@article{madison_tahir_broeck_phan_horn_sozzani_2024, title={Cell-material interactions in 3D bioprinted plant cells}, url={https://doi.org/10.1101/2024.01.30.578043}, DOI={10.1101/2024.01.30.578043}, abstractNote={3D bioprinting is an additive manufacturing technology with promise towards facilitating tissue engineering and single-cell investigations of cellular development and microenvironment responses. 3D bioprinting is still a new technology in the field of plant biology so its optimization with plant cells is still widely needed. Here, we present a study in which 3D bioprinting parameters, such as needle gauge, extrusion pressure, and scaffold type, were all tested in 3D bioprinted Tobacco BY-2 cells to evaluate how cell viability is responsive to each parameter. As a result, this study revealed an optimal range of extrusion pressures and needle gauges that resulted in an optimum cell viability. Furthermore, this study applied the identified optimal 3D bioprinting parameters to a different cell line, Arabidopsis root protoplasts, and stress condition, phosphate starvation, to confirm that the identified parameters were optimal in a different species, cell type, and cellular microenvironment. This suggested that phosphate-starved bioprinted Arabidopsis cells were less viable by 7 days, which was consistent with whole root phosphate starvation responses. As a result, the 3D bioprinter optimization yielded optimal cell viabilities in both BY-2 and Arabidopsis cells and facilitated an applied investigation into phosphate starvation stress.}, author={Madison, Imani and Tahir, Maimouna and Broeck, Lisa Van and Phan, Linh and Horn, Timothy and Sozzani, Rosangela}, year={2024}, month={Feb} }
 @article{haverroth_gobble_bradley_harris-gilliam_fischer_williams_long_sozzani_2024, title={The Black American experience: Answering the global challenge of broadening participation in STEM/agriculture}, volume={1}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koae002}, DOI={10.1093/plcell/koae002}, journal={PLANT CELL}, author={Haverroth, Eduardo and Gobble, Mariah and Bradley, Latosha and Harris-Gilliam, Kailyn and Fischer, Alicia and Williams, Cranos and Long, Terri and Sozzani, Rosangela}, year={2024}, month={Jan} }
 @article{van den broeck_bhosale_song_fonseca de lima_ashley_zhu_zhu_van de cotte_neyt_ortiz_et al._2023, title={Functional annotation of proteins for signaling network inference in non-model species}, volume={14}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-023-40365-z}, DOI={10.1038/s41467-023-40365-z}, abstractNote={Abstract Molecular biology aims to understand cellular responses and regulatory dynamics in complex biological systems. However, these studies remain challenging in non-model species due to poor functional annotation of regulatory proteins. To overcome this limitation, we develop a multi-layer neural network that determines protein functionality directly from the protein sequence. We annotate kinases and phosphatases in Glycine max . We use the functional annotations from our neural network, Bayesian inference principles, and high resolution phosphoproteomics to infer phosphorylation signaling cascades in soybean exposed to cold, and identify Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as key temperature regulators. Importantly, the signaling cascade inference does not rely upon known kinase motifs or interaction data, enabling de novo identification of kinase-substrate interactions. Conclusively, our neural network shows generalization and scalability, as such we extend our predictions to Oryza sativa , Zea mays , Sorghum bicolor , and Triticum aestivum . Taken together, we develop a signaling inference approach for non-model species leveraging our predicted kinases and phosphatases.}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Van den Broeck, Lisa and Bhosale, Dinesh Kiran and Song, Kuncheng and Fonseca de Lima, Cássio Flavio and Ashley, Michael and Zhu, Tingting and Zhu, Shanshuo and Van De Cotte, Brigitte and Neyt, Pia and Ortiz, Anna C. and et al.}, year={2023}, month={Aug} }
 @article{bennett_brady_dinneny_helariutta_sozzani_2023, title={Obituary Philip N. Benfey (1953-2023)}, volume={58}, ISSN={["1878-1551"]}, DOI={10.1016/j.devcel.2023.10.013}, abstractNote={“When I started to work in systems biology, I kept running across this term ‘emergent behavior,’ and it was really not clear to me, and so as with many things for me, an analogy was very helpful. The analogy I’d like to propose to you is that of a flock of birds, the idea being the following, that you can study a single bird as much as you like and you will never understand how a flock works, because a flock is all about the interactions between birds, and those interactions can lead to some really interesting complex behavior …”—Philip Benfey Professor Philip Benfey, a leading figure in plant biology, passed away on September 26, 2023, at the age of 70. Philip will be deeply missed by his family and friends. He adored his wife, Elisabeth, and their children, Sam and Julian. He was very proud of their achievements. We extend our heartfelt condolences to them as well as to his wider family, his current and former trainees, and his colleagues and friends as we all mourn his loss. Philip has been a giant presence in the field of plant biology over the past several decades—literally, scientifically, and legacy-wise. Everyone who met Philip could not help but be impressed by his imposing physical presence, his intelligence, and his scientific vision. Philip considered himself an “accidental scientist,” who after touring the world for 6 years ended up at the University of Paris VI. From there he went to graduate school at Harvard Medical School, where he completed his thesis with Phil Leder. Thereafter, he performed postdoctoral work with Nam-Hai Chua at the Rockefeller University. His independent career featured several distinct phases and approaches, each marked by a seminal scientific discovery or research innovation. Philip’s impressive independent career took off at NYU, where he adopted the Arabidopsis root as his experimental model to study the genetic regulation of plant development. He pioneered genetic screens to isolate root mutants influencing radial patterning. As a result, his lab identified a pair of GRAS family transcription factors, SHORT-ROOT (SHR) and SCARECROW (SCR), that specify the asymmetric cell division and subsequent cell specification processes separating endodermal and cortex tissue identities. Philip’s team later discovered that SHR is a mobile transcription factor that is produced in the innermost vascular domain of the root and moves from there, through the plasmodesmata, to the adjacent endodermal/cortex stem cell.1Nakajima K. Sena G. Nawy T. Benfey P.N. Intercellular movement of the putative transcription factor SHR in root patterning.Nature. 2001; 413: 307-311https://doi.org/10.1038/35095061Crossref PubMed Scopus (648) Google Scholar In this stem cell, SHR then forms a complex with SCR, and this complex is required for the asymmetric division separating the two cell layers. The formation of this complex also provides a sequestration mechanism to restrict the further movement of SHR and thereby to regulate the number of cell layers in the root. Although prior to this study it had been shown that proteins, even transcription factors, can move through plasmodesmata, the SHR-SCR model on radial patterning was the first to highlight the importance of mobile transcription factors, today a widely recognized principle of plant development. Throughout this period, Philip’s team worked closely with the lab of Ben Scheres at Utrecht University, investigating the interaction of the SHR-SCR module with other transcription factors and developmental signals that define radial patterning and provide the basis for our current understanding. After moving to Duke in 2002, Philip published a series of highly influential papers describing a transformative research approach. While plant single-cell transcriptomics are now de rigueur, his work was truly ahead of its time. Philip believed that resolving gene expression in Arabidopsis root tissues in space and time could help identify the full complement of factors required for cell-type patterning and acquisition of identity. He, along with Ken Birnbaum, took advantage of fluorescent activated cell sorting (FACS) coupled with the many transcriptional reporter lines that mark individual cell types or populations of cell types in the root. FACS was and is a frequently used tool in animal research, but he was able to convince cytometry facility operators to let plant biologists load in their protoplasts to have the machine recognize GFP-positive cells; and scientists in the lab trained in RNA extraction from very small sample sizes. Microarray analysis on this material subsequently reported near-transcriptome-scale gene expression. Since a cell’s developmental trajectory can be tracked along the root’s longitudinal axis, simply cutting a root into several pieces along this axis and isolating RNA/performing microarray analysis, plus some clever computational tools, could capture gene expression in time over the root’s longitudinal axis. Successive papers in Science, including Brady et al., 2007,2Brady S.M. Orlando D.A. Lee J.Y. Wang J.Y. Koch J. Dinneny J.R. Mace D. Ohler U. Benfey P.N. A high-resolution root spatiotemporal map reveals dominant expression patterns.Science. 2007; 318: 801-806https://doi.org/10.1126/science.1146265Crossref PubMed Scopus (888) Google Scholar demonstrated a wealth of expression pattern types and their changes over a cell type’s developmental trajectory. These data are now used by scientists all over the world to determine the expression pattern of their gene(s) of interest. These methods were used to further profile whole-transcriptome gene expression when RNAseq was in its infancy, followed by small RNA levels, protein, and metabolite abundance. These datasets served as a framework for the annotation of every single-cell transcriptome paper that has recently been published. Philip next pioneered systems biology approaches to propel the field of plant developmental biology forward to become more predictive and quantitative. His team exploited these approaches to discover how asymmetric cell division is regulated in roots. By cleverly utilizing fluorescence-activated cell sorting and single-cell gene expression analysis, he discovered a direct connection between developmental subnetworks and the cell division machinery. Philip later explored how emergent behavior transcends a series of switches influenced by high (for asymmetric cell divisions) and low concentrations (for symmetric cell divisions) of proteins. Philip recognized that to understand complex regulatory processes it is critical to quantitatively analyze protein movement and protein-protein interactions in time and space. This led Philip and Ross Sozzani’s teams to study the SHR-SCR regulatory network, where intercellular movement of SHR and interaction with its target SCR controls root patterning and cell fate specification.3Clark N.M. Hinde E. Winter C.M. Fisher A.P. Crosti G. Blilou I. Gratton E. Benfey P.N. Sozzani R. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.Elife. 2016; 5e14770Crossref Scopus (68) Google Scholar Key parameters such as SHR mobility, oligomeric state, and association with SCR were quantified using advanced spectroscopy techniques and incorporated into a mathematical model. This seminal quantitative systems biology paper revealed that the timing of SHR protein movement and SHR-SCR stoichiometry play critical regulatory roles during root development. While able to generate seminal research discoveries at the disciplinary interface, Philip considered himself first and foremost a developmental biologist and used plants as an ideal model system to explore questions of cell fate determination. However, the standard practice in developmental biology, of minimizing the impact of the environment on the organism to study such processes, is counter to the nature of roots, which grow in intimate association with the complex and dynamic soil environment. If tissue-specific transcriptomics revealed a rich regulatory landscape for each cell, how much of this architecture was dependent on the specific environmental conditions under which the plants were grown? To address this question, Philip’s lab generated the first spatial maps of roots exposed to environmental stresses, including iron and sulfur deprivation, high salinity, and low pH.4Dinneny J.R. Long T.A. Wang J.Y. Jung J.W. Mace D. Pointer S. Barron C. Brady S.M. Schiefelbein J. Benfey P.N. Cell identity mediates the response of Arabidopsis roots to abiotic stress.Science. 2008; 320: 942-945https://doi.org/10.1126/science.1153795Crossref PubMed Scopus (599) Google Scholar Many of the transcriptional responses were regulated in a cell-type-specific manner, which resulted in major shifts in cell-type function, with many canonical functions only occurring under a narrow range of environmental conditions. Thus, this work showed that plants offered profound insights into the intricacies of cell identity. This identity is intrinsically linked to the environment, which serves as a critical factor in determining how this cellular property is realized through gene expression. While Philip was a stalwart proponent of Arabidopsis as a model system, his interest in understanding plants with more complex root systems, and in applying this knowledge to solve real-world problems, led to deep dives into the use of crop plants, especially rice, and the development of innovative phenotyping approaches. From custom-fabricated microfluidic devices to the use of optical tomography and image analysis algorithms, which generated three-dimensional representations of root system architecture,5Topp C.N. Iyer-Pascuzzi A.S. Anderson J.T. Lee C.-R. Zurek P.R. Symonova O. Zheng Y. Bucksch A. Mileyko Y. Galkovskyi T. et al.3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture.Proc. Natl. Acad. Sci. USA. 2013; 110: 1695-1704Crossref PubMed Scopus (0) Google Scholar Philip was essential in identifying nascent technologies that could be applied to this emerging area. Such work inspired Philip to establish two companies, Grassroots Biotechnology and Hi Fidelity Genetics, which leveraged these innovative methods to advance crop biotechnology solutions. Philip’s impact on the field of plant biology extends far beyond his pioneering basic and applied research discoveries and the technological innovations outlined above. What set Philip apart from his peer group was the unparalleled roll call of international researchers who worked in his laboratory and are now leaders in the plant biology field around the world. These several generations of researchers Philip has mentored arguably represent his greatest scientific legacy.}, number={22}, journal={DEVELOPMENTAL CELL}, author={Bennett, Malcolm J. and Brady, Siobhan M. and Dinneny, Jose R. and Helariutta, Yka and Sozzani, Ross}, year={2023}, month={Nov}, pages={2413–2415} }
 @article{madison_gillan_peace_gabrieli_broeck_jones_sozzani_2023, title={Phosphate starvation: response mechanisms and solutions}, volume={8}, ISSN={["1460-2431"]}, url={https://doi.org/10.1093/jxb/erad326}, DOI={10.1093/jxb/erad326}, abstractNote={Phosphorus is essential to plant growth and agricultural crop yields, yet the challenges associated with phosphorus fertilization in agriculture, such as aquatic runoff pollution and poor phosphorus bioavailability, are increasingly difficult to manage. Comprehensively understanding the dynamics of phosphorus uptake and signaling mechanisms will inform the development of strategies to address these issues. This review describes regulatory mechanisms used by specific tissues in the root apical meristem to sense and uptake phosphate from the rhizosphere. The major regulatory mechanisms and related hormone crosstalk underpinning phosphate starvation responses, cellular phosphate homeostasis, and plant adaptations to phosphate starvation are also discussed in this review. In addition, this review overviews the major mechanism of plant systemic phosphate starvation responses. Finally, this review discusses recent promising genetic engineering strategies for improving crop phosphorus use and computational approaches that may help further design strategies for improved plant phosphate acquisition. The mechanisms and approaches presented in this review include a wide variety of species not only including Arabidopsis thaliana but also including crop species such as Oryza sativa (rice), Glycine max (soybean), and Triticum aestivum (wheat) to address both general and species-specific mechanisms and strategies. The aspects of phosphorus deficiency responses and recently employed strategies of improving phosphate acquisition that are detailed in this review may provide insights on the mechanisms or phenotypes that may be targeted in efforts to improve crop phosphorus content and plant growth in low phosphorus soils.}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Madison, Imani and Gillan, Lydia and Peace, Jasmine and Gabrieli, Flavio and Broeck, Lisa and Jones, Jacob L. and Sozzani, Rosangela}, editor={Ort, DonaldEditor}, year={2023}, month={Aug} }
 @inproceedings{mahatma_broeck_morffy_staller_strader_sozzani_2023, title={Prediction and functional characterization of transcriptional activation domains}, url={https://doi.org/10.1109/CISS56502.2023.10089768}, DOI={10.1109/CISS56502.2023.10089768}, abstractNote={Gene expression is induced by transcription factors (TFs) through their activation domains (ADs). However, ADs are unconserved, intrinsically disordered sequences without a secondary structure, making it challenging to recognize and predict these regions and limiting our ability to identify TFs. Here, we address this challenge by leveraging a neural network approach to systematically predict ADs. As input for our neural network, we used computed properties for amino acid (AA) side chain and secondary structure, rather than relying on the raw sequence. Moreover, to shed light on the features learned by our neural network and greatly increase interpretability, we computed the input properties most important for an accurate prediction. Our findings further highlight the importance of aromatic and negatively charged AA and reveal the importance of unknown AA properties. Taking advantage of these most important features, we used an unsupervised learning approach to classify the ADs into 10 subclasses, which can further be explored for AA specificity and AD functionality. Overall, our pipeline, relying on supervised and unsupervised machine learning, shed light on the non-linear properties of ADs.}, author={Mahatma, Saloni and Broeck, Lisa Van and Morffy, Nicholas and Staller, Max V and Strader, Lucia C and Sozzani, Rosangela}, year={2023}, month={Mar} }
 @article{gaudinier_broeck_moreno-risueño_rodriguez-medina_sozzani_brady_2023, title={Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation}, url={https://doi.org/10.1101/2023.12.05.570292}, DOI={10.1101/2023.12.05.570292}, abstractNote={Nitrogen (N) is an essential macronutrient and its bioavailability plays a major role in how plant development is tuned to environmental nutrient status. To find novel factors in early root system architecture responses to N conditions, we performed Arabidopsis thaliana root transcriptome profiling of a short-term time course in limiting and sufficient N conditions. Using this data, we inferred transcriptional regulatory networks in each condition, which revealed the N-condition specific responses of jasmonate regulation; transcriptional factor (TF) ERF107 plays a more generalized role in lateral root development while TF LBD13 is specific to N-limiting conditions. Further, we used a single cell LR cell-type specific transcriptome dataset to model and analyze the roles of TFs LBD13, ERF107, and PDF2 in early stages of LR development. Linking the N time course transcriptomics, LR mutant phenotypes, and cell-type specific single cell profiling, these approaches provide multiple lines of evidence to find and test the roles of TFs that are involved in early root patterning responses to N conditions.}, author={Gaudinier, Allison and Broeck, Lisa Van and Moreno-Risueño, Miguel and Rodriguez-Medina, Joel and Sozzani, Rosangela and Brady, Siobhan M.}, year={2023}, month={Dec} }
 @article{beretta_franchini_din_lacchini_broeck_sozzani_orozco-arroyo_caporali_adam_jouannic_et al._2023, title={The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice}, volume={4}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.16229}, DOI={10.1111/tpj.16229}, abstractNote={The architecture of the rice inflorescence is an important determinant of crop yield. The length of the inflorescence and the number of branches are among the key factors determining the number of spikelets, and thus grains, that a plant will develop. Especially the timing of the identity transition from indeterminate branch meristem to determinate spikelet meristem regulates the complexity of the inflorescence. In this context, the ALOG gene TAWAWA1 (TAW1) has been shown to delay the transition to determinate spikelet development in rice. Recently, by combining precise laser microdissection of inflorescence meristems with RNA-seq we observed that two ALOG genes, Oryza sativa OsG1-like 1 (OsG1L1) and OsG1L2, have an expression profile similar to TAW1. Here we report that osg1l1 and osg1l2 loss-of-function CRISPR mutants have similar phenotypes as the previously published taw mutant, suggesting that these genes might act on related pathways during inflorescence development. Transcriptome analysis of the osg1l2 mutant suggested interactions of OsG1L2 with other known inflorescence architecture regulators and the datasets were used for the construction of a gene regulatory network (GRN) proposing interactions among genes potentially involved in controlling inflorescence development in rice. We selected in this GRN the homeodomain-leucine zipper transcription factor encoding gene OsHOX14 for further characterisation. The spatio-temporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new players involved in rice inflorescence development.}, journal={PLANT JOURNAL}, author={Beretta, Veronica M. and Franchini, Emanuela and Din, Israr Ud and Lacchini, Elia and Broeck, Lisa and Sozzani, Rosangela and Orozco-Arroyo, Gregorio and Caporali, Elisabetta and Adam, Helene and Jouannic, Stefan and et al.}, year={2023}, month={Apr} }
 @article{ortiz_de smet_sozzani_locke_2022, title={Field-grown soybean shows genotypic variation in physiological and seed composition responses to heat stress during seed development}, volume={195}, ISSN={0098-8472}, url={http://dx.doi.org/10.1016/j.envexpbot.2021.104768}, DOI={10.1016/j.envexpbot.2021.104768}, abstractNote={An average temperature increase between 2.6 and 4.8 °C, along with more frequent extreme temperatures, will challenge crop productivity by the end of the century. To investigate genotypic variation in soybean response to elevated temperature, six soybean (Glycine max) genotypes were subjected to elevated air temperature of + 4.5 °C above ambient for 28 days in open-top field chambers. Gas exchange and chlorophyll fluorescence were measured before and during heating and yield as well as seed composition were evaluated at maturity. Results show that long-term elevated air temperature increased nighttime respiration, increased the maximum velocity of carboxylation by Rubisco, impacted seed protein concentration, and reduced seed oil concentration across genotypes. The genotypes in this study varied in temperature responses for photosynthetic CO2 assimilation, stomatal conductance, photosystem II operating efficiency, quantum efficiency of CO2 assimilation, and seed protein concentration at maturity. These diverse responses among genotypes to elevated air temperature during seed development in the field, reveal the potential for soybean heat tolerance to be improved through breeding and underlines the importance of identifying efficient selection strategies for stress-tolerant crops.}, journal={Environmental and Experimental Botany}, publisher={Elsevier BV}, author={Ortiz, Anna C. and De Smet, Ive and Sozzani, Rosangela and Locke, Anna M.}, year={2022}, month={Mar}, pages={104768} }
 @article{thomas_broeck_spurney_sozzani_frank_2022, title={Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation}, volume={34}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koab246}, DOI={10.1093/plcell/koab246}, abstractNote={Graft incompatibility is a poorly understood phenomenon that presents a serious agricultural challenge. Unlike immediate incompatibility that results in rapid death, delayed incompatibility can take months or even years to manifest, creating a significant economic burden for perennial crop production. To gain insight into the genetic mechanisms underlying this phenomenon, we developed a model system with Solanum lycopersicum ‘tomato’ and Capsicum annuum ‘pepper’ heterografting, which expresses signs of anatomical junction failure within the first week of grafting. By generating a detailed timeline for junction formation we were able to pinpoint the cellular basis for this delayed incompatibility. Furthermore, we infer gene regulatory networks for compatible self-grafts versus incompatible heterografts based on these key anatomical events, which predict core regulators for grafting. Finally, we delve into the role of vascular development in graft formation and validate SlWOX4 as a regulator for grafting in tomato. Notably, SlWOX4 is the first gene to be functionally implicated in vegetable crop grafting.}, number={1}, journal={PLANT CELL}, publisher={Oxford University Press (OUP)}, author={Thomas, Hannah and Broeck, Lisa and Spurney, Ryan and Sozzani, Rosangela and Frank, Margaret}, year={2022}, month={Jan}, pages={535–556} }
 @article{muhammad_clark_haque_williams_sozzani_long_2022, title={POPEYE intercellular localization mediates cell-specific iron deficiency responses}, volume={8}, ISSN={["1532-2548"]}, url={https://doi.org/10.1093/plphys/kiac357}, DOI={10.1093/plphys/kiac357}, abstractNote={Plants must tightly regulate iron (Fe) sensing, acquisition, transport, mobilization, and storage to ensure sufficient levels of this essential micronutrient. POPEYE (PYE) is an iron responsive transcription factor that positively regulates the iron deficiency response, while also repressing genes essential for maintaining iron homeostasis. However, little is known about how PYE plays such contradictory roles. Under iron-deficient conditions pPYE:GFP accumulates in the root pericycle while pPYE:PYE-GFP is localized to the nucleus in all Arabidopsis (Arabidopsis thaliana) root cells, suggesting that PYE may have cell-specific dynamics and functions. Using scanning fluorescence correlation spectroscopy (scanning FCS) and cell-specific promoters, we found that PYE-GFP moves between different cells and that the tendency for movement corresponds with transcript abundance. While localization to the cortex, endodermis, and vasculature is required to manage changes in iron availability, vasculature and endodermis localization of PYE-GFP protein exacerbated pye-1 defects and elicited a host of transcriptional changes that are detrimental to iron mobilization. Our findings indicate that PYE acts as a positive regulator of iron deficiency response by regulating iron bioavailability differentially across cells, which may trigger iron uptake from the surrounding rhizosphere and impact root energy metabolism.}, journal={PLANT PHYSIOLOGY}, publisher={Oxford University Press (OUP)}, author={Muhammad, DurreShahwar and Clark, Natalie M. and Haque, Samiul and Williams, Cranos M. and Sozzani, Rosangela and Long, Terri A.}, year={2022}, month={Aug} }
 @article{adhikari_aryal_redpath_broeck_ashrafi_philbrick_jacobs_sozzani_louws_2022, title={RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry}, volume={12}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2021.805771}, abstractNote={Two hemibiotrophic pathogens, Colletotrichum acutatum (Ca) and C. gloeosporioides (Cg), cause anthracnose fruit rot and anthracnose crown rot in strawberry (Fragaria × ananassa Duchesne), respectively. Both Ca and Cg can initially infect through a brief biotrophic phase, which is associated with the production of intracellular primary hyphae that can infect host cells without causing cell death and establishing hemibiotrophic infection (HBI) or quiescent (latent infections) in leaf tissues. The Ca and Cg HBI in nurseries and subsequent distribution of asymptomatic infected transplants to fruit production fields is the major source of anthracnose epidemics in North Carolina. In the absence of complete resistance, strawberry varieties with good fruit quality showing rate-reducing resistance have frequently been used as a source of resistance to Ca and Cg. However, the molecular mechanisms underlying the rate-reducing resistance or susceptibility to Ca and Cg are still unknown. We performed comparative transcriptome analyses to examine how rate-reducing resistant genotype NCS 10-147 and susceptible genotype ‘Chandler’ respond to Ca and Cg and identify molecular events between 0 and 48 h after the pathogen-inoculated and mock-inoculated leaf tissues. Although plant response to both Ca and Cg at the same timepoint was not similar, more genes in the resistant interaction were upregulated at 24 hpi with Ca compared with those at 48 hpi. In contrast, a few genes were upregulated in the resistant interaction at 48 hpi with Cg. Resistance response to both Ca and Cg was associated with upregulation of MLP-like protein 44, LRR receptor-like serine/threonine-protein kinase, and auxin signaling pathway, whereas susceptibility was linked to modulation of the phenylpropanoid pathway. Gene regulatory network inference analysis revealed candidate transcription factors (TFs) such as GATA5 and MYB-10, and their downstream targets were upregulated in resistant interactions. Our results provide valuable insights into transcriptional changes during resistant and susceptible interactions, which can further facilitate assessing candidate genes necessary for resistance to two hemibiotrophic Colletotrichum spp. in strawberry.}, journal={FRONTIERS IN GENETICS}, author={Adhikari, Tika B. and Aryal, Rishi and Redpath, Lauren E. and Broeck, Lisa and Ashrafi, Hamid and Philbrick, Ashley N. and Jacobs, Raymond L. and Sozzani, Rosangela and Louws, Frank J.}, year={2022}, month={Mar} }
 @article{broeck_spurney_fisher_schwartz_clark_nguyen_madison_gobble_long_sozzani_2021, title={A hybrid model connecting regulatory interactions with stem cell divisions in the root}, volume={2}, url={https://doi.org/10.1017/qpb.2021.1}, DOI={10.1017/qpb.2021.1}, abstractNote={Abstract Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5) and SHORTROOT (SHR), regulate divisions in the root stem cell niche. However, how these proteins coordinately function to establish systemic behaviour is not well understood. We propose a non-cell autonomous role for WOX5 in the cortex endodermis initial (CEI) and identify a regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR 1, that coordinates CEI divisions. Here, we show with a multi-scale hybrid model integrating ordinary differential equations (ODEs) and agent-based modeling that quiescent center (QC) and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behaviour, which led us to predict cell-type-specific expression dynamics of SHR, SCARECROW, WOX5, AN3 and CYCLIND6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions.}, journal={Quantitative Plant Biology}, publisher={Cambridge University Press (CUP)}, author={Broeck, Lisa Van and Spurney, Ryan J. and Fisher, Adam P. and Schwartz, Michael and Clark, Natalie M. and Nguyen, Thomas T. and Madison, Imani and Gobble, Mariah and Long, Terri and Sozzani, Rosangela}, year={2021} }
 @article{roszak_heo_blob_toyokura_sugiyama_balaguer_lau_hamey_cirrone_madej_et al._2021, title={Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization}, volume={374}, ISSN={["1095-9203"]}, DOI={10.1126/science.aba5531}, abstractNote={Description Root meristem controls The plant meristem, a small cluster of stem cells generates all of the cell types necessary for the plant’s indeterminate growth pattern. Roszak et al. use single-cell analyses to follow development from the stem cell to the enucleated cell of the phloem vasculature. In the root of the small mustard plant Arabidopsis, this process takes just over 3 days, and the developmental trajectory spans more than a dozen different cell states. A transcriptional program initially held under repressive control is released as those initial repressors dissipate. Reciprocal repression by regulators early and late in the developmental trajectory control a rapid switch in the differentiation program. —PJH Single-cell analysis shows how the generalized root meristem builds a range of specialized tissues. INTRODUCTION The plant root grows indeterminately. Continual birth and maturation of cells in a gradient along the root longitudinal axis requires tissue-wide coordination of cell division with cell differentiation. Within the root, a single cell file of developing protophloem is surrounded by other tissues, with each cell type differentiating at its characteristic pace. Despite communication of protophloem cells with the surrounding environment, the developmental program of phloem, within the plant’s vasculature, is accelerated compared with certain surrounding cell types. Here, we take advantage of the fast pace of protophloem differentiation and the cellular changes that it undergoes to dissect its developmental trajectory using high-resolution imaging and single-cell omics. RATIONALE Single-cell RNA-sequencing (scRNA-seq) analysis as applied to the study of organogenesis typically creates maps of transcriptome activity in various tissue types. Although these approaches characterize gene expression within cells of an organ, the ability to reconstruct the step-by-step changes in cells during maturation is often limited. High-resolution profiling will sample each cellular state along a developmental trajectory and associate each state with developmental changes that lead to cellular specialization. To understand the developmental progression of root phloem cells at a single-cell resolution as related to cellular specializations, we used cell sorting to profile Arabidopsis thaliana root tissue and map protophloem-specific transcripts, scRNA-seq to identify molecular transition as cells mature, and live-cell imaging to map molecular states to morphological and cellular events during differentiation. RESULTS Long-term live imaging enabled us to determine the duration of the developmental stages and the time one cell spends in each position of the trajectory during protophloem sieve element maturation. We then mapped single-cell transcriptomes corresponding to the 19 cell stages of protophloem development from birth to enucleation. Combining single-cell transcriptomics with cell behavior data from live-imaging experiments, we established seven developmental phases of protophloem development, including early lineage bifurcations, transition from proliferation to differentiation, and, finally, cell enucleation. The ability to connect cellular development such as lineage bifurcation and enucleation to molecular states using scRNA-seq allowed us to uncover genetic mechanisms that coordinate cellular maturation. First, our analysis revealed the importance of RHO OF PLANTS (ROP) GTPase signaling during early phloem development when the protophloem cell lineage bifurcates to generate metaphloem sieve element and procambium. We found that the expression of the phloem-enriched components of ROP GTPase signaling is triggered by lineage-specific PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors. PEARs also promote phloem differentiation by transcriptional activation of the gene encoding ALTERED PHLOEM DEVELOPMENT (APL), which regulates protophloem sieve element enucleation. In the absence of PEARs, transcription of APL, NAC DOMAIN CONTAINING PROTEIN 45/86 (NAC45/86), and NAC45/86-DEPENDENT EXONUCLEASE-DOMAIN PROTEIN 4 (NEN4) is not activated in the protophloem cell lineage and cell enucleation fails. The genetic cascade, with PEARs handing off late maturation to APL, represents a largely autonomous phloem-specific circuit regulating maturation. However, we could also connect the timing of the genetic cascade to broadly expressed master regulators of meristem maturation. Protophloem sieve element differentiation program is temporally coordinated with the rest of the meristem by the broadly acting PLETHORA factors emanating from the stem cell niche. We showed that, although distributed across different tissues, PLETHORA factors directly repress expression of APL, counteracting PEARs close to the stem cell niche. The precise timing of developmental mechanisms was critical for proper phloem development; “fail-safe” mechanisms ensured orderly developmental transitions. For example, activation of late genes accompanied repression of early genes of the phloem differentiation program. Ectopic expression of selected late phloem genes in early dividing cells inhibited cell division and promoted cell expansion, two features that characterize late phloem. CONCLUSION Using cell sorting, live-microscopy lineage tracing, and transcriptomics, we built a high-resolution blueprint of the genetic program that guides protophloem development. We document even short developmental phases such as cell enucleation, which takes place every 2 hours. Deep, high-resolution single-cell sequencing of the underlying gene-regulatory network revealed a “seesaw” mechanism of reciprocal genetic repression that triggered rapid developmental transitions. Further analysis of this network revealed an interaction of broad versus tissue-specific transcription factors that orchestrates timing of sieve element differentiation. Developmental trajectory of protophloem sieve element. Interactions between transcription factors guiding protophloem sieve element development and the length of the identified developmental phases (I to VII). Arrows indicate transcriptional activation. T bars indicate transcriptional inhibition. Colored arrows depict positive and inhibitory interactions identified for early and late factors, respectively, underlying a “seesaw” model. Gray bar indicates PEAR expression domain. Wedge indicates the PLETHORA protein gradient. Credit: Image by Pawel Roszak and Bernhard Blob In the plant meristem, tissue-wide maturation gradients are coordinated with specialized cell networks to establish various developmental phases required for indeterminate growth. Here, we used single-cell transcriptomics to reconstruct the protophloem developmental trajectory from the birth of cell progenitors to terminal differentiation in the Arabidopsis thaliana root. PHLOEM EARLY DNA-BINDING-WITH-ONE-FINGER (PEAR) transcription factors mediate lineage bifurcation by activating guanosine triphosphatase signaling and prime a transcriptional differentiation program. This program is initially repressed by a meristem-wide gradient of PLETHORA transcription factors. Only the dissipation of PLETHORA gradient permits activation of the differentiation program that involves mutual inhibition of early versus late meristem regulators. Thus, for phloem development, broad maturation gradients interface with cell-type-specific transcriptional regulators to stage cellular differentiation.}, number={6575}, journal={SCIENCE}, author={Roszak, Pawel and Heo, Jung-Ok and Blob, Bernhard and Toyokura, Koichi and Sugiyama, Yuki and Balaguer, Maria Angels de Luis and Lau, Winnie W. Y. and Hamey, Fiona and Cirrone, Jacopo and Madej, Ewelina and et al.}, year={2021}, month={Dec}, pages={1577-+} }
 @misc{schwartz_peters_hunt_abdul-matin_broeck_sozzani_2021, title={Divide and Conquer: The Initiation and Proliferation of Meristems}, volume={40}, ISSN={["1549-7836"]}, url={http://dx.doi.org/10.1080/07352689.2021.1915228}, DOI={10.1080/07352689.2021.1915228}, abstractNote={Abstract In contrast to animals, which complete organogenesis early in their development, plants continuously produce organs, and structures throughout their entire lifecycle. Plants achieve the continuous growth of organs through the initiation and maintenance of meristems that populate the plant body. Plants contain two apical meristems, one at the shoot and one root, to produce the lateral organs of the shoot and the cell files of the root, respectively. Additional meristems within the plant produce branches while others produce the cell types within the vasculature system. Throughout development, plants must balance producing organs and maintaining their meristems, which requires tightly controlled regulations. This review focuses on the various plant meristems, how cells within these meristems maintain their identity, and particularly the molecular players that regulate stem cell maintenance. In addition, we summarize cell types which share molecular features with meristems, but do not follow the same rules regarding maintenance, including pericycle and rachis founder cells. Together, these populations of cells contribute to the entire organogenesis of plants.}, number={2}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, publisher={Informa UK Limited}, author={Schwartz, Michael F. and Peters, Rachel and Hunt, Aitch M. and Abdul-Matin, Abdul-Khaliq and Broeck, Lisa and Sozzani, Rosangela}, year={2021}, month={Mar}, pages={147–156} }
 @article{orozco-navarrete_song_casanal_sozzani_flors_sanchez-sevilla_trinkl_hoffmann_merchante_schwab_et al._2021, title={Down-regulation of Fra a 1.02 in strawberry fruits causes transcriptomic and metabolic changes compatible with an altered defense response}, volume={8}, ISSN={["2052-7276"]}, DOI={10.1038/s41438-021-00492-4}, abstractNote={Abstract The strawberry Fra a 1 proteins belong to the class 10 Pathogenesis-Related (PR-10) superfamily. In strawberry, a large number of members have been identified, but only a limited number is expressed in the fruits. In this organ, Fra a 1.01 and Fra a 1.02 are the most abundant Fra proteins in the green and red fruits, respectively, however, their function remains unknown. To know the function of Fra a 1.02 we have generated transgenic lines that silence this gene, and performed metabolomics, RNA-Seq, and hormonal assays. Previous studies associated Fra a 1.02 to strawberry fruit color, but the analysis of anthocyanins in the ripe fruits showed no diminution in their content in the silenced lines. Gene ontology (GO) analysis of the genes differentially expressed indicated that oxidation/reduction was the most represented biological process. Redox state was not apparently altered since no changes were found in ascorbic acid and glutathione (GSH) reduced/oxidized ratio, but GSH content was reduced in the silenced fruits. In addition, a number of glutathione-S-transferases (GST) were down-regulated as result of Fra a 1.02-silencing. Another highly represented GO category was transport which included a number of ABC and MATE transporters. Among the regulatory genes differentially expressed WRKY33.1 and WRKY33.2 were down-regulated, which had previously been assigned a role in strawberry plant defense. A reduced expression of the VQ23 gene and a diminished content of the hormones JA, SA, and IAA were also found. These data might indicate that Fra a 1.02 participates in the defense against pathogens in the ripe strawberry fruits.}, number={1}, journal={HORTICULTURE RESEARCH}, author={Orozco-Navarrete, Begona and Song, Jina and Casanal, Ana and Sozzani, Rosangela and Flors, Victor and Sanchez-Sevilla, Jose F. and Trinkl, Johanna and Hoffmann, Thomas and Merchante, Catharina and Schwab, Wilfried and et al.}, year={2021}, month={Mar} }
 @article{thomas_broeck_spurney_sozzani_frank_2021, title={Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation}, volume={2}, url={https://doi.org/10.1101/2021.02.26.433082}, DOI={10.1101/2021.02.26.433082}, abstractNote={Abstract Graft incompatibility is a poorly understood phenomenon that presents a serious agricultural challenge. Unlike immediate incompatibility that results in rapid death, delayed incompatibility can take months or even years to manifest, creating a significant economic burden for perennial crop production. To gain insight into the genetic mechanisms underlying this phenomenon, we developed a model system with Solanum lycopersicum ‘tomato’ and Capsicum annuum ‘pepper’ heterografting, which expresses signs of anatomical junction failure within the first week of grafting. By generating a detailed timeline for junction formation we were able to pinpoint the cellular basis for this delayed incompatibility. Furthermore, we infer gene regulatory networks for compatible self-grafts versus incompatible heterografts based on these key anatomical events, which predict core regulators for grafting. Finally, we delve into the role of vascular development in graft formation and validate SlWOX4 as a regulator for grafting in tomato. Notably, SlWOX4 is the first gene to be functionally implicated in vegetable crop grafting.}, publisher={Cold Spring Harbor Laboratory}, author={Thomas, Hannah and Broeck, Lisa Van and Spurney, Ryan and Sozzani, Rosangela and Frank, Margaret}, year={2021}, month={Feb} }
 @article{clark_nolan_wang_song_montes_valentine_guo_sozzani_yin_walley_2021, title={Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis}, volume={12}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-021-26165-3}, abstractNote={Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets and unravel the molecular signaling events of BR response in Arabidopsis. We profile the levels of 26,669 transcripts, 9,533 protein groups, and 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths of time. We then construct a network inference pipeline called Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) to integrate these data. We use our network predictions to identify putative phosphorylation sites on BES1 and experimentally validate their importance. Additionally, we identify BRONTOSAURUS (BRON) as a transcription factor that regulates cell division, and we show that BRON expression is modulated by BR-responsive kinases and transcription factors. This work demonstrates the power of integrative network analysis applied to multi-omic data and provides fundamental insights into the molecular signaling events occurring during BR response.}, number={1}, journal={NATURE COMMUNICATIONS}, author={Clark, Natalie M. and Nolan, Trevor M. and Wang, Ping and Song, Gaoyuan and Montes, Christian and Valentine, Conner T. and Guo, Hongqing and Sozzani, Rosangela and Yin, Yanhai and Walley, Justin W.}, year={2021}, month={Oct} }
 @article{betegon-putze_mercadal_bosch_planas-riverola_marques-bueno_vilarrasa-blasi_frigola_burkart_martinez_conesa_et al._2021, title={Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots}, volume={17}, ISSN={["1744-4292"]}, DOI={10.15252/msb.20209864}, abstractNote={Root growth and development are essential features for plant survival and the preservation of terrestrial ecosystems. In the Arabidopsis primary root apex, stem-cell specific transcription factors BRAVO and WOX5 co-localize at the Quiescent Center (QC) cells, where they repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Here, by using empirical evidence and mathematical modeling, we establish the precise regulatory and molecular interactions between BRAVO and WOX5. We found that BRAVO and WOX5 regulate each other besides forming a transcription factor complex in the QC necessary to preserve overall root growth and architecture. Our results unveil the importance of transcriptional regulatory circuits at the quiescent and stem cells to the control of organ initiation and growth of plant tissues.}, number={6}, journal={MOLECULAR SYSTEMS BIOLOGY}, author={Betegon-Putze, Isabel and Mercadal, Josep and Bosch, Nadja and Planas-Riverola, Ainoa and Marques-Bueno, Mar and Vilarrasa-Blasi, Josep and Frigola, David and Burkart, Rebecca C. and Martinez, Cristina and Conesa, Ana and et al.}, year={2021}, month={Jun} }
 @article{spurney_schwartz_gobble_sozzani_broeck_2021, title={Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification}, volume={2328}, ISBN={["978-1-0716-1533-1"]}, ISSN={["1940-6029"]}, DOI={10.1007/978-1-0716-1534-8_4}, abstractNote={Gene expression data analysis and the prediction of causal relationships within gene regulatory networks (GRNs) have guided the identification of key regulatory factors and unraveled the dynamic properties of biological systems. However, drawing accurate and unbiased conclusions requires a comprehensive understanding of relevant tools, computational methods, and their workflows. The topics covered in this chapter encompass the entire workflow for GRN inference including: (1) experimental design; (2) RNA sequencing data processing; (3) differentially expressed gene (DEG) selection; (4) clustering prior to inference; (5) network inference techniques; and (6) network visualization and analysis. Moreover, this chapter aims to present a workflow feasible and accessible for plant biologists without a bioinformatics or computer science background. To address this need, TuxNet, a user-friendly graphical user interface that integrates RNA sequencing data analysis with GRN inference, is chosen for the purpose of providing a detailed tutorial.}, journal={MODELING TRANSCRIPTIONAL REGULATION}, author={Spurney, Ryan and Schwartz, Michael and Gobble, Mariah and Sozzani, Rosangela and Broeck, Lisa}, year={2021}, pages={47–65} }
 @article{crook_willoughby_hazak_okuda_vandermolen_soyars_cattaneo_clark_sozzani_hothorn_et al._2020, title={BAM1/2 receptor kinase signaling drives CLE peptide-mediated formative cell divisions in Arabidopsis roots}, volume={117}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.2018565117}, abstractNote={Significance Proper elaboration of the plant body plan requires that cell division patterns are coordinated during development in complex tissues. Activation of cell cycle machinery is critical for this process, but it is not clear how or if this links to cell-to-cell communication networks that are important during development. Here we show that key cell divisions that generate the plant root are controlled by cell-to-cell signaling peptides which act through plant-specific receptor kinases to control expression of a specific cyclinD cell cycle regulatory gene. We show that cyclinD gene expression depends on both receptor signaling and the SHORT-ROOT transcription factor to ensure timely and robust cell division patterns.}, number={51}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Crook, Ashley D. and Willoughby, Andrew C. and Hazak, Ora and Okuda, Satohiro and VanDerMolen, Kylie R. and Soyars, Cara L. and Cattaneo, Pietro and Clark, Natalie M. and Sozzani, Rosangela and Hothorn, Michael and et al.}, year={2020}, month={Dec}, pages={32750–32756} }
 @inbook{buckner_madison_melvin_long_sozzani_williams_2020, title={BioVision Tracker: A semi-automated image analysis software for spatiotemporal gene expression tracking in Arabidopsis thaliana}, volume={160}, ISBN={9780128215333}, ISSN={0091-679X}, url={http://dx.doi.org/10.1016/bs.mcb.2020.04.017}, DOI={10.1016/bs.mcb.2020.04.017}, abstractNote={Fluorescence microscopy can produce large quantities of data that reveal the spatiotemporal behavior of gene expression at the cellular level in plants. Automated or semi-automated image analysis methods are required to extract data from these images. These data are helpful in revealing spatial and/or temporal-dependent processes that influence development in the meristematic region of plant roots. Tracking spatiotemporal gene expression in the meristem requires the processing of multiple microscopy imaging channels (one channel used to image root geometry which serves as a reference for relating locations within the root, and one or more channels used to image fluorescent gene expression signals). Many automated image analysis methods rely on the staining of cell walls with fluorescent dyes to capture cellular geometry and overall root geometry. However, in long time-course imaging experiments, dyes may fade which hinders spatial assessment in image analysis. Here, we describe a procedure for analyzing 3D microscopy images to track spatiotemporal gene expression signals using the MATLAB-based BioVision Tracker software. This software requires either a fluorescence image or a brightfield image to analyze root geometry and a fluorescence image to capture and track temporal changes in gene expression.}, booktitle={Methods in Cell Biology}, publisher={Elsevier}, author={Buckner, Eli and Madison, Imani and Melvin, Charles and Long, Terri and Sozzani, Rosangela and Williams, Cranos}, year={2020}, pages={419–436} }
 @article{van norman_strader_sozzani_2020, title={Editorial overview: Directionality and precision - how signaling and gene regulation drive plant development and growth}, volume={57}, ISSN={["1879-0356"]}, DOI={10.1016/j.pbi.2020.11.001}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Van Norman, Jaimie M. and Strader, Lucia C. and Sozzani, Rosangela}, year={2020}, month={Oct}, pages={A1–A3} }
 @article{broeck_spurney_fisher_schwartz_clark_nguyen_madison_gobble_long_sozzani_2020, title={Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions}, url={https://doi.org/10.1101/2020.11.30.404426}, DOI={10.1101/2020.11.30.404426}, abstractNote={Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WOX5 and SHR, regulate divisions in the root stem cell niche (SCN). However, how these proteins coordinately function to establish systemic behavior is not well understood. We propose a non-cell autonomous role for WOX5 in the CEI and identify a regulator, AN3/GIF1, that coordinates CEI divisions. Here we show with a multiscale hybrid model integrating ODEs and agent-based modeling that QC and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behavior, which led us to predict cell-type-specific expression dynamics of SHR, SCR, WOX5, AN3, and CYCD6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions. Thumbnail image}, author={Broeck, Lisa Van and Spurney, Ryan J. and Fisher, Adam P. and Schwartz, Michael and Clark, Natalie M. and Nguyen, Thomas T. and Madison, Imani and Gobble, Mariah and Long, Terri and Sozzani, Rosangela}, year={2020}, month={Dec} }
 @article{van den broeck_gordon_inzé_williams_sozzani_2020, title={Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling}, volume={11}, ISSN={1664-8021}, url={http://dx.doi.org/10.3389/fgene.2020.00457}, DOI={10.3389/fgene.2020.00457}, abstractNote={Plant responses to environmental and intrinsic signals are tightly controlled by multiple transcription factors (TFs). These TFs and their regulatory connections form gene regulatory networks (GRNs), which provide a blueprint of the transcriptional regulations underlying plant development and environmental responses. This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs. Additionally, this review describes network inference techniques that leverage gene expression data to predict regulatory interactions. These computational and experimental methodologies yield complex networks that can identify new regulatory interactions, driving novel hypotheses. Biological properties that contribute to the complexity of GRNs are also described in this review. These include network topology, network size, transient binding of TFs to DNA, and competition between multiple upstream regulators. Finally, this review highlights the potential of machine learning approaches to leverage gene expression data to predict phenotypic outputs.}, journal={Frontiers in Genetics}, publisher={Frontiers Media SA}, author={Van den Broeck, Lisa and Gordon, Max and Inzé, Dirk and Williams, Cranos and Sozzani, Rosangela}, year={2020}, month={May} }
 @inbook{madison_melvin_buckner_williams_sozzani_long_2020, title={MAGIC: Live imaging of cellular division in plant seedlings using lightsheet microscopy}, volume={160}, ISBN={9780128215333}, ISSN={0091-679X}, url={http://dx.doi.org/10.1016/bs.mcb.2020.04.004}, DOI={10.1016/bs.mcb.2020.04.004}, abstractNote={Imaging technologies have been used to understand plant genetic and developmental processes, from the dynamics of gene expression to tissue and organ morphogenesis. Although the field has advanced incredibly in recent years, gaps remain in identifying fine and dynamic spatiotemporal intervals of target processes, such as changes to gene expression in response to abiotic stresses. Lightsheet microscopy is a valuable tool for such studies due to its ability to perform long-term imaging at fine intervals of time and at low photo-toxicity of live vertically oriented seedlings. In this chapter, we describe a detailed method for preparing and imaging Arabidopsis thaliana seedlings for lightsheet microscopy via a Multi-Sample Imaging Growth Chamber (MAGIC), which allows simultaneous imaging of at least four samples. This method opens new avenues for acquiring imaging data at a high temporal resolution, which can be eventually probed to identify key regulatory time points and any spatial dependencies of target developmental processes.}, booktitle={Methods in Cell Biology}, publisher={Elsevier}, author={Madison, Imani and Melvin, Charles and Buckner, Eli and Williams, Cranos and Sozzani, Rosangela and Long, Terri}, year={2020}, pages={405–418} }
 @article{clark_van den broeck_guichard_stager_tanner_blilou_grossmann_iyer-pascuzzi_maizel_sparks_et al._2020, title={Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big}, volume={71}, ISSN={1543-5008 1545-2123}, url={http://dx.doi.org/10.1146/annurev-arplant-050718-100038}, DOI={10.1146/annurev-arplant-050718-100038}, abstractNote={The acquisition of quantitative information on plant development across a range of temporal and spatial scales is essential to understand the mechanisms of plant growth. Recent years have shown the emergence of imaging methodologies that enable the capture and analysis of plant growth, from the dynamics of molecules within cells to the measurement of morphometric and physiological traits in field-grown plants. In some instances, these imaging methods can be parallelized across multiple samples to increase throughput. When high throughput is combined with high temporal and spatial resolution, the resulting image-derived data sets could be combined with molecular large-scale data sets to enable unprecedented systems-level computational modeling. Such image-driven functional genomics studies may be expected to appear at an accelerating rate in the near future given the early success of the foundational efforts reviewed here. We present new imaging modalities and review how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale. Expected final online publication date for the Annual Review of Plant Biology, Volume 71 is April 29, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, number={1}, journal={Annual Review of Plant Biology}, publisher={Annual Reviews}, author={Clark, Natalie M. and Van den Broeck, Lisa and Guichard, Marjorie and Stager, Adam and Tanner, Herbert G. and Blilou, Ikram and Grossmann, Guido and Iyer-Pascuzzi, Anjali S. and Maizel, Alexis and Sparks, Erin E. and et al.}, year={2020}, month={Apr}, pages={789–816} }
 @article{clark_fisher_berckmans_van den broeck_nelson_nguyen_bustillo-avendaño_zebell_moreno-risueno_simon_et al._2020, title={Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division}, volume={117}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.2002166117}, DOI={10.1073/pnas.2002166117}, abstractNote={Significance The spatiotemporal regulation of stem cell division is important for proper cell differentiation and organ growth. Here we examine the roles of the transcription factors SHORTROOT (SHR) and SCARECROW (SCR) in two different stem cells: the cortex endodermis initials (CEI), which actively divide, and the quiescent center (QC), which is less mitotically active. We constructed a mathematical model that predicts putative SHR regulators, which were experimentally validated, and suggests that the SHR-SCR complex promotes CEI division but represses QC division. Through the cyclic process of experimentally validating model predictions that in turn inform the mathematical model, we gained insight into how protein complex stoichiometry and transcriptional regulation contribute to differences in the timing of divisions between specialized cell types. Stem cells divide and differentiate to form all of the specialized cell types in a multicellular organism. In the Arabidopsis root, stem cells are maintained in an undifferentiated state by a less mitotically active population of cells called the quiescent center (QC). Determining how the QC regulates the surrounding stem cell initials, or what makes the QC fundamentally different from the actively dividing initials, is important for understanding how stem cell divisions are maintained. Here we gained insight into the differences between the QC and the cortex endodermis initials (CEI) by studying the mobile transcription factor SHORTROOT (SHR) and its binding partner SCARECROW (SCR). We constructed an ordinary differential equation model of SHR and SCR in the QC and CEI which incorporated the stoichiometry of the SHR-SCR complex as well as upstream transcriptional regulation of SHR and SCR. Our model prediction, coupled with experimental validation, showed that high levels of the SHR-SCR complex are associated with more CEI division but less QC division. Furthermore, our model prediction allowed us to propose the putative upstream SHR regulators SEUSS and WUSCHEL-RELATED HOMEOBOX 5 and to experimentally validate their roles in QC and CEI division. In addition, our model established the timing of QC and CEI division and suggests that SHR repression of QC division depends on formation of the SHR homodimer. Thus, our results support that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche.}, number={26}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Clark, Natalie M. and Fisher, Adam P. and Berckmans, Barbara and Van den Broeck, Lisa and Nelson, Emily C. and Nguyen, Thomas T. and Bustillo-Avendaño, Estefano and Zebell, Sophia G. and Moreno-Risueno, Miguel A. and Simon, Rüdiger and et al.}, year={2020}, month={Jun}, pages={15332–15342} }
 @article{spurney_broeck_clark_fisher_balaguer_sozzani_2020, title={tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks}, volume={101}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.14558}, DOI={10.1111/tpj.14558}, abstractNote={Summary Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA‐sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet , a user‐friendly platform that can process raw RNA‐sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline ( hisat 2 + cufflinks package) and infer GRNs from these processed data. tuxnet is implemented as a graphical user interface and can mine gene regulations, either by applying a dynamic Bayesian network (DBN) inference algorithm, genist , or a regression tree‐based pipeline, rtp‐star . We obtained time‐course expression data of a PERIANTHIA ( PAN ) inducible line and inferred a GRN using genist to illustrate the use of tuxnet while gaining insight into the regulations downstream of the Arabidopsis root stem cell regulator PAN . Using rtp‐star , we inferred the network of ATHB13 , a downstream gene of PAN, for which we obtained wild‐type and mutant expression profiles. Additionally, we generated two networks using temporal data from developmental leaf data and spatial data from root cell‐type data to highlight the use of tuxnet to form new testable hypotheses from previously explored data. Our case studies feature the versatility of tuxnet when using different types of gene expression data to infer networks and its accessibility as a pipeline for non‐bioinformaticians to analyze transcriptome data, predict causal regulations, assess network topology and identify key regulators.}, number={3}, journal={PLANT JOURNAL}, author={Spurney, Ryan J. and Broeck, Lisa and Clark, Natalie M. and Fisher, Adam P. and Balaguer, Maria A. de Luis and Sozzani, Rosangela}, year={2020}, month={Feb}, pages={716–730} }
 @article{buckner_madison_chou_matthiadis_melvin_sozzani_williams_long_2019, title={Automated Imaging, Tracking, and Analytics Pipeline for Differentiating Environmental Effects on Root Meristematic Cell Division}, volume={10}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2019.01487}, DOI={10.3389/fpls.2019.01487}, abstractNote={Exposure of plants to abiotic stresses, whether individually or in combination, triggers dynamic changes to gene regulation. These responses induce distinct changes in phenotypic characteristics, enabling the plant to adapt to changing environments. For example, iron deficiency and heat stress have been shown to alter root development by reducing primary root growth and reducing cell proliferation, respectively. Currently, identifying the dynamic temporal coordination of genetic responses to combined abiotic stresses remains a bottleneck. This is, in part, due to an inability to isolate specific intervals in developmental time where differential activity in plant stress responses plays a critical role. Here, we observed that iron deficiency, in combination with temporary heat stress, suppresses the expression of iron deficiency-responsive pPYE::LUC (POPEYE::luciferase) and pBTS::LUC (BRUTUS::luciferase) reporter genes. Moreover, root growth was suppressed less under combined iron deficiency and heat stress than under either single stress condition. To further explore the interaction between pathways, we also created a computer vision pipeline to extract, analyze, and compare high-dimensional dynamic spatial and temporal cellular data in response to heat and iron deficiency stress conditions at high temporal resolution. Specifically, we used fluorescence light sheet microscopy to image Arabidopsis thaliana roots expressing CYCB1;1:GFP, a marker for cell entry into mitosis, every 20 min for 24 h exposed to either iron sufficiency, iron deficiency, heat stress, or combined iron deficiency and heat stress. Our pipeline extracted spatiotemporal metrics from these time-course data. These metrics showed that the persistency and timing of CYCB1;1:GFP signal were uniquely different under combined iron deficiency and heat stress conditions versus the single stress conditions. These metrics also indicated that the spatiotemporal characteristics of the CYCB1;1:GFP signal under combined stress were more dissimilar to the control response than the response seen under iron deficiency for the majority of the 24-h experiment. Moreover, the combined stress response was less dissimilar to the control than the response seen under heat stress. This indicated that pathways activated when the plant is exposed to both iron deficiency and heat stress affected CYCB1;1:GFP spatiotemporal function antagonistically}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Buckner, Eli and Madison, Imani and Chou, Hsuan and Matthiadis, Anna and Melvin, Charles E. and Sozzani, Rosangela and Williams, Cranos and Long, Terri A.}, year={2019}, month={Nov} }
 @article{vallarino_merchante_sánchez‐sevilla_luis balaguer_pott_ariza_casañal_posé_vioque_amaya_et al._2019, title={Characterizing the involvement of
            FaMADS9
            in the regulation of strawberry fruit receptacle development}, volume={18}, ISBN={1467-7652}, ISSN={1467-7644 1467-7652}, url={http://dx.doi.org/10.1111/pbi.13257}, DOI={10.1111/pbi.13257}, abstractNote={Abstract FaMADS9 is the strawberry (Fragaria x ananassa) gene that exhibits the highest homology to the tomato (Solanum lycopersicum) RIN gene. Transgenic lines were obtained in which FaMADS9 was silenced. The fruits of these lines did not show differences in basic parameters, such as fruit firmness or colour, but exhibited lower Brix values in three of the four independent lines. The gene ontology MapMan category that was most enriched among the differentially expressed genes in the receptacles at the white stage corresponded to the regulation of transcription, including a high percentage of transcription factors and regulatory proteins associated with auxin action. In contrast, the most enriched categories at the red stage were transport, lipid metabolism and cell wall. Metabolomic analysis of the receptacles of the transformed fruits identified significant changes in the content of maltose, galactonic acid‐1,4‐lactone, proanthocyanidins and flavonols at the green/white stage, while isomaltose, anthocyanins and cuticular wax metabolism were the most affected at the red stage. Among the regulatory genes that were differentially expressed in the transgenic receptacles were several genes previously linked to flavonoid metabolism, such as MYB10, DIV, ZFN1, ZFN2, GT2, and GT5, or associated with the action of hormones, such as abscisic acid, SHP, ASR, GTE7 and SnRK2.7. The inference of a gene regulatory network, based on a dynamic Bayesian approach, among the genes differentially expressed in the transgenic receptacles at the white and red stages, identified the genes KAN1, DIV, ZFN2 and GTE7 as putative targets of FaMADS9. A MADS9‐specific CArG box was identified in the promoters of these genes.}, number={4}, journal={Plant Biotechnology Journal}, publisher={Wiley}, author={Vallarino, José G. and Merchante, Catharina and Sánchez‐Sevilla, José F. and Luis Balaguer, María Angels and Pott, Delphine M. and Ariza, María T. and Casañal, Ana and Posé, David and Vioque, Amalia and Amaya, Iraida and et al.}, year={2019}, month={Oct}, pages={929–943} }
 @article{haque_ahmad_clark_williams_sozzani_2019, title={Computational prediction of gene regulatory networks in plant growth and development}, volume={47}, ISSN={1369-5266}, url={http://www.sciencedirect.com/science/article/pii/S1369526618300839}, DOI={10.1016/j.pbi.2018.10.005}, abstractNote={Plants integrate a wide range of cellular, developmental, and environmental signals to regulate complex patterns of gene expression. Recent advances in genomic technologies enable differential gene expression analysis at a systems level, allowing for improved inference of the network of regulatory interactions between genes. These gene regulatory networks, or GRNs, are used to visualize the causal regulatory relationships between regulators and their downstream target genes. Accordingly, these GRNs can represent spatial, temporal, and/or environmental regulations and can identify functional genes. This review summarizes recent computational approaches applied to different types of gene expression data to infer GRNs in the context of plant growth and development. Three stages of GRN inference are described: first, data collection and analysis based on the dataset type; second, network inference application based on data availability and proposed hypotheses; and third, validation based on in silico, in vivo, and in planta methods. In addition, this review relates data collection strategies to biological questions, organizes inference algorithms based on statistical methods and data types, discusses experimental design considerations, and provides guidelines for GRN inference with an emphasis on the benefits of integrative approaches, especially when a priori information is limited. Finally, this review concludes that computational frameworks integrating large-scale heterogeneous datasets are needed for a more accurate (e.g. fewer false interactions), detailed (e.g. discrimination between direct versus indirect interactions), and comprehensive (e.g. genetic regulation under various conditions and spatial locations) inference of GRNs.}, journal={Current Opinion in Plant Biology}, publisher={Elsevier BV}, author={Haque, Samiul and Ahmad, Jabeen S. and Clark, Natalie M. and Williams, Cranos M. and Sozzani, Rosangela}, year={2019}, month={Feb}, pages={96–105} }
 @article{smet_sevilem_luis balaguer_wybouw_mor_miyashima_blob_roszak_jacobs_boekschoten_et al._2019, title={DOF2.1 Controls Cytokinin-Dependent Vascular Cell Proliferation Downstream of TMO5/LHW}, volume={29}, ISSN={["1879-0445"]}, DOI={10.1016/j.cub.2018.12.041}, abstractNote={To create a three-dimensional structure, plants rely on oriented cell divisions and cell elongation. Oriented cell divisions are specifically important in procambium cells of the root to establish the different vascular cell types [1, 2]. These divisions are in part controlled by the auxin-controlled TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW) transcription factor complex [3-7]. Loss-of-function of tmo5 or lhw clade members results in strongly reduced vascular cell file numbers, whereas ectopic expression of both TMO5 and LHW can ubiquitously induce periclinal and radial cell divisions in all cell types of the root meristem. TMO5 and LHW interact only in young xylem cells, where they promote expression of two direct target genes involved in the final step of cytokinin (CK) biosynthesis, LONELY GUY3 (LOG3) and LOG4 [8, 9] Therefore, CK was hypothesized to act as a mobile signal from the xylem to trigger divisions in the neighboring procambium cells [3, 6]. To unravel how TMO5/LHW-dependent cytokinin regulates cell proliferation, we analyzed the transcriptional responses upon simultaneous induction of both transcription factors. Using inferred network analysis, we identified AT2G28510/DOF2.1 as a cytokinin-dependent downstream target gene. We further showed that DOF2.1 controls specific procambium cell divisions without inducing other cytokinin-dependent effects such as the inhibition of vascular differentiation. In summary, our results suggest that DOF2.1 and its closest homologs control vascular cell proliferation, thus leading to radial expansion of the root.}, number={3}, journal={CURRENT BIOLOGY}, author={Smet, Wouter and Sevilem, Iris and Luis Balaguer, Maria Angels and Wybouw, Brecht and Mor, Eliana and Miyashima, Shunsuke and Blob, Bernhard and Roszak, Pawel and Jacobs, Thomas B. and Boekschoten, Mark and et al.}, year={2019}, month={Feb}, pages={520-+} }
 @article{miyashima_roszak_sevilem_toyokura_blob_heo_mellor_help-rinta-rahko_otero_smet_et al._2019, title={Mobile PEAR transcription factors integrate hormone and miRNA cues to prime cambial growth}, volume={565}, ISSN={0028-0836, 1476-4687}, url={http://www.nature.com/articles/s41586-018-0839-y}, DOI={10.1038/s41586-018-0839-y}, abstractNote={Apical growth in plants initiates upon seed germination, whereas radial growth is primed only during early ontogenesis in procambium cells and activated later by the vascular cambium1. Although it is not known how radial growth is organized and regulated in plants, this system resembles the developmental competence observed in some animal systems, in which pre-existing patterns of developmental potential are established early on2,3. Here we show that in Arabidopsis the initiation of radial growth occurs around early protophloem-sieve-element cell files of the root procambial tissue. In this domain, cytokinin signalling promotes the expression of a pair of mobile transcription factors—PHLOEM EARLY DOF 1 (PEAR1) and PHLOEM EARLY DOF 2 (PEAR2)—and their four homologues (DOF6, TMO6, OBP2 and HCA2), which we collectively name PEAR proteins. The PEAR proteins form a short-range concentration gradient that peaks at protophloem sieve elements, and activates gene expression that promotes radial growth. The expression and function of PEAR proteins are antagonized by the HD-ZIP III proteins, well-known polarity transcription factors4—the expression of which is concentrated in the more-internal domain of radially non-dividing procambial cells by the function of auxin, and mobile miR165 and miR166 microRNAs. The PEAR proteins locally promote transcription of their inhibitory HD-ZIP III genes, and thereby establish a negative-feedback loop that forms a robust boundary that demarks the zone of cell division. Taken together, our data establish that during root procambial development there exists a network in which a module that links PEAR and HD-ZIP III transcription factors integrates spatial information of the hormonal domains and miRNA gradients to provide adjacent zones of dividing and more-quiescent cells, which forms a foundation for further radial growth. Radial growth in the roots of Arabidopsis, which is mediated by gene expression activated by the mobile PEAR1 and PEAR2 transcription factors, is initiated around protophloem-sieve-element cell files of procambial tissue.}, number={7740}, journal={Nature}, author={Miyashima, Shunsuke and Roszak, Pawel and Sevilem, Iris and Toyokura, Koichi and Blob, Bernhard and Heo, Jung-ok and Mellor, Nathan and Help-Rinta-Rahko, Hanna and Otero, Sofia and Smet, Wouter and et al.}, year={2019}, month={Jan}, pages={490–494} }
 @article{powers_holehouse_korasick_schreiber_clark_jing_emenecker_han_tycksen_hwang_et al._2019, title={Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana}, volume={76}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2019.06.044}, abstractNote={The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development. The auxin response factor (ARF) transcription factor family regulates auxin-responsive gene expression and exhibits nuclear localization in regions of high auxin responsiveness. Here we show that the ARF7 and ARF19 proteins accumulate in micron-sized assemblies within the cytoplasm of tissues with attenuated auxin responsiveness. We found that the intrinsically disordered middle region and the folded PB1 interaction domain of ARFs drive protein assembly formation. Mutation of a single lysine within the PB1 domain abrogates cytoplasmic assemblies, promotes ARF nuclear localization, and results in an altered transcriptome and morphological defects. Our data suggest a model in which ARF nucleo-cytoplasmic partitioning regulates auxin responsiveness, providing a mechanism for cellular competence for auxin signaling.}, number={1}, journal={MOLECULAR CELL}, author={Powers, Samantha K. and Holehouse, Alex S. and Korasick, David A. and Schreiber, Katherine H. and Clark, Natalie M. and Jing, Hongwei and Emenecker, Ryan and Han, Soeun and Tycksen, Eric and Hwang, Ildoo and et al.}, year={2019}, month={Oct}, pages={177-+} }
 @article{clark_buckner_fisher_nelson_nguyen_simmons_balaguer_butler-smith_sheldon_bergmann_et al._2019, title={Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks}, volume={10}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-019-13132-2}, abstractNote={Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood. Here, we find that, in the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks. Development of a mathematical model of TCX2 expression allows us to show that TCX2 orchestrates the coordinated division of different stem cell types. Our results highlight that genes expressed across different stem cell types ensure cross-communication among cells, allowing them to divide and develop harmonically together.}, journal={NATURE COMMUNICATIONS}, author={Clark, Natalie M. and Buckner, Eli and Fisher, Adam P. and Nelson, Emily C. and Nguyen, Thomas T. and Simmons, Abigail R. and Balaguer, Maria A. de Luis and Butler-Smith, Tiara and Sheldon, Parnell J. and Bergmann, Dominique C. and et al.}, year={2019}, month={Dec} }
 @article{di mambro_svolacchia_dello ioio_pierdonati_salvi_pedrazzini_vitale_perilli_sozzani_benfey_et al._2019, title={The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size}, volume={29}, ISSN={["1879-0445"]}, DOI={10.1016/j.cub.2019.02.022}, abstractNote={Plant developmental plasticity relies on the activities of meristems, regions where stem cells continuously produce new cells [1]. The lateral root cap (LRC) is the outermost tissue of the root meristem [1], and it is known to play an important role during root development [2-6]. In particular, it has been shown that mechanical or genetic ablation of LRC cells affect meristem size [7, 8]; however, the molecular mechanisms involved are unknown. Root meristem size and, consequently, root growth depend on the position of the transition zone (TZ), a boundary that separates dividing from differentiating cells [9, 10]. The interaction of two phytohormones, cytokinin and auxin, is fundamental in controlling the position of the TZ [9, 10]. Cytokinin via the ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) control auxin distribution within the meristem, generating an instructive auxin minimum that positions the TZ [10]. We identify a cytokinin-dependent molecular mechanism that acts in the LRC to control the position of the TZ and meristem size. We show that auxin levels within the LRC cells depends on PIN-FORMED 5 (PIN5), a cytokinin-activated intracellular transporter that pumps auxin from the cytoplasm into the endoplasmic reticulum, and on irreversible auxin conjugation mediated by the IAA-amino synthase GRETCHEN HAGEN 3.17 (GH3.17). By titrating auxin in the LRC, the PIN5 and the GH3.17 genes control auxin levels in the entire root meristem. Overall, our results indicate that the LRC serves as an auxin sink that, under the control of cytokinin, regulates meristem size and root growth.}, number={7}, journal={CURRENT BIOLOGY}, author={Di Mambro, Riccardo and Svolacchia, Noemi and Dello Ioio, Raffaele and Pierdonati, Emanuela and Salvi, Elena and Pedrazzini, Emanuela and Vitale, Alessandro and Perilli, Serena and Sozzani, Rosangela and Benfey, Philip N. and et al.}, year={2019}, month={Apr}, pages={1199-+} }
 @article{o'lexy_kasai_clark_fujiwara_sozzani_gallagher_2018, title={Exposure to heavy metal stress triggers changes in plasmodesmatal permeability via deposition and breakdown of callose}, volume={69}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/ery171}, abstractNote={As sessile organisms, plants continually modify their growth to adapt to changes in their environment. Here we show that significant changes in plasmodesmatal permeability underlie root responses to nutrient stress.}, number={15}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={O'Lexy, Ruthsabel and Kasai, Koji and Clark, Natalie and Fujiwara, Toru and Sozzani, Rosangela and Gallagher, Kimberly L.}, year={2018}, month={Jul}, pages={3715–3728} }
 @article{shibata_breuer_kawamura_clark_rymen_braidwood_morohashi_busch_benfey_sozzani_et al._2018, title={GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis}, volume={145}, ISSN={["1477-9129"]}, DOI={10.1242/dev.159707}, abstractNote={ABSTRACT How plants determine the final size of growing cells is an important, yet unresolved, issue. Root hairs provide an excellent model system with which to study this as their final cell size is remarkably constant under constant environmental conditions. Previous studies have demonstrated that a basic helix-loop helix transcription factor ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4) promotes root hair growth, but how hair growth is terminated is not known. In this study, we demonstrate that a trihelix transcription factor GT-2-LIKE1 (GTL1) and its homolog DF1 repress root hair growth in Arabidopsis. Our transcriptional data, combined with genome-wide chromatin-binding data, show that GTL1 and DF1 directly bind the RSL4 promoter and regulate its expression to repress root hair growth. Our data further show that GTL1 and RSL4 regulate each other, as well as a set of common downstream genes, many of which have previously been implicated in root hair growth. This study therefore uncovers a core regulatory module that fine-tunes the extent of root hair growth by the orchestrated actions of opposing transcription factors. Summary: Arabidopsis gtl1 df1 double mutants and tissue-specific overexpression of GTL1 and DF1 demonstrate that both GTL1 and DF1 negatively regulate root hair growth by directly repressing RSL4.}, number={3}, journal={DEVELOPMENT}, author={Shibata, Michitaro and Breuer, Christian and Kawamura, Ayako and Clark, Natalie M. and Rymen, Bart and Braidwood, Luke and Morohashi, Kengo and Busch, Wolfgang and Benfey, Philip N. and Sozzani, Rosangela and et al.}, year={2018}, month={Feb} }
 @inbook{clark_fisher_sozzani_2018, place={New York, NY}, series={Methods in Molecular Biology}, title={Identifying Differentially Expressed Genes Using Fluorescence-Activated Cell Sorting (FACS) and RNA Sequencing from Low Input Samples}, volume={1819}, ISBN={978-1-4939-8617-0 978-1-4939-8618-7}, url={http://link.springer.com/10.1007/978-1-4939-8618-7_6}, DOI={10.1007/978-1-4939-8618-7_6}, abstractNote={Cell type-specific gene expression profiles are useful for understanding genes that are important for the development of different tissues and organs. Here, we describe how to perform fluorescence-activated cell sorting (FACS) on Arabidopsis root protoplasts to isolate specific cell types in the root. We then detail how to extract and process RNA from a very low number of cells (≥40 cells) for RNA sequencing (RNA seq). Finally, we describe how to process RNA seq data using TopHat and how to identify differentially expressed genes using PoissonSeq.}, booktitle={Computational Cell Biology}, publisher={Springer New York}, author={Clark, Natalie M. and Fisher, Adam P. and Sozzani, Rosangela}, editor={Stechow, Louise von and Santos Delgado, AlbertoEditors}, year={2018}, pages={139–151}, collection={Methods in Molecular Biology} }
 @inproceedings{buckner_ottley_williams_luis balaguer_melvin_sozzani_2018, place={Honolulu, HI}, title={Tracking Gene Expression via Light Sheet Microscopy and Computer Vision in Living Organisms}, ISBN={978-1-5386-3646-6}, url={https://ieeexplore.ieee.org/document/8512416/}, DOI={10.1109/EMBC.2018.8512416}, abstractNote={Automated tracking of spatiotemporal gene expression using in vivo microscopy images have given great insight into understanding developmental processes in multicellular organisms. Many existing analysis tools rely on the fluorescent tagging of cell wall or cell nuclei localized proteins to assess position, orientation, and overall shape of an organism; information necessary for determining locations of gene expression activity. Particularly in plants, organism lines that have fluorescent tags can take months to develop, which can be time consuming and costly. We propose an automated solution for analyzing spatial characteristics of gene expression without the necessity of fluorescent tagged cell walls or cell nuclei. Our solution indicates, segments, and tracks gene expression using a fluorescent imaging channel of a light sheet microscope while determining gene expression location within an organism from a Brightfield (non-fluorescent) imaging channel. We use the images obtained from the Arabidopsis thaliana root as a proof of concept for our solution by studying the effects of heat shock stress on CYCLIN B1 protein production.}, booktitle={2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)}, publisher={IEEE}, author={Buckner, Eli and Ottley, Chanae and Williams, Cranos and Luis Balaguer, Angels de and Melvin, Charles E. and Sozzani, Rosangela}, year={2018}, month={Jul}, pages={818–821} }
 @article{di mambro_de ruvo_pacifici_salvi_sozzani_benfey_busch_novak_ljung_di paola_et al._2017, title={Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root}, volume={114}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1705833114}, abstractNote={Significance The maintenance of boundaries between neighboring groups of distinct cell types is vital during development of multicellular organisms, as groups of cells with distinct functions must be kept physically separated to guarantee correct control of organ and body growth and function. In the Arabidopsis root, the transition zone is a developmental boundary in the meristem that separates dividing from differentiating cells. Here, we infer that a well-defined and tightly controlled minimum of the hormone auxin acts as a signal to establish the position of the transition zone by controlling the developmental switch from cell division to cell differentiation. We provide the mechanistic and genetic basis of how another hormone, cytokinin, controls and positions this auxin minimum, thus regulating root size. In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the Arabidopsis root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin’s control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size.}, number={36}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Di Mambro, Riccardo and De Ruvo, Micol and Pacifici, Elena and Salvi, Elena and Sozzani, Rosangela and Benfey, Philip N. and Busch, Wolfgang and Novak, Ondrej and Ljung, Karin and Di Paola, Luisa and et al.}, year={2017}, month={Sep}, pages={E7641–E7649} }
 @article{liao_melvin_sozzani_jones_elston_jones_2017, title={Dose-Duration Reciprocity for G protein activation: Modulation of kinase to substrate ratio alters cell signaling}, volume={12}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0190000}, abstractNote={In animal cells, activation of heterotrimeric G protein signaling generally occurs when the system’s cognate signal exceeds a threshold, whereas in plant cells, both the amount and the exposure time of at least one signal, D-glucose, are used toward activation. This unusual signaling property called Dose-Duration Reciprocity, first elucidated in the genetic model Arabidopsis thaliana, is achieved by a complex that is comprised of a 7-transmembrane REGULATOR OF G SIGNALING (RGS) protein (AtRGS1), a Gα subunit that binds and hydrolyzes nucleotide, a Gβγ dimer, and three WITH NO LYSINE (WNK) kinases. D-glucose is one of several signals such as salt and pathogen-derived molecular patterns that operates through this protein complex to activate G protein signaling by WNK kinase transphosphorylation of AtRGS1. Because WNK kinases compete for the same substrate, AtRGS1, we hypothesize that activation is sensitive to the AtRGS1 amount and that modulation of the AtRGS1 pool affects the response to the stimulant. Mathematical simulation revealed that the ratio of AtRGS1 to the kinase affects system sensitivity to D-glucose, and therefore illustrates how modulation of the cellular AtRGS1 level is a means to change signal-induced activation. AtRGS1 levels change under tested conditions that mimic physiological conditions therefore, we propose a previously-unknown mechanism by which plants react to changes in their environment.}, number={12}, journal={PLOS ONE}, author={Liao, Kang-Ling and Melvin, Charles E. and Sozzani, Rosangela and Jones, Roger D. and Elston, Timothy C. and Jones, Alan M.}, year={2017}, month={Dec} }
 @article{wendrich_moller_li_saiga_sozzani_benfey_de rybel_weijers_2017, title={Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem}, volume={114}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1707400114}, abstractNote={Significance Plants have the ability to live and grow for many thousands of years due to the activity of groups of cells called meristems. Meristems contain stem cells that can survive the entire life of the plant and ensure the continuous supply of new cells. Stem cells are thought to be qualitatively different compared with their neighboring daughter cells. Here we show that in the case of the proximal root meristem, there does not seem to be such an on-off type of organization. We show that the majority of transcripts, together with other cellular properties, gradually transition from stem cell activity to differentiation, by opposing gradients. This impacts our understanding of meristem organization and will determine the direction of future research. In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem, a group of slowly dividing quiescent center cells is thought to limit stem cell activity to directly neighboring cells, thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction to the more gradual changes in cell division potential and differentiation that occur as cells move further away from the quiescent center. To address this paradox and to infer molecular organization of the root meristem, we used a whole-genome approach to determine dominant transcriptional patterns along root ontogeny zones. We found that the prevalent patterns are expressed in two opposing gradients. One is characterized by genes associated with development, the other enriched in differentiation genes. We confirmed these transcript gradients, and demonstrate that these translate to gradients in protein accumulation and gradual changes in cellular properties. We also show that gradients are genetically controlled through multiple pathways. Based on these findings, we propose that cells in the Arabidopsis root meristem gradually transition from stem cell activity toward differentiation.}, number={42}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Wendrich, Jos R. and Moller, Barbara K. and Li, Song and Saiga, Shunsuke and Sozzani, Rosangela and Benfey, Philip N. and De Rybel, Bert and Weijers, Dolf}, year={2017}, month={Oct}, pages={E8922–E8929} }
 @article{coneva_frank_balaguer_li_sozzani_chitwood_2017, title={Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii}, volume={175}, ISSN={["1532-2548"]}, DOI={10.1104/pp.17.00790}, abstractNote={Leaf thickness in desert-adapted tomato is characterized by the anatomic and transcriptional alterations that are uncovered by QTL analysis of introgression lines. Thicker leaves allow plants to grow in water-limited conditions. However, our understanding of the genetic underpinnings of this highly functional leaf shape trait is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato Solanum pennellii and identified quantitative trait loci. We report evidence of a complex genetic architecture of this trait and roles for both genetic and environmental factors. Several ILs with thick leaves have dramatically elongated palisade mesophyll cells and, in some cases, increased leaf ploidy. We characterized the thick IL2-5 and IL4-3 in detail and found increased mesophyll cell size and leaf ploidy levels, suggesting that endoreduplication underpins leaf thickness in tomato. Next, we queried the transcriptomes and inferred dynamic Bayesian networks of gene expression across early leaf ontogeny in these lines to compare the molecular networks that pattern leaf thickness. We show that thick ILs share S. pennellii-like expression profiles for putative regulators of cell shape and meristem determinacy as well as a general signature of cell cycle-related gene expression. However, our network data suggest that leaf thickness in these two lines is patterned at least partially by distinct mechanisms. Consistent with this hypothesis, double homozygote lines combining introgression segments from these two ILs show additive phenotypes, including thick leaves, higher ploidy levels, and larger palisade mesophyll cells. Collectively, these data establish a framework of genetic, anatomical, and molecular mechanisms that pattern leaf thickness in desert-adapted tomato.}, number={1}, journal={PLANT PHYSIOLOGY}, author={Coneva, Viktoriya and Frank, Margaret H. and Balaguer, Maria A. de Luis and Li, Mao and Sozzani, Rosangela and Chitwood, Daniel H.}, year={2017}, month={Sep}, pages={376–391} }
 @inbook{de luis balaguer_sozzani_2017, place={New York, NY}, series={Methods in Molecular Biology}, title={Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach}, volume={1629}, ISBN={978-1-4939-7124-4 978-1-4939-7125-1}, url={http://link.springer.com/10.1007/978-1-4939-7125-1_21}, DOI={10.1007/978-1-4939-7125-1_21}, abstractNote={Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs), and we then explain how to approximate DBN-based GRN models with continuous models. In addition, we show a MATLAB implementation of the key steps of this method, which we use to infer an Arabidopsis root GRN.}, booktitle={Plant Gene Regulatory Networks}, publisher={Springer New York}, author={Luis Balaguer, Maria Angels de and Sozzani, Rosangela}, editor={Kaufmann, Kerstin and Mueller-Roeber, BerndEditors}, year={2017}, pages={331–348}, collection={Methods in Molecular Biology} }
 @inbook{clark_sozzani_2017, place={New York, NY}, series={Methods in Molecular Biology}, title={Measuring Protein Movement, Oligomerization State, and Protein–Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (Scanning FCS)}, volume={1610}, ISBN={978-1-4939-7001-8 978-1-4939-7003-2}, url={http://link.springer.com/10.1007/978-1-4939-7003-2_16}, DOI={10.1007/978-1-4939-7003-2_16}, abstractNote={Scanning fluorescence correlation spectroscopy (scanning FCS) can be used to determine protein movement, oligomerization state, and protein–protein interaction. Here, we describe how to use the scanning FCS techniques of raster image correlation spectroscopy (RICS) and pair correlation function (pCF) to determine the rate and direction of protein movement. In addition, we detail how number and brightness (N&B) and cross-correlation analyses can be used to determine oligomerization state and binding ratios of protein complexes. We specifically describe how to acquire suitable images for scanning FCS analysis using the model plant Arabidopsis and how to perform the various analyses using the SimFCS software.}, booktitle={Plant Genomics}, publisher={Springer New York}, author={Clark, Natalie M. and Sozzani, Rosangela}, editor={Busch, WolfgangEditor}, year={2017}, pages={251–266}, collection={Methods in Molecular Biology} }
 @article{balaguer_fisher_clark_fernandez-espinosa_moller_weijers_lohmann_williams_lorenzo_sozzani_et al._2017, title={Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells}, volume={114}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1707566114}, abstractNote={Significance We developed a computational pipeline that uses gene expression datasets for inferring relationships among genes and predicting their importance. We showed that the capacity of our pipeline to integrate spatial and temporal transcriptional datasets improves the performance of inference algorithms. The combination of this pipeline with Arabidopsis stem cell-specific data resulted in networks that capture the regulations of stem cell-enriched genes in the stem cells and throughout root development. Our combined approach of molecular biology, computational biology, and mathematical biology, led to successful findings of factors that could play important roles in stem cell regulation and, in particular, quiescent center function. Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference. We leveraged the topology of our networks to infer potential major regulators. Specifically, through mathematical modeling and experimental validation, we identified PERIANTHIA (PAN) as an important molecular regulator of quiescent center function. The results presented in this work show that our combination of molecular biology, computational biology, and mathematical modeling is an efficient approach to identify candidate factors that function in the stem cells.}, number={36}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Balaguer, M. A. D. and Fisher, A. P. and Clark, N. M. and Fernandez-Espinosa, M. G. and Moller, B. K. and Weijers, D. and Lohmann, J. U. and Williams, C. and Lorenzo, O. and Sozzani, Rosangela and et al.}, year={2017}, month={Sep}, pages={E7632–E7640} }
 @article{fisher_sozzani_2016, title={Gene and networks regulating the root stem cell niche of Arabidopsis}, volume={29}, ISSN={["1879-0356"]}, DOI={10.1016/j.pbi.2015.11.002}, abstractNote={Stem cells are the source of different cell types and tissues in all multicellular organisms. In plants, the balance between stem cell self-renewal and differentiation of their progeny is crucial for correct tissue and organ formation. How transcriptional programs precisely control stem cell maintenance and identity, and what are the regulatory programs influencing stem cell asymmetric cell division (ACD), are key questions that researchers have sought to address for the past decade. Successful efforts in genetic, molecular, and developmental biology, along with mathematical modeling, have identified some of the players involved in stem cell regulation. In this review, we will discuss several studies that characterized many of the genetic programs and molecular mechanisms regulating stem cell ACD and their identity in the Arabidopsis root. We will also highlight how the growing use of mathematical modeling provides a comprehensive and quantitative perspective on the design rules governing stem cell ACDs.}, journal={Curr Opin Plant Biol}, author={Fisher, A.P. and Sozzani, R.}, year={2016}, month={Feb}, pages={38–43} }
 @article{slattery_grennan_sivaguru_sozzani_ort_2016, title={Light sheet microscopy reveals more gradual light attenuation in light-green versus dark-green soybean leaves}, volume={67}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erw246}, abstractNote={Highlight Light sheet microscopy, a novel approach to quantifying light profiles, showed more gradual light attenuation in light-green soybean leaves compared to dark-green soybean.}, number={15}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Slattery, Rebecca A. and Grennan, Aleel K. and Sivaguru, Mayandi and Sozzani, Rosangela and Ort, Donald R.}, year={2016}, month={Aug}, pages={4697–4709} }
 @article{de luis balaguer_ramos-pezzotti_rahhal_melvin_johannes_horn_sozzani_2016, title={Multi-sample Arabidopsis Growth and Imaging Chamber (MAGIC) for long term imaging in the ZEISS Lightsheet Z.1}, volume={419}, ISSN={1095-564X}, DOI={10.1016/j.ydbio.2016.05.029}, abstractNote={Time-course imaging experiments on live organisms are critical for understanding the dynamics of growth and development. Light-sheet microscopy has advanced the field of long-term imaging of live specimens by significantly reducing photo-toxicity and allowing fast acquisition of three-dimensional data over time. However, current light-sheet technology does not allow the imaging of multiple plant specimens in parallel. To achieve higher throughput, we have developed a Multi-sample Arabidopsis Growth and Imaging Chamber (MAGIC) that provides near-physiological imaging conditions and allows high-throughput time-course imaging experiments in the ZEISS Lightsheet Z.1. Here, we illustrate MAGIC's imaging capabilities by following cell divisions, as an indicator of plant growth and development, over prolonged time periods. To automatically quantify the number of cell divisions in long-term experiments, we present a FIJI-based image processing pipeline. We demonstrate that plants imaged with our chamber undergo cell divisions for >16 times longer than those with the glass capillary system supplied by the ZEISS Z1.}, number={1}, journal={Developmental Biology}, author={Luis Balaguer, Maria Angels de and Ramos-Pezzotti, Marina and Rahhal, Morjan B. and Melvin, Charles E. and Johannes, Eva and Horn, Timothy J. and Sozzani, Rosangela}, year={2016}, month={Jan}, pages={19–25} }
 @article{clark_hinde_winter_fisher_crosti_blilou_gratton_benfey_sozzani_2016, title={Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy}, volume={5}, journal={Elife}, author={Clark, N. M. and Hinde, E. and Winter, C. M. and Fisher, A. P. and Crosti, G. and Blilou, I. and Gratton, E. and Benfey, P. N. and Sozzani, R.}, year={2016} }
 @article{moreno-risueno_sozzani_yardimici_petricka_vernoux_blilou_alonso_winter_ohler_scheres_et al._2015, title={Bird and Scarecrow proteins organize tissue formation in Arabidopsis roots}, volume={350}, ISSN={["1095-9203"]}, DOI={10.1126/science.aad1171}, abstractNote={Multifunctional root regulators The growing plant root undergoes a variety of developmental steps that determine thickness and branching as the roots elaborate. Moreno-Risueno et al. identify a suite of transcription factors, some of which mobilize between cells, that regulate shifting fates during root growth. The same set of transcription factors governs identity and proliferation of the stem cells as well as the fates of daughter cells. Science, this issue p. 426 Plant tissue organization is maintained at all formative steps during root growth by the same set of transcription factors. Tissue patterns are dynamically maintained. Continuous formation of plant tissues during postembryonic growth requires asymmetric divisions and the specification of cell lineages. We show that the BIRDs and SCARECROW regulate lineage identity, positional signals, patterning, and formative divisions throughout Arabidopsis root growth. These transcription factors are postembryonic determinants of the ground tissue stem cells and their lineage. Upon further activation by the positional signal SHORT-ROOT (a mobile transcription factor), they direct asymmetric cell divisions and patterning of cell types. The BIRDs and SCARECROW with SHORT-ROOT organize tissue patterns at all formative steps during growth, ensuring developmental plasticity.}, number={6259}, journal={Science}, author={Moreno-Risueno, MA. and Sozzani, R. and Yardimici, GG. and Petricka, JJ. and Vernoux, T. and Blilou, I. and Alonso, J. and Winter, CM. and Ohler, U. and Scheres, B. and et al.}, year={2015}, pages={426–430} }
 @misc{sozzani_busch_spalding_benfey_2014, title={Advanced imaging techniques for the study of plant growth and development}, volume={19}, ISSN={["1878-4372"]}, DOI={10.1016/j.tplants.2013.12.003}, abstractNote={•Integration of imaging tools with genome-wide approaches and modeling. •Quantitative measurements to describe biological systems at cellular resolution over time. •Recent developments in the field of imaging. •Vision-based methods (2D high-throughput and non-destructive methods). A variety of imaging methodologies are being used to collect data for quantitative studies of plant growth and development from living plants. Multi-level data, from macroscopic to molecular, and from weeks to seconds, can be acquired. Furthermore, advances in parallelized and automated image acquisition enable the throughput to capture images from large populations of plants under specific growth conditions. Image-processing capabilities allow for 3D or 4D reconstruction of image data and automated quantification of biological features. These advances facilitate the integration of imaging data with genome-wide molecular data to enable systems-level modeling. A variety of imaging methodologies are being used to collect data for quantitative studies of plant growth and development from living plants. Multi-level data, from macroscopic to molecular, and from weeks to seconds, can be acquired. Furthermore, advances in parallelized and automated image acquisition enable the throughput to capture images from large populations of plants under specific growth conditions. Image-processing capabilities allow for 3D or 4D reconstruction of image data and automated quantification of biological features. These advances facilitate the integration of imaging data with genome-wide molecular data to enable systems-level modeling. laser microscopy that allows image acquisition of fluorescent molecules producing images with high horizontal resolution and depth selectivity. technique in which the sample is illuminated perpendicular to the direction of observation. 3D image computed from multiple 2D projections from different angles obtained by interaction of matter and X-rays. apparatus in which small volumes of liquid can be controlled. integrated and automated approach to track cell lineages over time, in which images of organs are acquired from multiple angles, computationally merged and segmented. 3D image computed from multiple 2D projections from different angles obtained by optical microscopy. genome regions that underlie the quantitative variation of a trait. collection of lines, each containing chromosomes which constitute a genetic mosaic of two parental lines. light sheet illumination-based microscopy allowing for image acquisition with high-spatial and temporal resolution. microscopy technique that can yield images with a resolution higher than the diffraction limit would allow.}, number={5}, journal={TRENDS IN PLANT SCIENCE}, author={Sozzani, Rosangela and Busch, Wolfgang and Spalding, Edgar P. and Benfey, Philip N.}, year={2014}, month={May}, pages={304–310} }
 @misc{clark_balaguer_sozzani_2014, title={Experimental data and computational modeling link auxin gradient and development in the Arabidopsis root}, volume={5}, journal={Frontiers in Plant Science}, author={Clark, N. M. and Balaguer, M. A. D. and Sozzani, R.}, year={2014} }
 @article{gallagher_sozzani_lee_2014, title={Intercellular Protein Movement: Deciphering the Language of Development}, volume={30}, ISSN={["1530-8995"]}, DOI={10.1146/annurev-cellbio-100913-012915}, abstractNote={Development in multicellular organisms requires the coordinated production of a large number of specialized cell types through sophisticated signaling mechanisms. Non-cell-autonomous signals are one of the key mechanisms by which organisms coordinate development. In plants, intercellular movement of transcription factors and other mobile signals, such as hormones and peptides, is essential for normal development. Through a combination of different approaches, a large number of non-cell-autonomous signals that control plant development have been identified. We review some of the transcriptional regulators that traffic between cells, as well as how changes in symplasmic continuity affect and are affected by development. We also review current models for how mobile signals move via plasmodesmata and how movement is inhibited. Finally, we consider challenges in and new tools for studying protein movement.}, journal={ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 30}, author={Gallagher, Kimberly L. and Sozzani, Rosangela and Lee, Chin-Mei}, year={2014}, pages={207–233} }
 @misc{kajala_ramakrishna_fisher_bergmann_de smet_sozzani_weijers_brady_2014, title={Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants}, volume={113}, ISSN={["1095-8290"]}, DOI={10.1093/aob/mcu065}, abstractNote={BACKGROUND
Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic ('niche-controlled') or intrinsic regulatory mechanisms and are fundamentally important in plant development.


SCOPE
This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells.


CONCLUSIONS
Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.}, number={7}, journal={ANNALS OF BOTANY}, author={Kajala, Kaisa and Ramakrishna, Priya and Fisher, Adam and Bergmann, Dominique C. and De Smet, Ive and Sozzani, Rosangela and Weijers, Dolf and Brady, Siobhan M.}, year={2014}, month={Jun}, pages={1083–1105} }
 @misc{sozzani_iyer-pascuzzi_2014, title={Postembryonic control of root meristem growth and development}, volume={17}, ISSN={["1879-0356"]}, DOI={10.1016/j.pbi.2013.10.005}, abstractNote={Organ development in multicellular organisms is dependent on the proper balance between cell proliferation and differentiation. In the Arabidopsis root apical meristem, meristem growth is the result of cell divisions in the proximal meristem and cell differentiation in the elongation and differentiation zones. Hormones, transcription factors and small peptides underpin the molecular mechanisms governing these processes. Computer modeling has aided our understanding of the dynamic interactions involved in stem cell maintenance and meristem activity. Here we review recent advances in our understanding of postembryonic root stem cell maintenance and control of meristem size.}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Sozzani, Rosangela and Iyer-Pascuzzi, Anjali}, year={2014}, month={Feb}, pages={7–12} }
 @article{moubayidin_di mambro_sozzani_pacifici_salvi_terpstra_bao_van dijken_dello ioio_perilli_et al._2013, title={Spatial Coordination between Stem Cell Activity and Cell Differentiation in the Root Meristem}, volume={26}, ISSN={15345807}, url={https://linkinghub.elsevier.com/retrieve/pii/S1534580713003882}, DOI={10.1016/j.devcel.2013.06.025}, abstractNote={A critical issue in development is the coordination of the activity of stem cell niches with differentiation of their progeny to ensure coherent organ growth. In the plant root, these processes take place at opposite ends of the meristem and must be coordinated with each other at a distance. Here, we show that in Arabidopsis, the gene SCR presides over this spatial coordination. In the organizing center of the root stem cell niche, SCR directly represses the expression of the cytokinin-response transcription factor ARR1, which promotes cell differentiation, controlling auxin production via the ASB1 gene and sustaining stem cell activity. This allows SCR to regulate, via auxin, the level of ARR1 expression in the transition zone where the stem cell progeny leaves the meristem, thus controlling the rate of differentiation. In this way, SCR simultaneously controls stem cell division and differentiation, ensuring coherent root growth.}, number={4}, journal={Developmental Cell}, author={Moubayidin, Laila and Di Mambro, Riccardo and Sozzani, Rosangela and Pacifici, Elena and Salvi, Elena and Terpstra, Inez and Bao, Dongping and van Dijken, Anja and Dello Ioio, Raffaele and Perilli, Serena and et al.}, year={2013}, month={Aug}, pages={405–415} }
 @article{cruz-ramírez_díaz-triviño_blilou_grieneisen_sozzani_zamioudis_miskolczi_nieuwland_benjamins_dhonukshe_et al._2012, title={A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division}, volume={150}, ISSN={1097-4172}, DOI={10.1016/j.cell.2012.07.017}, abstractNote={<h2>Summary</h2> In plants, where cells cannot migrate, asymmetric cell divisions (ACDs) must be confined to the appropriate spatial context. We investigate tissue-generating asymmetric divisions in a stem cell daughter within the <i>Arabidopsis</i> root. Spatial restriction of these divisions requires physical binding of the stem cell regulator SCARECROW (SCR) by the RETINOBLASTOMA-RELATED (RBR) protein. In the stem cell niche, SCR activity is counteracted by phosphorylation of RBR through a cyclinD6;1-CDK complex. This cyclin is itself under transcriptional control of SCR and its partner SHORT ROOT (SHR), creating a robust bistable circuit with either high or low SHR-SCR complex activity. Auxin biases this circuit by promoting <i>CYCD6;1</i> transcription. Mathematical modeling shows that ACDs are only switched on after integration of radial and longitudinal information, determined by SHR and auxin distribution, respectively. Coupling of cell-cycle progression to protein degradation resets the circuit, resulting in a "flip flop" that constrains asymmetric cell division to the stem cell region.}, number={5}, journal={Cell}, author={Cruz-Ramírez, Alfredo and Díaz-Triviño, Sara and Blilou, Ikram and Grieneisen, Verônica A. and Sozzani, Rosangela and Zamioudis, Christos and Miskolczi, Pál and Nieuwland, Jeroen and Benjamins, René and Dhonukshe, Pankaj and et al.}, year={2012}, month={Aug}, pages={1002–1015} }
 @article{liberman_sozzani_benfey_2012, title={Integrative systems biology: an attempt to describe a simple weed}, volume={15}, ISSN={1879-0356}, DOI={10.1016/j.pbi.2012.01.004}, abstractNote={Genome-scale studies hold great promise for revealing novel plant biology. Because of the complexity of these techniques, numerous considerations need to be made before embarking on a study. Here we focus on the Arabidopsis model system because of the wealth of available genome-scale data. Many approaches are available that provide genome-scale information regarding the state of a given organism (e.g. genomics, epigenomics, transcriptomics, proteomics, metabolomics interactomics, ionomics, phenomics, etc.). Integration of all of these types of data will be necessary for a comprehensive description of Arabidopsis. In this review we propose that 'triangulation' among transcriptomics, proteomics and metabolomics is a meaningful approach for beginning this integrative analysis and uncovering a systems level perspective of Arabidopsis biology.}, number={2}, journal={Current Opinion in Plant Biology}, author={Liberman, Louisa M. and Sozzani, Rosangela and Benfey, Philip N.}, year={2012}, month={Apr}, pages={162–167} }
 @article{engstrom_andersen_gumulak-smith_hu_orlova_sozzani_bowman_2011, title={Arabidopsis homologs of the petunia hairy meristem gene are required for maintenance of shoot and root indeterminacy}, volume={155}, ISSN={1532-2548}, DOI={10.1104/pp.110.168757}, abstractNote={Maintenance of indeterminacy is fundamental to the generation of plant architecture and a central component of the plant life strategy. Indeterminacy in plants is a characteristic of shoot and root meristems, which must balance maintenance of indeterminacy with organogenesis. The Petunia hybrida HAIRY MERISTEM (HAM) gene, a member of the GRAS family of transcriptional regulators, promotes shoot indeterminacy by an undefined non-cell-autonomous signaling mechanism(s). Here, we report that Arabidopsis (Arabidopsis thaliana) mutants triply homozygous for knockout alleles in three Arabidopsis HAM orthologs (Atham1,2,3 mutants) exhibit loss of indeterminacy in both the shoot and root. In the shoot, the degree of penetrance of the loss-of-indeterminacy phenotype of Atham1,2,3 mutants varies among shoot systems, with arrest of the primary vegetative shoot meristem occurring rarely or never, secondary shoot meristems typically arresting prior to initiating organogenesis, and inflorescence and flower meristems exhibiting a phenotypic range extending from wild type (flowers) to meristem arrest preempting organogenesis (flowers and inflorescence). Atham1,2,3 mutants also exhibit aberrant shoot phyllotaxis, lateral organ abnormalities, and altered meristem morphology in functioning meristems of both rosette and inflorescence. Root meristems of Atham1,2,3 mutants are significantly smaller than in the wild type in both longitudinal and radial axes, a consequence of reduced rates of meristem cell division that culminate in root meristem arrest. Atham1,2,3 phenotypes are unlikely to reflect complete loss of HAM function, as a fourth, more distantly related Arabidopsis HAM homolog, AtHAM4, exhibits overlapping function with AtHAM1 and AtHAM2 in promoting shoot indeterminacy.}, number={2}, journal={Plant Physiology}, author={Engstrom, Eric M. and Andersen, Carl M. and Gumulak-Smith, Juliann and Hu, John and Orlova, Evguenia and Sozzani, Rosangela and Bowman, John L.}, year={2011}, month={Feb}, pages={735–750} }
 @article{sozzani_benfey_2011, title={High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype}, volume={12}, ISSN={1474-760X}, url={https://doi.org/10.1186/gb-2011-12-3-219}, DOI={10.1186/gb-2011-12-3-219}, abstractNote={High-throughput phenotyping approaches (phenomics) are being combined with genome-wide genetic screens to identify alterations in phenotype that result from gene inactivation. Here we highlight promising technologies for 'phenome-scale' analyses in multicellular organisms.}, number={3}, journal={Genome Biology}, author={Sozzani, Rosangela and Benfey, Philip N.}, year={2011}, month={Mar}, pages={219} }
 @article{sozzani_cui_moreno-risueno_busch_van norman_vernoux_brady_dewitte_murray_benfey_2010, title={Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth}, volume={466}, ISSN={0028-0836 1476-4687}, url={http://dx.doi.org/10.1038/nature09143}, DOI={10.1038/nature09143}, abstractNote={The development of multicellular organisms relies on the coordinated control of cell divisions leading to proper patterning and growth. The molecular mechanisms underlying pattern formation, particularly the regulation of formative cell divisions, remain poorly understood. In Arabidopsis, formative divisions generating the root ground tissue are controlled by SHORTROOT (SHR) and SCARECROW (SCR). Here we show, using cell-type-specific transcriptional effects of SHR and SCR combined with data from chromatin immunoprecipitation-based microarray experiments, that SHR regulates the spatiotemporal activation of specific genes involved in cell division. Coincident with the onset of a specific formative division, SHR and SCR directly activate a D-type cyclin; furthermore, altering the expression of this cyclin resulted in formative division defects. Our results indicate that proper pattern formation is achieved through transcriptional regulation of specific cell-cycle genes in a cell-type- and developmental-stage-specific context. Taken together, we provide evidence for a direct link between developmental regulators, specific components of the cell-cycle machinery and organ patterning.}, number={7302}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Sozzani, R. and Cui, H. and Moreno-Risueno, M. A. and Busch, W. and Van Norman, J. M. and Vernoux, T. and Brady, S. M. and Dewitte, W. and Murray, J. A. H. and Benfey, P. N.}, year={2010}, month={Jul}, pages={128–132} }
 @article{sozzani_maggio_giordo_umana_ascencio-ibañez_hanley-bowdoin_bergounioux_cella_albani_2010, title={The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis}, volume={72}, ISSN={1573-5028}, DOI={10.1007/s11103-009-9577-8}, abstractNote={An emerging view of plant cell cycle regulators, including the E2F transcription factors, implicates them in the integration of cell proliferation and development. Arabidopsis encodes six E2F proteins that can act as activators or repressors of E2F-responsive genes. E2FA, E2FB and E2FC interact with the retinoblastoma-like RBR protein and bind to DNA together with their DP partners. In contrast, E2FD, E2FE and E2FF (also known as DEL2, DEL1 and DEL3) are atypical E2Fs that possess duplicated DNA binding regions, lack trans-activating and RBR-binding domains and are believed to act as transcriptional inhibitors/repressors. E2FE/DEL1 has been shown to inhibit the endocycle and E2FF/DEL3 appears to control cell expansion but the role of E2FD/DEL2 has not been reported so far. In this study, we investigated the expression of E2FD/DEL2 and analysed the accumulation of its product. These studies revealed that E2FD/DEL2 accumulation is subject to negative post-translational regulation mediated by the plant hormone auxin. Moreover, the analysis of mutant and transgenic plants characterized by altered expression of E2FD/DEL2 has revealed that this atypical E2F can affect plant growth by promoting cell proliferation and repressing cell elongation. Overexpression of E2FD/DEL2 increased the expression of E2FA, E2FB and E2FE/DEL1 whereas its inactivation led to the up-regulation of genes encoding repressors of cell division. These results suggest that E2FD/DEL2 is part of a regulatory network that controls the balance between cell proliferation and development in Arabidopsis.}, number={4-5}, journal={Plant Molecular Biology}, author={Sozzani, Rosangela and Maggio, Caterina and Giordo, Roberta and Umana, Elisabetta and Ascencio-Ibañez, Jose Trinidad and Hanley-Bowdoin, Linda and Bergounioux, Catherine and Cella, Rino and Albani, Diego}, year={2010}, month={Mar}, pages={381–395} }
 @article{sozzani_cui_moreno-risueno_busch_van norman_vernoux_brady_dewitte_murray_benfey_2010, title={The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root}, volume={466}, number={7302}, journal={Nature}, author={Sozzani, R. and Cui, H. and Moreno-Risueno, M.A. and Busch, W. and Van Norman, J.M. and Vernoux, T. and Brady, S.M. and Dewitte, W. and Murray, J.A. and Benfey, P.N.}, year={2010}, pages={128–132} }
 @article{benfey_cui_twigg_long_iyer-pascuzzi_tsukagoshi_sozzani_jackson_van norman_moreno-risueno_2009, title={Development rooted in interwoven networks}, volume={331}, ISSN={0012-1606}, url={http://dx.doi.org/10.1016/j.ydbio.2009.05.012}, DOI={10.1016/j.ydbio.2009.05.012}, abstractNote={Freshwater planarians appear to utilize inductive signals to specify their germ cell lineage: germ cells are believed to form post-embryonically from the pluripotent somatic stem cells, known as neoblasts. Previously, we identified a planarian homolog of nanos (Smed-nanos) and demonstrated by RNA interference (RNAi) that this gene is required for the development, maintenance, and regeneration of planarian germ cells. We have performed microarray analyses to compare gene expression profiles between planarians with early germ cells and those without them. We identified ∼300 genes that are significantly down-regulated in animals lacking early germ cells. This data set contains genes implicated in germ cell development in other organisms, conserved genes not yet reported to have germ cell-related functions, and novel genes. Analysis using putative domain functions (Clusters of Orthologous Groups) suggested diverse molecular functions, including cytoskeletal components, metabolism, RNA processing and modification, transcription, as well as signal transduction. Top hits have been validated by in situ hybridization. Functional analyses of these genes via RNA interference are being carried out. Thus far, we have identified several genes that, when knocked down by RNAi, cause various defects in germ cell development, including: impaired testes development; loss of spermatogonial stem cells; meiotic failure; and defects in sperm elongation. This work will contribute to our knowledge of conserved regulators of germ cell differentiation. (Supported by NIH-NICHD R01-HD043403.)}, number={2}, journal={Developmental Biology}, publisher={Elsevier BV}, author={Benfey, Philip N. and Cui, Hongchang and Twigg, Richard and Long, Terri and Iyer-Pascuzzi, Anjali and Tsukagoshi, Hironaka and Sozzani, Rosangela and Jackson, Terry and Van Norman, Jaimie and Moreno-Risueno, Miguel}, year={2009}, month={Jul}, pages={386} }
 @article{ni_sozzani_blanchet_domenichini_reuzeau_cella_bergounioux_raynaud_2009, title={The Arabidopsis MCM2 gene is essential to embryo development and its over-expression alters root meristem function}, volume={184}, ISSN={1469-8137}, DOI={10.1111/j.1469-8137.2009.02961.x}, abstractNote={* Minichromosome maintenance (MCM) proteins are subunits of the pre-replication complex that probably function as DNA helicases during the S phase of the cell cycle. Here, we investigated the function of AtMCM2 in Arabidopsis. * To gain an insight into the function of AtMCM2, we combined loss- and gain-of-function approaches. To this end, we analysed two null alleles of AtMCM2, and generated transgenic plants expressing AtMCM2 downstream of the constitutive 35S promoter. * Disruption of AtMCM2 is lethal at a very early stage of embryogenesis, whereas its over-expression results in reduced growth and inhibition of endoreduplication. In addition, over-expression of AtMCM2 induces the formation of additional initials in the columella root cap. In the plt1,2 mutant, defective for root apical meristem maintenance, over-expression of AtMCM2 induces lateral root initiation close to the root tip, a phenotype not reported in the wild-type or in plt1,2 mutants, even when cell cycle regulators, such as AtCYCD3;1, were over-expressed. * Taken together, our results provide evidence for the involvement of AtMCM2 in DNA replication, and suggest that it plays a crucial role in root meristem function.}, number={2}, journal={The New Phytologist}, author={Ni, Di An and Sozzani, Rosangela and Blanchet, Sophie and Domenichini, Séverine and Reuzeau, Christophe and Cella, Rino and Bergounioux, Catherine and Raynaud, Cécile}, year={2009}, month={Oct}, pages={311–322} }
 @article{ascencio-ibáñez_sozzani_lee_chu_wolfinger_cella_hanley-bowdoin_2008, title={Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection}, volume={148}, ISSN={0032-0889}, DOI={10.1104/pp.108.121038}, abstractNote={Geminiviruses are small DNA viruses that use plant replication machinery to amplify their genomes. Microarray analysis of the Arabidopsis (Arabidopsis thaliana) transcriptome in response to cabbage leaf curl virus (CaLCuV) infection uncovered 5,365 genes (false discovery rate <0.005) differentially expressed in infected rosette leaves at 12 d postinoculation. Data mining revealed that CaLCuV triggers a pathogen response via the salicylic acid pathway and induces expression of genes involved in programmed cell death, genotoxic stress, and DNA repair. CaLCuV also altered expression of cell cycle-associated genes, preferentially activating genes expressed during S and G2 and inhibiting genes active in G1 and M. A limited set of core cell cycle genes associated with cell cycle reentry, late G1, S, and early G2 had increased RNA levels, while core cell cycle genes linked to early G1 and late G2 had reduced transcripts. Fluorescence-activated cell sorting of nuclei from infected leaves revealed a depletion of the 4C population and an increase in 8C, 16C, and 32C nuclei. Infectivity studies of transgenic Arabidopsis showed that overexpression of CYCD3;1 or E2FB, both of which promote the mitotic cell cycle, strongly impaired CaLCuV infection. In contrast, overexpression of E2FA or E2FC, which can facilitate the endocycle, had no apparent effect. These results showed that geminiviruses and RNA viruses interface with the host pathogen response via a common mechanism, and that geminiviruses modulate plant cell cycle status by differentially impacting the CYCD/retinoblastoma-related protein/E2F regulatory network and facilitating progression into the endocycle.}, number={1}, journal={Plant Physiology}, author={Ascencio-Ibáñez, José Trinidad and Sozzani, Rosangela and Lee, Tae-Jin and Chu, Tzu-Ming and Wolfinger, Russell D. and Cella, Rino and Hanley-Bowdoin, Linda}, year={2008}, month={Sep}, pages={436–454} }
 @article{sozzani_maggio_varotto_canova_bergounioux_albani_cella_2006, title={Interplay between Arabidopsis Activating Factors E2Fb and E2Fa in Cell Cycle Progression and Development}, volume={140}, ISSN={0032-0889, 1532-2548}, url={http://www.plantphysiol.org/content/140/4/1355}, DOI={10.1104/pp.106.077990}, abstractNote={Eukaryotic E2Fs are conserved transcription factors playing crucial and antagonistic roles in several pathways related to cell division, DNA repair, and differentiation. In plants, these processes are strictly intermingled at the growing zone to produce postembryonic development in response to internal signals and environmental cues. Of the six AtE2F proteins found in Arabidopsis (Arabidopsis thaliana), only AtE2Fa and AtE2Fb have been clearly indicated as activators of E2F-responsive genes. AtE2Fa activity was shown to induce S phase and endoreduplication, whereas the function of AtE2Fb and the interrelationship between these two transcription factors was unclear. We have investigated the role played by the AtE2Fb gene during cell cycle and development performing in situ RNA hybridization, immunolocalization of the AtE2Fb protein in planta, and analysis of AtE2Fb promoter activity in transgenic plants. Overexpression of AtE2Fb in transgenic Arabidopsis plants led to striking modifications of the morphology of roots, cotyledons, and leaves that can be ascribed to stimulation of cell division. The accumulation of the AtE2Fb protein in these lines was paralleled by an increased expression of E2F-responsive G1/S and G2/M marker genes. These results suggest that AtE2Fa and AtE2Fb have specific expression patterns and play similar but distinct roles during cell cycle progression.}, number={4}, journal={Plant Physiology}, author={Sozzani, Rosangela and Maggio, Caterina and Varotto, Serena and Canova, Sabrina and Bergounioux, Catherine and Albani, Diego and Cella, Rino}, year={2006}, month={Apr}, pages={1355–1366} }
 @article{raynaud_sozzani_glab_domenichini_perennes_cella_kondorosi_bergounioux_2006, title={Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis}, volume={47}, ISSN={0960-7412}, DOI={10.1111/j.1365-313X.2006.02799.x}, abstractNote={The proliferating cell nuclear antigen (PCNA) functions as a sliding clamp for DNA polymerase, and is thus a key actor in DNA replication. It is also involved in DNA repair, maintenance of heterochromatic regions throughout replication, cell cycle regulation and programmed cell death. Identification of PCNA partners is therefore necessary for understanding these processes. Here we identify two Arabidopsis SET-domain proteins that interact with PCNA: ATXR5 and ATXR6. A truncated ATXR5Deltaex2, incapable of interacting with PCNA, also occurs in planta. ATXR6, upregulated during the S phase, is upregulated by AtE2F transcription factors, suggesting that it is required for S-phase progression. The two proteins differ in their subcellular localization: ATXR5 has a dual localization in plastids and in the nucleus, whereas ATXR6 is solely nuclear. This indicates that the two proteins may play different roles in plant cells. However, overexpression of either ATXR5 or ATXR6 causes male sterility because of the degeneration of defined cell types. Taken together, our results suggest that both proteins may play a role in the cell cycle or DNA replication, and that the activity of ATXR5 may be regulated via its subcellular localization.}, number={3}, journal={The Plant Journal: For Cell and Molecular Biology}, author={Raynaud, Cécile and Sozzani, Rosangela and Glab, Nathalie and Domenichini, Séverine and Perennes, Claudette and Cella, Rino and Kondorosi, Eva and Bergounioux, Catherine}, year={2006}, month={Aug}, pages={395–407} }