@article{reyes_flores-vergara_guerra-peraza_rajabu_desai_hiromoto-ruiz_ndunguru_hanley-bowdoin_kjemtrup_ascencio-ibanez_et al._2017, title={A VIGS screen identifies immunity in the Arabidopsis Pla-1 accession to viruses in two different genera of the Geminiviridae}, volume={92}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.13716}, abstractNote={Summary}, number={5}, journal={PLANT JOURNAL}, author={Reyes, Maria Ines and Flores-Vergara, Miguel A. and Guerra-Peraza, Orlene and Rajabu, Cyprian and Desai, Jigar and Hiromoto-Ruiz, Yokiko H. and Ndunguru, Joseph and Hanley-Bowdoin, Linda and Kjemtrup, Susanne and Ascencio-Ibanez, Jose T. and et al.}, year={2017}, month={Dec}, pages={796–807} }
 @article{gong_flores-vergara_hong_chu_lim_franks_liu_xu_physiology_2016, title={SEUSS Integrates Gibberellin Signaling with Transcriptional Inputs from the SHR-SCR-SCL3 Module to Regulate Middle Cortex Formation in the Arabidopsis Root}, volume={170}, ISSN={["1532-2548"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84959314828&partnerID=MN8TOARS}, DOI={10.1104/pp.15.01501}, abstractNote={The transcription factor SEU promotes middle cortex formation through a network of transcription factor interactions. A decade of studies on middle cortex (MC) formation in the root endodermis of Arabidopsis (Arabidopsis thaliana) have revealed a complex regulatory network that is orchestrated by several GRAS family transcription factors, including SHORT-ROOT (SHR), SCARECROW (SCR), and SCARECROW-LIKE3 (SCL3). However, how their functions are regulated remains obscure. Here we show that mutations in the SEUSS (SEU) gene led to a higher frequency of MC formation. seu mutants had strongly reduced expression of SHR, SCR, and SCL3, suggesting that SEU positively regulates these genes. Our results further indicate that SEU physically associates with upstream regulatory sequences of SHR, SCR, and SCL3; and that SEU has distinct genetic interactions with these genes in the control of MC formation, with SCL3 being epistatic to SEU. Similar to SCL3, SEU was repressed by the phytohormone GA and induced by the GA biosynthesis inhibitor paclobutrazol, suggesting that SEU acts downstream of GA signaling to regulate MC formation. Consistently, we found that SEU mediates the regulation of SCL3 by GA signaling. Together, our study identifies SEU as a new critical player that integrates GA signaling with transcriptional inputs from the SHR-SCR-SCL3 module to regulate MC formation in the Arabidopsis root.}, number={3}, journal={PLANT PHYSIOLOGY}, publisher={American Society of Plant Biologists (ASPB)}, author={Gong, X. and Flores-Vergara, M.A. and Hong, J.H. and Chu, H. and Lim, J. and Franks, Robert G. and Liu, Z. and Xu, J. and physiology, Plant}, year={2016}, month={Mar}, pages={1675–1683} }
 @article{villarino_hu_manrique_flores-vergara_sehra_robles_brumos_stepanova_colombo_sundberg_et al._2016, title={Transcriptomic Signature of the SHATTERPROOF2 Expression Domain Reveals the Meristematic Nature of Arabidopsis Gynoecial Medial Domain}, volume={171}, ISSN={["1532-2548"]}, url={http://europepmc.org/abstract/med/26983993}, DOI={10.1104/pp.15.01845}, abstractNote={Transcriptional profiles of spatially and temporally restricted cell populations from the Arabidopsis gynoecium reveals the meristematic nature of the gynoecial medial domain. Plant meristems, like animal stem cell niches, maintain a pool of multipotent, undifferentiated cells that divide and differentiate to give rise to organs. In Arabidopsis (Arabidopsis thaliana), the carpel margin meristem is a vital meristematic structure that generates ovules from the medial domain of the gynoecium, the female floral reproductive structure. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present a novel approach to analyze the transcriptional signature of the medial domain of the Arabidopsis gynoecium, highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Using a floral synchronization system and a SHATTERPROOF2 (SHP2) domain-specific reporter, paired with FACS and RNA sequencing, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. This analysis reveals a set of genes that are differentially expressed within the SHP2 expression domain, including genes that have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Global analyses of the transcriptomic data set indicate a similarity of the pSHP2-expressing cell population to previously characterized meristematic domains, further supporting the meristematic nature of this gynoecial tissue. Our method identifies additional genes including novel isoforms, cis-natural antisense transcripts, and a previously unrecognized member of the REPRODUCTIVE MERISTEM family of transcriptional regulators that are potential novel regulators of medial domain development. This data set provides genome-wide transcriptional insight into the development of the carpel margin meristem in Arabidopsis.}, number={1}, journal={PLANT PHYSIOLOGY}, author={Villarino, Gonzalo H. and Hu, Qiwen and Manrique, Silvia and Flores-Vergara, Miguel and Sehra, Bhupinder and Robles, Linda and Brumos, Javier and Stepanova, Anna N. and Colombo, Lucia and Sundberg, Eva and et al.}, year={2016}, month={May}, pages={42–61} }
 @article{flores_reyes_robertson_kjemtrup_2015, title={Persistent Virus-Induced Gene Silencing in Asymptomatic Accessions of Arabidopsis}, volume={1284}, ISBN={["978-1-4939-2443-1"]}, ISSN={["1064-3745"]}, DOI={10.1007/978-1-4939-2444-8_15}, abstractNote={Coupled with the advantages afforded by the model plant Arabidopsis, virus-induced gene silencing (VIGS) offers a rapid means to assess gene function. The geminivirus vector based on Cabbage leaf curl virus described here has the benefits of small insert size and persistent silencing of the target gene through the life cycle of the plant. Here, we show that genetic variation in the vast collection of Arabidopsis accessions can be leveraged to ameliorate viral symptomology that accompanies the VIGS procedure. The plasticity of phenotypes under different day lengths or temperature conditions can be exploited to achieve maximum silencing efficacy in either vegetative or inflorescence tissue, according to the question being asked. Protocols and vectors for Agro-infiltration of primary leaves, subapical pricking in older plants, and microprojectile bombardment are described.}, journal={PLANT FUNCTIONAL GENOMICS: METHODS AND PROTOCOLS, 2ND EDITION}, author={Flores, Miguel A. and Reyes, Maria I. and Robertson, Dominique and Kjemtrup, Susanne}, year={2015}, pages={305–322} }
 @article{pascuzzi_flores-vergara_lee_sosinski_vaughn_hanley-bowdoin_thompson_allen_2014, title={In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts}, volume={26}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.113.121194}, abstractNote={This work uses tiling microarrays to map S/MARs on Arabidopsis chromosome 4. S/MARs were found to be spaced more closely than in the large plant and animal genomes studied to date and preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation. Most S/MARs occur near gene transcription start sites, and these genes show an increased probability of expression. Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.}, number={1}, journal={PLANT CELL}, author={Pascuzzi, Pete E. and Flores-Vergara, Miguel A. and Lee, Tae-Jin and Sosinski, Bryon and Vaughn, Matthew W. and Hanley-Bowdoin, Linda and Thompson, William F. and Allen, George C.}, year={2014}, month={Jan}, pages={102–120} }
 @article{allen_flores-vergara_krasnyanski_kumar_thompson_2006, title={A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide}, volume={1}, ISSN={["1750-2799"]}, DOI={10.1038/nprot.2006.384}, abstractNote={We describe a modification of the DNA extraction method, in which cetyltrimethylammonium bromide (CTAB) is used to extract nucleic acids from plant tissues. In contrast to the original method, the modified CTAB procedure is faster, omits the selective precipitation and CsCl gradient steps, uses less expensive and toxic reagents, requires only inexpensive laboratory equipment and is more readily adapted to high-throughput DNA extraction. This protocol yields approximately 5-30 microg of total DNA from 200 mg of tissue fresh weight, depending on plant species and tissue source. It can be completed in as little as 5-6 h.}, number={5}, journal={NATURE PROTOCOLS}, author={Allen, G. C. and Flores-Vergara, M. A. and Krasnyanski, S. and Kumar, S. and Thompson, W. F.}, year={2006}, pages={2320–2325} }