@article{amses_simmons_longcore_mondo_seto_jeronimo_bonds_quandt_davis_chang_et al._2022, title={Diploid-dominant life cycles characterize the early evolution of Fungi}, volume={119}, ISSN={["1091-6490"]}, DOI={10.1073/pnas.2116841119}, abstractNote={Significance It has been assumed that fungi are characterized by a haploid-dominant life cycle with a general absence of mitosis in the diploid stage (haplontic life cycles). However, this characterization is based largely on information for Dikarya, a group of fungi that contains mushrooms, lichens, molds, yeasts, and most described fungi. We now appreciate that most early-diverging lineages of fungi are not Dikarya and share traits with protists, such as flagellated life stages. Here, we generated an improved phylogeny of the fungi by generating genome sequences of 69 zoosporic fungi. We show, using the estimated heterozygosity of these genomes, that many fungal lineages have diploid-dominant life cycles (diplontic). This finding forces us to rethink the early evolution of the fungal cell.}, number={36}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Amses, Kevin R. and Simmons, D. Rabern and Longcore, Joyce E. and Mondo, Stephen J. and Seto, Kensuke and Jeronimo, Gustavo H. and Bonds, Anne E. and Quandt, C. Alisha and Davis, William J. and Chang, Ying and et al.}, year={2022}, month={Sep} }
 @article{lin_buchler_2022, title={Gene expression noise accelerates the evolution of a biological oscillator}, volume={3}, url={https://doi.org/10.1101/2022.03.21.485207}, DOI={10.1101/2022.03.21.485207}, abstractNote={Gene expression is a biochemical process, where stochastic binding and unbinding events naturally generate fluctuations and cell-to-cell variability in gene dynamics. These fluctuations typically have destructive consequences for proper biological dynamics and function (e.g., loss of timing and synchrony in biological oscillators). Here, we show that gene expression noise counter-intuitively accelerates the evolution of a biological oscillator and, thus, can impart a benefit to living organisms. We used computer simulations to evolve two mechanistic models of a biological oscillator at different levels of gene expression noise. We first show that gene expression noise induces oscillatory-like dynamics in regions of parameter space that cannot oscillate in the absence of noise. We then demonstrate that these noise-induced oscillations generate a fitness landscape whose gradient robustly and quickly guides evolution by mutation towards robust and self-sustaining oscillation. These results suggest that noise can help dynamical systems evolve or learn new behavior by revealing cryptic dynamic phenotypes outside the bifurcation point. Graphical Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Lin, Yen Ting and Buchler, Nicolas E.}, year={2022}, month={Mar} }
 @article{zhang_ho_buchler_gordan_2021, title={Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions}, volume={31}, ISSN={["1549-5469"]}, url={https://doi.org/10.1101/gr.275145.120}, DOI={10.1101/gr.275145.120}, abstractNote={Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e., paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are coexpressed in the cell and thus can compete for target sites across the genome. However, this competition is rarely taken into account when studying the in vivo binding patterns of eukaryotic TFs. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. Using yeast proteins Cbf1 and Pho4 as our model system, we designed a high-throughput quantitative assay to capture the genomic binding profiles of competing TFs in a cell-free system. Our data show that Cbf1 and Pho4 greatly influence each other's occupancy by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs’ expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive TF binding patterns in vitro are also followed in vivo, in the complex cellular environment. Furthermore, the Cbf1-Pho4 competition for genomic sites, as characterized in vitro using our new assay, plays a critical role in the specific activation of their target genes in the cell. Overall, our study highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.}, number={7}, journal={GENOME RESEARCH}, publisher={Cold Spring Harbor Laboratory}, author={Zhang, Yuning and Ho, Tiffany D. and Buchler, Nicolas E. and Gordan, Raluca}, year={2021}, month={Jul}, pages={1216-+} }
 @article{medina_buchler_2020, title={Chytrid fungi.}, volume={5}, url={http://europepmc.org/abstract/med/32428492}, DOI={10.1016/j.cub.2020.02.076}, abstractNote={Fungi have distinguishing traits, such as hyphae and cell walls, that evolved in a fungal ancestor over one billion years ago. Chytrid fungi are some of the earliest diverging fungal lineages that retained features of the opisthokont ancestor of animals and fungi (Figure 1). For example, chytrids make reproductive cells known as zoospores that swim with a motile cilium or crawl like an amoeba. The aim of this primer is to introduce the reader to the life cycle, biology, and ecology of chytrids and other zoosporic fungi. We highlight how chytrids are well positioned to elucidate both the cell biology of the animal–fungal ancestor and the evolution of derived fungal features. Life first evolved in the ocean and the last eukaryotic common ancestor (LECA) likely swam and engulfed organic matter via phagocytosis. Based on the shared features found across eukaryotes, LECA had a nucleus, mitochondria, an endo-membrane system, actin and tubulin cytoskeleton, and a centriole for building a mitotic spindle and cilium. LECA gave rise to diverse eukaryotes, some of which remained in aquatic environments and others which colonized land over 500 million years ago. Fungi (e.g. chytrids, rusts, molds, mushrooms, and yeast) are a large eukaryotic kingdom found in many environments and ecological niches. These eukaryotes are decomposers that live on organic matter or as parasites of plants and animals. Fungi are also important symbionts: they are partners of algae and cyanobacteria in lichens or they form mycorrhizae that colonize plant roots and extract water and nutrients from soil in exchange for sugars. The successful expansion and colonization of terrestrial environments by the plant and fungal kingdoms is likely the consequence of a symbiotic relationship between early fungi and photosynthetic algae. Fungi are closely related to animals through a common opisthokont ancestor that lived in an aquatic environment over one billion years ago (Figure 1). Chytrids and other early-diverging fungi have persisted in this ancestral habitat and have retained traits that make them well adapted to foraging for resources in water. For example, chytrids produce spores (known as zoospores) that lack a cell wall and swim via a motile cilium and/or crawl on surfaces via amoeboid motion (Figure 1). The presence of a centriole and a motile cilium is unique to chytrids and other zoosporic fungi within the fungal kingdom. The cilium is attached to a basal body that contains a classic centriole with nine circularly arranged triplet microtubules that nucleate the axoneme. Similar to many animal cells, chytrids resorb the cilium and the centriole is repurposed as a centrosome to organize the mitotic spindle for nuclear division cycles. The fungal ancestor evolved new traits (‘derived traits’) that are shared by all fungi including chytrids. For example, the chytrid life cycle includes a vegetative body (‘thallus’) with a cell wall and hyphal-like feeding structure known as a rhizoid (Figure 1). Fungal hyphae are branching, filamentous tubes that penetrate organic matter and secrete digestive enzymes to extract nutrients for cell growth. Hyphae grow into substrates by depositing cell wall materials and remodeling enzymes at the hyphal tip via directed vesicle trafficking on a cytoskeletal network. The cell wall is critical because it holds large, hydrostatic pressures caused by internal osmolytes, which generate the biomechanical forces that drive cell wall expansion at the hyphal tip. As in other fungi, the hyphal-like rhizoid is important for colonizing substrates and extracting nutrients to fuel chytrid cell growth. We use the term zoosporic fungi to describe chytrids and other early diverging fungi that have a zoospore stage during their life cycle (Figure 2A). Meta-genomic sequencing has shown that zoosporic fungi comprise much of the unknown fungal diversity in aquatic environments. Zoosporic fungi span at least three phyla (Cryptomycota, Chytridiomycota, and Blastocladiomycota). The Cryptomycota are the deepest lineage and include the genus Rozella, which parasitizes chytrids (Figure 2B), and other uncultured parasites of fungi, amoeba, oomycetes and algae. The Cryptomycota also include the Microsporidia, which are common animal parasites that have small, fast-evolving eukaryotic genomes and that have lost their cilium. Despite their lack of a zoospore stage, phylogenetic analyses place Microsporidia within the Cryptomycota. The Chytridiomycota and Blastocladiomycota are later-diverging phyla that are better studied than the Cryptomycota. The Chytridiomycota (commonly called ‘chytrids’) are found in aquatic and terrestrial habitats, and are saprotrophs as well as parasites of algae, plants and animals (e.g. the amphibian pathogen Batrachochytrium). These chytrids play an important role in aquatic food webs by infecting large, inedible algae and producing small zoospores (Figure 2C) that are edible to zooplankton. Anaerobic, multi-ciliated Neocallimastigomycota in ruminants (e.g. sheep, cattle) are a well-characterized subgroup of this phylum that have evolved hydrogen-producing organelles known as hydrogenosomes (Figure 2D). The rumen microbiome contains eubacteria, archaea, ciliates, and chytrids that collectively ferment plant material to produce volatile fatty acids and microbial protein for their animal host. The rumen chytrids penetrate plant tissue with their hyphal-like structures, secrete cellulases, and help breakdown highly recalcitrant carbohydrates for the microbiome. The Blastocladiomycota include saprotrophs as well as parasites of fungi, algae, plants and invertebrates (Figure 2E). Although zoosporic, and once classified as Chytridiomycota, the Blastocladiomycota differ from the other chytrids in the complexity of their thallus and life cycle: they can have haplodiplontic alternation of generations (much like land plants) and exhibit multicellular haploid (gametophyte) and multicellular diploid thalli (sporophyte). While asexual reproduction is through zoospores, sexual reproduction involves motile gametes of opposite sexes with different sizes and coloration that attract and swim towards each other through pheromone signaling. The Blastocladiomycota have diverse body plans with some species (e.g. Allomyces) developing true hyphae (nucleated, with pseudo-septa and polarized indeterminate growth with an apical organizing center, similar to the Spitzenkörper found in filamentous fungi). Chytrid species can differ considerably in their life history, morphology, metabolism, and sub-cellular organelles. However, many chytrids exhibit a similar life cycle that progresses from zoospore to thallus to sporangium (Figure 3A). Chytrid zoospores range from 2–10 microns in diameter and have a single posterior motile cilium, although anaerobic chytrids of the rumen can have multiple cilia (Figure 2D). Zoospore ultrastructure (e.g. basal body and associated sub-structures) is diverse and is often used to identify and classify chytrid species. Chytrids swim with a motile cilium and some species can switch to amoeboid crawling when attached to a surface. Zoospores have a single nucleus and are quiescent, i.e. inactive cell division cycle and no growth. They sustain the energetic demands for motility by catabolizing lipids and storage carbohydrates that were maternally provisioned by the chytrid sporangium during zoosporogenesis in the previous life cycle. Lipid droplets are often visible when observing chytrid zoospores by light microscopy (Figure 2E). Although chytrid zoospores are metabolically active, they do not produce new DNA, RNA, or proteins until after germination. Zoospores are translationally inactive and contain inactive ribosomes pre-loaded with maternal mRNAs. In the Blastocladiomycota, inactive mRNA–ribosomes are packaged into an organelle associated with the nucleus called the nuclear cap (Figure 2E). Ribosome activity in the zoospore is blocked in the elongation stage by an inhibitor whose identity remains unknown. It is unclear how universal this mechanism might be across all chytrids; however, it has been established that some Chytridiomycota zoospores are also translationally inactive. Once chytrid zoospores find an appropriate niche, they encyst by retracting their motile cilium and building a fungal cell wall (Figure 3A). The mechanics of ciliary retraction are diverse with at least four scenarios (lash-around, body-twist, straight in, and vesicular) that can vary depending on the species or the environment. In the lash-around retraction, the cilium lashes around the immobile zoospore body resulting in a sheath-less axoneme coiled inside the membrane. In the body-twist retraction, the zoospore body twists or rotates while the cilium remains passive, with the same resulting axoneme coiled under the membrane. In the straight-in retraction, the immobile cilium slowly reduces length, entering the immobile zoospore body at the point of attachment. Finally, for vesicular retraction, the axoneme coils or loops within itself in a vesicle of the cilia membrane, progressively shortening the cilium until the vesicle reaches and fuses into the main zoospore body (Figure 3B). The cell biology and mechanisms used by zoospores for retraction are still an open question, but its diversity of form and plasticity may reflect the structural diversity seen in the chytrid zoospore basal body and associated structures. Much like metazoan cells, retraction of the cilium liberates the centrioles for cell division that occurs during chytrid growth. It may also repurpose ciliary components for germination or other cellular processes until new protein is synthesized in the chytrid. Upon encystment, changes in the regulation of the actin cytoskeleton shift the chytrid from a naked motility specialist (ciliary swimming and crawling) to a foraging specialist with a fungal cell wall and turgor-driven polarized growth. The germinating cyst usually forms a single germ tube that later expands and branches into a hyphal-like rhizoidal system (Figure 3A). Zoospores in some Chytridiomycota crawl using pseudopod-based alpha-motility, which is driven by the expansion of branched-actin filament networks via the Arp2/3 complex. Chytrid species whose zoospores crawl contain activators of branched-actin assembly (WASP, SCAR/WAVE), which are correlated with crawling and alpha-motility in other eukaryotes. Once the zoospores encyst and germinate, there is a shift in actin cytoskeleton organization to actin patches and cables that extend into the germ tube and rhizoids. This architecture is typical of fungi, where actin patches are associated with endocytosis and cell wall deposition, whereas actin cables are pathways for targeted delivery of exocytic vesicles. In some chytrids, the nucleus remains in the cyst during germ tube expansion and the cyst will develop into a spherical reproductive structure called the sporangium (Figure 3A). In other species, the nucleus can migrate into the rhizoid and eventually trigger the growth and formation of a sporangium outside the original cyst. During the formation of the sporangium, a nucleus goes through multiple rounds of nuclear division without cytokinesis to create a shared compartment of nuclei known as a coenocyte. This is later followed by ciliogenesis (i.e. the conversion of centrioles into basal bodies and the building of motile cilia), membrane invagination and the coordinated encapsulation of individual nuclei, cilia and other organelles into single cells to form new zoospores. Membrane cellularization of a coenocytic compartment is an ancestral process that occurs in pre-metazoan lineages and animal embryogenesis. In appropriate environmental conditions, the mature zoospores are released through one or multiple pores (called discharge papillae) that open in the cell wall (Figure 3C). Upon release from a sporangium, chytrid zoospores swim or crawl to find new niches. The zoospores can swim for hours to days with speeds of up to 100 microns per second. The motion consists of swimming in mostly straight lines with rapid changes in direction, interspersed with long breaks of crawling in some species. Zoospores sense both chemical cues and use light cues to locate hosts or substrates. Chemotaxis assays have shown that zoospores will swim towards specific nutrients (e.g. sugars, proteins, fatty acids, amino acids) usually associated with target hosts or substrates. Likewise, phototaxis assays have shown that zoospores of different species will swim towards green or blue light. A type-I opsin (also known as bacteriorhodopsin) fused to guanylate-cyclase drives the phototaxis of zoospores in Blastocladiella emersonii (Blastocladiomycota). The mechanism of phototransduction of this type-I opsin is reminiscent of the phototransduction pathway of animal G-protein-coupled ciliary opsins. This type-I opsin is homologous to the one used by pre-metazoan choanoflagellates to drive ciliary movement and contractility of the multi-cell colony. The diversity of type-I opsins seen in chytrids and choanoflagellates have optogenetic potential. For example, Blastocladiella ‘CyclOp’ was recently developed for sensitive and fast control of cGMP levels in target cells and animals. Chemotaxis also drives sexual reproduction in the Allomyces (Blastocladiomycota) in which motile male and female gametes produced by male and female gametangia (Figure 3D) swim towards each other using pheromone signaling. Although the chemical structure of the male pheromone (parisin) is unknown, the female pheromone (sirenin) is a sesquiterpene. Strikingly, sirenin can activate the human sperm CatSper calcium channel, much like progesterone. CatSper is essential for hyperactivation of the sperm’s cilium and plays a role in chemotaxis towards the egg. Interestingly, chytrids have orthologs of CatSper and calcium signaling is involved in sirenin signaling. The chytrid pheromone receptor and its mechanism of action remain unknown, but we anticipate that chytrids will be useful organisms for understanding the conserved mechanisms of sexual chemotaxis, calcium signaling, and the regulation of swimming motility via CatSper. Basic research in animal and fungal model organisms elucidated conserved mechanisms and regulators of eukaryotic cell biology (e.g. cell cycle). However, these closely related eukaryotes also evolved new features and adaptations over the last one billion years. The common ancestor of most fungi committed to a cellular morphology and sessile life cycle that produces hyphae that grow into their substrates and durable spores that disperse via air currents or ejection. These adaptations are useful for a saprophytic or parasitic lifestyle in a terrestrial environment, but they emerged when the fungal ancestor was still living in aquatic environments. Chytrids are an early-diverging fungal lineage that likely reflect a transitional phase in the evolution of terrestrial fungi, not unlike amphibious animals. Chytrid genomes are also unique because they contain ancestral, animal-like genes and regulatory networks that were lost in most other fungi. For example, the fungal cell cycle was rewired by a viral domain that eventually replaced the ancestral G1/S regulator in most fungi. The ancestral and viral regulators and G1/S pathways still coexist in chytrids. This same viral domain also created a large family of transcription factors that regulate fungal-specific processes, such as hyphal morphogenesis. As such, chytrids are promising organisms to help understand the molecular evolution of derived fungal features and the conservation of ancestral features.}, journal={Current biology : CB}, author={Medina, EM and Buchler, NE}, year={2020}, month={May} }
 @article{medina_robinson_bellingham-johnstun_ianiri_laplante_fritz-laylin_buchler_2020, title={Genetic transformation of Spizellomyces punctatus, a resource for studying chytrid biology and evolutionary cell biology}, url={https://doi.org/10.7554/eLife.52741}, DOI={10.7554/eLife.52741}, abstractNote={Chytrids are early-diverging fungi that share features with animals that have been lost in most other fungi. They hold promise as a system to study fungal and animal evolution, but we lack genetic tools for hypothesis testing. Here, we generated transgenic lines of the chytrid Spizellomyces punctatus, and used fluorescence microscopy to explore chytrid cell biology and development during its life cycle. We show that the chytrid undergoes multiple rounds of synchronous nuclear division, followed by cellularization, to create and release many daughter ‘zoospores’. The zoospores, akin to animal cells, crawl using actin-mediated cell migration. After forming a cell wall, polymerized actin reorganizes into fungal-like cortical patches and cables that extend into hyphal-like structures. Actin perinuclear shells form each cell cycle and polygonal territories emerge during cellularization. This work makes Spizellomyces a genetically tractable model for comparative cell biology and understanding the evolution of fungi and early eukaryotes.}, journal={eLife}, author={Medina, Edgar M and Robinson, Kristyn A and Bellingham-Johnstun, Kimberly and Ianiri, Giuseppe and Laplante, Caroline and Fritz-Laylin, Lillian K and Buchler, Nicolas E}, year={2020}, month={May} }
 @article{chen_lin_gallegos_hazlett_gomez-schiavon_yang_kalmeta_zhou_holtzman_gersbach_et al._2019, title={Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes}, volume={26}, ISSN={["2211-1247"]}, url={https://publons.com/publon/9042681/}, DOI={10.1016/j.celrep.2019.01.032}, abstractNote={Neuronal activity-inducible gene transcription correlates with rapid and transient increases in histone acetylation at promoters and enhancers of activity-regulated genes. Exactly how histone acetylation modulates transcription of these genes has remained unknown. We used single-cell in situ transcriptional analysis to show that Fos and Npas4 are transcribed in stochastic bursts in mouse neurons and that membrane depolarization increases mRNA expression by increasing burst frequency. We then expressed dCas9-p300 or dCas9-HDAC8 fusion proteins to mimic or block activity-induced histone acetylation locally at enhancers. Adding histone acetylation increased Fos transcription by prolonging burst duration and resulted in higher Fos protein levels and an elevation of resting membrane potential. Inhibiting histone acetylation reduced Fos transcription by reducing burst frequency and impaired experience-dependent Fos protein induction in the hippocampus in vivo. Thus, activity-inducible histone acetylation tunes the transcriptional dynamics of experience-regulated genes to affect selective changes in neuronal gene expression and cellular function.}, number={5}, journal={CELL REPORTS}, author={Chen, Liang-Fu and Lin, Yen Ting and Gallegos, David A. and Hazlett, Mariah F. and Gomez-Schiavon, Mariana and Yang, Marty G. and Kalmeta, Breanna and Zhou, Allen S. and Holtzman, Liad and Gersbach, Charles A. and et al.}, year={2019}, month={Jan}, pages={1174-+} }
 @article{gomez-schiavon_buchler_2019, title={Epigenetic switching as a strategy for quick adaptation while attenuating biochemical noise}, volume={15}, ISSN={["1553-7358"]}, url={https://publons.com/publon/27274058/}, DOI={10.1371/journal.pcbi.1007364}, abstractNote={Epigenetic switches are bistable, molecular systems built from self-reinforcing feedback loops that can spontaneously switch between heritable phenotypes in the absence of DNA mutation. It has been hypothesized that epigenetic switches first evolved as a mechanism of bet-hedging and adaptation, but the evolutionary trajectories and conditions by which an epigenetic switch can outcompete adaptation through genetic mutation remain unknown. Here, we used computer simulations to evolve a mechanistic, biophysical model of a self-activating genetic circuit, which can both adapt genetically through mutation and exhibit epigenetic switching. We evolved these genetic circuits under a fluctuating environment that alternatively selected for low and high protein expression levels. In all tested conditions, the population first evolved by genetic mutation towards a region of genotypes where genetic adaptation can occur faster after each environmental transition. Once in this region, the self-activating genetic circuit can exhibit epigenetic switching, which starts competing with genetic adaptation. We show a trade-off between either minimizing the adaptation time or increasing the robustness of the phenotype to biochemical noise. Epigenetic switching was superior in a fast fluctuating environment because it adapted faster than genetic mutation after an environmental transition, while still attenuating the effect of biochemical noise on the phenotype. Conversely, genetic adaptation was favored in a slowly fluctuating environment because it maximized the phenotypic robustness to biochemical noise during the constant environment between transitions, even if this resulted in slower adaptation. This simple trade-off predicts the conditions and trajectories under which an epigenetic switch evolved to outcompete genetic adaptation, shedding light on possible mechanisms by which bet-hedging strategies might emerge and persist in natural populations.}, number={10}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Gomez-Schiavon, Mariana and Buchler, Nicolas E.}, year={2019}, month={Oct} }
 @misc{medina_walsh_buchler_2019, title={Evolutionary innovation, fungal cell biology, and the lateral gene transfer of a viral KilA-N domain}, volume={58-59}, ISSN={["1879-0380"]}, url={https://publons.com/publon/34754702/}, DOI={10.1016/j.gde.2019.08.004}, abstractNote={Fungi are found in diverse ecological niches as primary decomposers, mutualists, or parasites of plants and animals. Although animals and fungi share a common ancestor, fungi dramatically diversified their life cycle, cell biology, and metabolism as they evolved and colonized new niches. This review focuses on a family of fungal transcription factors (Swi4/Mbp1, APSES, Xbp1, Bqt4) derived from the lateral gene transfer of a KilA-N domain commonly found in prokaryotic and eukaryotic DNA viruses. These virus-derived fungal regulators play central roles in cell cycle, morphogenesis, sexual differentiation, and quiescence. We consider the possible origins of KilA-N and how this viral DNA binding domain came to be intimately associated with fungal processes.}, journal={CURRENT OPINION IN GENETICS & DEVELOPMENT}, author={Medina, Edgar M. and Walsh, Evan and Buchler, Nicolas E.}, year={2019}, month={Oct}, pages={103–110} }
 @article{lin_buchler_2019, title={Exact and efficient hybrid Monte Carlo algorithm for accelerated Bayesian inference of gene expression models from snapshots of single-cell transcripts}, url={https://doi.org/10.1063/1.5110503}, DOI={10.1063/1.5110503}, abstractNote={Single cells exhibit a significant amount of variability in transcript levels, which arises from slow, stochastic transitions between gene expression states. Elucidating the nature of these states and understanding how transition rates are affected by different regulatory mechanisms require state-of-the-art methods to infer underlying models of gene expression from single cell data. A Bayesian approach to statistical inference is the most suitable method for model selection and uncertainty quantification of kinetic parameters using small data sets. However, this approach is impractical because current algorithms are too slow to handle typical models of gene expression. To solve this problem, we first show that time-dependent mRNA distributions of discrete-state models of gene expression are dynamic Poisson mixtures, whose mixing kernels are characterized by a piecewise deterministic Markov process. We combined this analytical result with a kinetic Monte Carlo algorithm to create a hybrid numerical method that accelerates the calculation of time-dependent mRNA distributions by 1000-fold compared to current methods. We then integrated the hybrid algorithm into an existing Monte Carlo sampler to estimate the Bayesian posterior distribution of many different, competing models in a reasonable amount of time. We demonstrate that kinetic parameters can be reasonably constrained for modestly sampled data sets if the model is known a priori. If there are many competing models, Bayesian evidence can rigorously quantify the likelihood of a model relative to other models from the data. We demonstrate that Bayesian evidence selects the true model and outperforms approximate metrics typically used for model selection.}, journal={The Journal of Chemical Physics}, author={Lin, Yen Ting and Buchler, Nicolas E.}, year={2019}, month={Jul} }
 @article{gowans_bridgers_zhang_dronamraju_burnetti_king_thiengmany_shinsky_bhanu_garcia_et al._2019, title={Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression}, volume={76}, ISSN={["1097-4164"]}, url={https://publons.com/publon/34754701/}, DOI={10.1016/j.molcel.2019.09.029}, abstractNote={Metabolic signaling to chromatin often underlies how adaptive transcriptional responses are controlled. While intermediary metabolites serve as co-factors for histone-modifying enzymes during metabolic flux, how these modifications contribute to transcriptional responses is poorly understood. Here, we utilize the highly synchronized yeast metabolic cycle (YMC) and find that fatty acid β-oxidation genes are periodically expressed coincident with the β-oxidation byproduct histone crotonylation. Specifically, we found that H3K9 crotonylation peaks when H3K9 acetylation declines and energy resources become limited. During this metabolic state, pro-growth gene expression is dampened; however, mutation of the Taf14 YEATS domain, a H3K9 crotonylation reader, results in de-repression of these genes. Conversely, exogenous addition of crotonic acid results in increased histone crotonylation, constitutive repression of pro-growth genes, and disrupted YMC oscillations. Together, our findings expose an unexpected link between metabolic flux and transcription and demonstrate that histone crotonylation and Taf14 participate in the repression of energy-demanding gene expression.}, number={6}, journal={MOLECULAR CELL}, author={Gowans, Graeme J. and Bridgers, Joseph B. and Zhang, Jibo and Dronamraju, Raghuvar and Burnetti, Anthony and King, Devin A. and Thiengmany, Aline V and Shinsky, Stephen A. and Bhanu, Natarajan V and Garcia, Benjamin A. and et al.}, year={2019}, month={Dec}, pages={909-+} }
 @article{mwimba_karapetyan_liu_marques_mcginnis_buchler_dong_2018, title={Daily humidity oscillation regulates the circadian clock to influence plant physiology}, volume={9}, ISSN={["2041-1723"]}, url={https://publons.com/publon/34754703/}, DOI={10.1038/s41467-018-06692-2}, abstractNote={Early circadian studies in plants by de Mairan and de Candolle alluded to a regulation of circadian clocks by humidity. However, this regulation has not been described in detail, nor has its influence on physiology been demonstrated. Here we report that, under constant light, circadian humidity oscillation can entrain the plant circadian clock to a period of 24 h probably through the induction of clock genes such as CIRCADIAN CLOCK ASSOCIATED 1. Under simulated natural light and humidity cycles, humidity oscillation increases the amplitude of the circadian clock and further improves plant fitness-related traits. In addition, humidity oscillation enhances effector-triggered immunity at night possibly to counter increased pathogen virulence under high humidity. These results indicate that the humidity oscillation regulates specific circadian outputs besides those co-regulated with the light-dark cycle.}, journal={NATURE COMMUNICATIONS}, author={Mwimba, Musoki and Karapetyan, Sargis and Liu, Lijing and Marques, Jorge and McGinnis, Erin M. and Buchler, Nicolas E. and Dong, Xinnian}, year={2018}, month={Oct} }
 @article{lin_buchler_2018, title={Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes}, volume={15}, url={https://doi.org/10.1098/rsif.2017.0804}, DOI={10.1098/rsif.2017.0804}, abstractNote={Single-cell experiments show that gene expression is stochastic and bursty, a feature that can emerge from slow switching between promoter states with different activities. In addition to slow chromatin and/or DNA looping dynamics, one source of long-lived promoter states is the slow binding and unbinding kinetics of transcription factors to promoters, i.e. the non-adiabatic binding regime. Here, we introduce a simple analytical framework, known as a piecewise deterministic Markov process (PDMP), that accurately describes the stochastic dynamics of gene expression in the non-adiabatic regime. We illustrate the utility of the PDMP on a non-trivial dynamical system by analysing the properties of a titration-based oscillator in the non-adiabatic limit. We first show how to transform the underlying chemical master equation into a PDMP where the slow transitions between promoter states are stochastic, but whose rates depend upon the faster deterministic dynamics of the transcription factors regulated by these promoters. We show that the PDMP accurately describes the observed periods of stochastic cycles in activator and repressor-based titration oscillators. We then generalize our PDMP analysis to more complicated versions of titration-based oscillators to explain how multiple binding sites lengthen the period and improve coherence. Last, we show how noise-induced oscillation previously observed in a titration-based oscillator arises from non-adiabatic and discrete binding events at the promoter site.}, number={138}, journal={Journal of The Royal Society Interface}, publisher={The Royal Society}, author={Lin, Yen Ting and Buchler, Nicolas E.}, year={2018}, month={Jan}, pages={20170804} }
 @article{hendler_medina_buchler_bruin_aharoni_2018, title={The evolution of a G1/S transcriptional network in yeasts}, volume={64}, url={https://publons.com/publon/2047243/}, DOI={10.1007/S00294-017-0726-3}, abstractNote={The G1-to-S cell cycle transition is promoted by the periodic expression of a large set of genes. In Saccharomyces cerevisiae G1/S gene expression is regulated by two transcription factor (TF) complexes, the MBF and SBF, which bind to specific DNA sequences, the MCB and SCB, respectively. Despite extensive research little is known regarding the evolution of the G1/S transcription regulation including the co-evolution of the DNA binding domains with their respective DNA binding sequences. We have recently examined the co-evolution of the G1/S TF specificity through the systematic generation and examination of chimeric Mbp1/Swi4 TFs containing different orthologue DNA binding domains in S. cerevisiae (Hendler et al. in PLoS Genet 13:e1006778. doi: 10.1371/journal.pgen.1006778 , 2017). Here, we review the co-evolution of G1/S transcriptional network and discuss the evolutionary dynamics and specificity of the MBF–MCB and SBF–SCB interactions in different fungal species.}, number={1}, journal={Current Genetics}, publisher={Springer Nature}, author={Hendler, Adi and Medina, Edgar M. and Buchler, Nicolas E. and Bruin, Robertus A. M. and Aharoni, Amir}, year={2018}, pages={81–86} }
 @article{gómez-schiavon_chen_west_buchler_2017, title={BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells}, volume={18}, url={https://doi.org/10.1186/s13059-017-1297-9}, DOI={10.1186/s13059-017-1297-9}, abstractNote={Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution in the measurement of the abundance and localization of nascent and mature RNA transcripts in fixed, single cells. We developed a computational pipeline (BayFish) to infer the kinetic parameters of gene expression from smFISH data at multiple time points after gene induction. Given an underlying model of gene expression, BayFish uses a Monte Carlo method to estimate the Bayesian posterior probability of the model parameters and quantify the parameter uncertainty given the observed smFISH data. We tested BayFish on synthetic data and smFISH measurements of the neuronal activity-inducible gene Npas4 in primary neurons.}, number={1}, journal={Genome Biology}, publisher={Springer Science and Business Media LLC}, author={Gómez-Schiavon, Mariana and Chen, Liang-Fu and West, Anne E. and Buchler, Nicolas E.}, year={2017}, month={Dec} }
 @article{liban_medina_tripathi_sengupta_henry_buchler_rubin_2017, title={Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family}, volume={114}, url={https://doi.org/10.1073/pnas.1619170114}, DOI={10.1073/pnas.1619170114}, abstractNote={Significance The retinoblastoma (Rb) pocket protein and E2F transcription factor families regulate cell division and are commonly deregulated in proliferating cancer cells. An important question has been what distinguishing molecular features of Rb and its interaction with E2F result in its unique potency as a tumor suppressor relative to its homologous proteins p107 and p130. Here we identify structures in Rb, p107, and E2Fs that determine the specificity in their association. We explain binding preferences with an X-ray crystal structure of a p107–E2F5–DP1 complex, and present phylogenetic analyses that implicate coevolving protein interactions between family members as a key determinant of their evolution. The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD–CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein–E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.}, number={19}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Liban, Tyler J. and Medina, Edgar M. and Tripathi, Sarvind and Sengupta, Satyaki and Henry, R. William and Buchler, Nicolas E. and Rubin, Seth M.}, year={2017}, month={May}, pages={4942–4947} }
 @article{hendler_medina_kishkevich_abu-qarn_klier_buchler_bruin_aharoni_2017, title={Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness}, volume={13}, url={https://publons.com/publon/2047240/}, DOI={10.1371/journal.pgen.1006778}, abstractNote={Transcriptional regulatory networks play a central role in optimizing cell survival. How DNA binding domains and cis-regulatory DNA binding sequences have co-evolved to allow the expansion of transcriptional networks and how this contributes to cellular fitness remains unclear. Here we experimentally explore how the complex G1/S transcriptional network evolved in the budding yeast Saccharomyces cerevisiae by examining different chimeric transcription factor (TF) complexes. Over 200 G1/S genes are regulated by either one of the two TF complexes, SBF and MBF, which bind to specific DNA binding sequences, SCB and MCB, respectively. The difference in size and complexity of the G1/S transcriptional network across yeast species makes it well suited to investigate how TF paralogs (SBF and MBF) and DNA binding sequences (SCB and MCB) co-evolved after gene duplication to rewire and expand the network of G1/S target genes. Our data suggests that whilst SBF is the likely ancestral regulatory complex, the ancestral DNA binding element is more MCB-like. G1/S network expansion took place by both cis- and trans- co-evolutionary changes in closely related but distinct regulatory sequences. Replacement of the endogenous SBF DNA-binding domain (DBD) with that from more distantly related fungi leads to a contraction of the SBF-regulated G1/S network in budding yeast, which also correlates with increased defects in cell growth, cell size, and proliferation.}, number={5}, journal={PLOS Genetics}, publisher={Public Library of Science (PLoS)}, author={Hendler, Adi and Medina, Edgar M. and Kishkevich, Anastasiya and Abu-Qarn, Mehtap and Klier, Steffi and Buchler, Nicolas E. and Bruin, Robertus A. M. and Aharoni, Amir}, editor={Snyder, MichaelEditor}, year={2017}, month={May}, pages={e1006778} }
 @article{tanouchi_pai_park_huang_buchler_you_2017, title={Long-term growth data of Escherichia coli at a single-cell level}, url={https://doi.org/10.1038/sdata.2017.36}, DOI={10.1038/sdata.2017.36}, abstractNote={Long-term, single-cell measurement of bacterial growth is extremely valuable information, particularly in the study of homeostatic aspects such as cell-size and growth rate control. Such measurement has recently become possible due to the development of microfluidic technology. Here we present data from single-cell measurements of Escherichia coli growth over 70 generations obtained for three different growth conditions. The data were recorded every minute, and contain time course data of cell length and fluorescent intensity of constitutively expressed yellow fluorescent protein.}, journal={Scientific Data}, author={Tanouchi, Yu and Pai, Anand and Park, Heungwon and Huang, Shuqiang and Buchler, Nicolas E. and You, Lingchong}, year={2017}, month={Mar} }
 @article{burnetti_aydin_buchler_2016, title={Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates.}, volume={27}, url={http://europepmc.org/abstract/med/26538026}, DOI={10.1091/mbc.e15-07-0454}, abstractNote={The interaction of two oscillators (cell division cycle and yeast metabolic cycle) with different frequencies is studied. Cell cycle Start is coupled with the initiation of high oxygen consumption and breakdown of storage carbohydrates across diverse strains and different growth rates.}, number={1}, journal={Molecular Biology of the Cell}, author={Burnetti, AJ and Aydin, M and Buchler, NE}, year={2016}, month={Jan}, pages={64–74,} }
 @article{medina_turner_gordân_skotheim_buchler_2016, title={Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi}, volume={5}, url={https://doi.org/10.7554/eLife.09492}, DOI={10.7554/eLife.09492}, abstractNote={Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.}, journal={eLife}, publisher={eLife Sciences Organisation, Ltd.}, author={Medina, Edgar M and Turner, Jonathan J and Gordân, Raluca and Skotheim, Jan M and Buchler, Nicolas E}, year={2016}, month={May} }
 @article{schaap_barrantes_minx_sasaki_anderson_bénard_biggar_buchler_bundschuh_chen_et al._2016, title={The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling}, volume={8}, url={https://publons.com/publon/2047248/}, DOI={10.1093/GBE/EVV237}, abstractNote={Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.}, number={1}, journal={Genome Biology and Evolution}, author={Schaap, P and Barrantes, I and Minx, P and Sasaki, N and Anderson, RW and Bénard, M and Biggar, KK and Buchler, NE and Bundschuh, R and Chen, X and et al.}, year={2016}, pages={109–125,} }
 @article{tanouchi_pai_park_huang_stamatov_buchler_you_2015, title={A noisy linear map underlies oscillations in cell size and gene expression in bacteria}, volume={523}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84937414579&partnerID=MN8TOARS}, DOI={10.1038/nature14562}, abstractNote={During bacterial growth, a cell approximately doubles in size before division, after which it splits into two daughter cells. This process is subjected to the inherent perturbations of cellular noise and thus requires regulation for cell-size homeostasis. The mechanisms underlying the control and dynamics of cell size remain poorly understood owing to the difficulty in sizing individual bacteria over long periods of time in a high-throughput manner. Here we measure and analyse long-term, single-cell growth and division across different Escherichia coli strains and growth conditions. We show that a subset of cells in a population exhibit transient oscillations in cell size with periods that stretch across several (more than ten) generations. Our analysis reveals that a simple law governing cell-size control-a noisy linear map-explains the origins of these cell-size oscillations across all strains. This noisy linear map implements a negative feedback on cell-size control: a cell with a larger initial size tends to divide earlier, whereas one with a smaller initial size tends to divide later. Combining simulations of cell growth and division with experimental data, we demonstrate that this noisy linear map generates transient oscillations, not just in cell size, but also in constitutive gene expression. Our work provides new insights into the dynamics of bacterial cell-size regulation with implications for the physiological processes involved.}, number={7560}, journal={Nature}, publisher={Nature Publishing Group}, author={Tanouchi, Yu and Pai, Anand and Park, Heungwon and Huang, Shuqiang and Stamatov, Rumen and Buchler, Nicolas E. and You, Lingchong}, year={2015}, month={Jun}, pages={357–360} }
 @article{rienzo_poveda-huertes_aydin_buchler_pascual-ahuir_proft_2015, title={Different mechanisms confer gradual control and memory at nutrient- and stress-regulated genes in yeast}, volume={35}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84944603437&partnerID=MN8TOARS}, DOI={10.1128/MCB.00729-15}, abstractNote={ABSTRACT Cells respond to environmental stimuli by fine-tuned regulation of gene expression. Here we investigated the dose-dependent modulation of gene expression at high temporal resolution in response to nutrient and stress signals in yeast. The GAL1 activity in cell populations is modulated in a well-defined range of galactose concentrations, correlating with a dynamic change of histone remodeling and RNA polymerase II (RNAPII) association. This behavior is the result of a heterogeneous induction delay caused by decreasing inducer concentrations across the population. Chromatin remodeling appears to be the basis for the dynamic GAL1 expression, because mutants with impaired histone dynamics show severely truncated dose-response profiles. In contrast, the GRE2 promoter operates like a rapid off/on switch in response to increasing osmotic stress, with almost constant expression rates and exclusively temporal regulation of histone remodeling and RNAPII occupancy. The Gal3 inducer and the Hog1 mitogen-activated protein (MAP) kinase seem to determine the different dose-response strategies at the two promoters. Accordingly, GAL1 becomes highly sensitive and dose independent if previously stimulated because of residual Gal3 levels, whereas GRE2 expression diminishes upon repeated stimulation due to acquired stress resistance. Our analysis reveals important differences in the way dynamic signals create dose-sensitive gene expression outputs.}, number={21}, journal={Molecular and Cellular Biology}, author={Rienzo, A. and Poveda-Huertes, D. and Aydin, S. and Buchler, N.E. and Pascual-Ahuir, A. and Proft, M.}, year={2015}, pages={3669–3683} }
 @article{zhou_wang_karapetyan_mwimba_marqués_buchler_dong_2015, title={Redox rhythm reinforces the circadian clock to gate immune response}, volume={523}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84936968103&partnerID=MN8TOARS}, DOI={10.1038/nature14449}, abstractNote={Recent studies have shown that in addition to the transcriptional circadian clock, many organisms, including Arabidopsis, have a circadian redox rhythm driven by the organism's metabolic activities. It has been hypothesized that the redox rhythm is linked to the circadian clock, but the mechanism and the biological significance of this link have only begun to be investigated. Here we report that the master immune regulator NPR1 (non-expressor of pathogenesis-related gene 1) of Arabidopsis is a sensor of the plant's redox state and regulates transcription of core circadian clock genes even in the absence of pathogen challenge. Surprisingly, acute perturbation in the redox status triggered by the immune signal salicylic acid does not compromise the circadian clock but rather leads to its reinforcement. Mathematical modelling and subsequent experiments show that NPR1 reinforces the circadian clock without changing the period by regulating both the morning and the evening clock genes. This balanced network architecture helps plants gate their immune responses towards the morning and minimize costs on growth at night. Our study demonstrates how a sensitive redox rhythm interacts with a robust circadian clock to ensure proper responsiveness to environmental stimuli without compromising fitness of the organism.}, number={7561}, journal={Nature}, publisher={Nature Publishing Group}, author={Zhou, Mian and Wang, Wei and Karapetyan, Sargis and Mwimba, Musoki and Marqués, Jorge and Buchler, Nicolas E. and Dong, Xinnian}, year={2015}, month={Jun}, pages={472–476} }
 @article{karapetyan_buchler_e_2015, title={Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators.}, volume={92}, url={http://europepmc.org/abstract/med/26764732}, DOI={10.1103/physreve.92.062712}, abstractNote={Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest sources of stochasticity is the binary noise that arises from the binding of a regulatory protein to a promoter in the chromosomal DNA. In this study, we focus on two minimal oscillators based on activator titration and repressor titration to understand the key parameters that are important for oscillations and for overcoming binary noise. We show that the rate of unbinding from the DNA, despite traditionally being considered a fast parameter, needs to be slow to broaden the space of oscillatory solutions. The addition of multiple, independent DNA binding sites further expands the oscillatory parameter space for the repressor-titration oscillator and lengthens the period of both oscillators. This effect is a combination of increased effective delay of the unbinding kinetics due to multiple binding sites and increased promoter ultrasensitivity that is specific for repression. We then use stochastic simulation to show that multiple binding sites increase the coherence of oscillations by mitigating the binary noise. Slow values of DNA unbinding rate are also effective in alleviating molecular noise due to the increased distance from the bifurcation point. Our work demonstrates how the number of DNA binding sites and slow unbinding kinetics, which are often omitted in biophysical models of gene circuits, can have a significant impact on the temporal and stochastic dynamics of genetic oscillators.}, number={6}, journal={Physical Review E}, author={Karapetyan, S. and Buchler, N.E. and E, Physical}, year={2015}, month={Dec}, pages={062712,} }
 @article{mazo-vargas_park_aydin_buchler_2014, title={Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy}, volume={25}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84908583872&partnerID=MN8TOARS}, DOI={10.1091/mbc.E14-07-1187}, abstractNote={Beetle luciferases and time-lapse luminescence microscopy were optimized to measure the dynamics of cell cycle genes in yeast with subminute time resolution. This method is faster and the cells are smaller than in previous work. It is shown that luciferase reporters are better than fluorescent proteins at tracking gene expression.}, number={22}, journal={Molecular Biology of the Cell}, author={Mazo-Vargas, A. and Park, H. and Aydin, M. and Buchler, N.E.}, year={2014}, pages={3699–3708} }
 @article{archambault_buchler_wilmes_jacobson_cross_2014, title={Two-Faced Cyclins with Eyes on the Targets}, volume={4}, url={https://publons.com/publon/2047264/}, DOI={10.4161/CC.4.1.1402}, abstractNote={We recently reported that the ‘hydrophobic patch’ (HP) of the Saccharomyces cerevisiae S-phase cyclin Clb5 facilitates its interaction with Orc6 (via its Cy or RXL motif), providing a mechanism that helps prevent re-replication from individual origins.1 This is the first finding of a biological function for an interaction between a cyclin and a cyclin-binding motif (Cy or RXL motif) in a target protein in Saccharomyces cerevisiae. It is also the first such example involving a B-type cyclin in any organism. Yet, some of our observations as well as work from other groups suggest that HP-RXL interactions are functionally important for cyclin-Cdk signaling to other targets. The evolutionary conservation of the HP motif suggests that it allows cyclins to carry out important and specialized functions.}, number={1}, journal={Cell Cycle}, author={Archambault, V. and Buchler, N.E. and Wilmes, G.M. and Jacobson, M.D. and Cross, F.R.}, year={2014}, pages={125–130} }
 @article{tanouchi_pai_buchler_you_2012, title={Programming stress-induced altruistic death in engineered bacteria}, volume={8}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84870835870&partnerID=MN8TOARS}, DOI={10.1038/msb.2012.57}, abstractNote={Programmed death is often associated with a bacterial stress response. This behavior appears paradoxical, as it offers no benefit to the individual. This paradox can be explained if the death is 'altruistic': the killing of some cells can benefit the survivors through release of 'public goods'. However, the conditions where bacterial programmed death becomes advantageous have not been unambiguously demonstrated experimentally. Here, we determined such conditions by engineering tunable, stress-induced altruistic death in the bacterium Escherichia coli. Using a mathematical model, we predicted the existence of an optimal programmed death rate that maximizes population growth under stress. We further predicted that altruistic death could generate the 'Eagle effect', a counter-intuitive phenomenon where bacteria appear to grow better when treated with higher antibiotic concentrations. In support of these modeling insights, we experimentally demonstrated both the optimality in programmed death rate and the Eagle effect using our engineered system. Our findings fill a critical conceptual gap in the analysis of the evolution of bacterial programmed death, and have implications for a design of antibiotic treatment.}, journal={Molecular Systems Biology}, author={Tanouchi, Y. and Pai, A. and Buchler, N.E. and You, L.}, year={2012} }
 @article{buchler_bai_2011, title={Chromatin: Bind at your own RSC}, volume={21}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79952802100&partnerID=MN8TOARS}, DOI={10.1016/j.cub.2011.01.060}, abstractNote={Recent work has identified a novel RSC–nucleosome complex that both strongly phases flanking nucleosomes and presents regulatory sites for ready access. These results challenge several widely held views.}, number={6}, journal={Current Biology}, author={Buchler, N.E. and Bai, L.}, year={2011} }
 @article{cross_buchler_skotheim_2011, title={Evolution of networks and sequences in eukaryotic cell cycle control}, volume={366}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-81055155486&partnerID=MN8TOARS}, DOI={10.1098/rstb.2011.0078}, abstractNote={The molecular networks regulating the G1–S transition in budding yeast and mammals are strikingly similar in network structure. However, many of the individual proteins performing similar network roles appear to have unrelated amino acid sequences, suggesting either extremely rapid sequence evolution, or true polyphyly of proteins carrying out identical network roles. A yeast/mammal comparison suggests that network topology, and its associated dynamic properties, rather than regulatory proteins themselves may be the most important elements conserved through evolution. However, recent deep phylogenetic studies show that fungal and animal lineages are relatively closely related in the opisthokont branch of eukaryotes. The presence in plants of cell cycle regulators such as Rb, E2F and cyclins A and D, that appear lost in yeast, suggests cell cycle control in the last common ancestor of the eukaryotes was implemented with this set of regulatory proteins. Forward genetics in non-opisthokonts, such as plants or their green algal relatives, will provide direct information on cell cycle control in these organisms, and may elucidate the potentially more complex cell cycle control network of the last common eukaryotic ancestor.}, number={1584}, journal={Philosophical Transactions of the Royal Society B: Biological Sciences}, author={Cross, F.R. and Buchler, N.E. and Skotheim, J.M.}, year={2011}, pages={3532–3544} }
 @article{buchler_cross_2009, title={Protein sequestration generates a flexible ultrasensitive response in a genetic network}, volume={5}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-67149138163&partnerID=MN8TOARS}, DOI={10.1038/msb.2009.30}, abstractNote={Ultrasensitive responses are crucial for cellular regulation. Protein sequestration, where an active protein is bound in an inactive complex by an inhibitor, can potentially generate ultrasensitivity. Here, in a synthetic genetic circuit in budding yeast, we show that sequestration of a basic leucine zipper transcription factor by a dominant-negative inhibitor converts a graded transcriptional response into a sharply ultrasensitive response, with apparent Hill coefficients up to 12. A simple quantitative model for this genetic network shows that both the threshold and the degree of ultrasensitivity depend upon the abundance of the inhibitor, exactly as we observed experimentally. The abundance of the inhibitor can be altered by simple mutation; thus, ultrasensitive responses mediated by protein sequestration are easily tuneable. Gene duplication of regulatory homodimers and loss-of-function mutations can create dominant negatives that sequester and inactivate the original regulator. The generation of flexible ultrasensitive responses is an unappreciated adaptive advantage that could explain the frequent evolutionary emergence of dominant negatives.}, journal={Molecular Systems Biology}, author={Buchler, N.E. and Cross, F.R.}, year={2009} }
 @article{buchler_louis_2008, title={Molecular Titration and Ultrasensitivity in Regulatory Networks}, volume={384}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-56949098506&partnerID=MN8TOARS}, DOI={10.1016/j.jmb.2008.09.079}, abstractNote={Protein sequestration occurs when an active protein is sequestered by a repressor into an inactive complex. Using mathematical and computational modeling, we show how this regulatory mechanism (called "molecular titration") can generate ultrasensitive or "all-or-none" responses that are equivalent to highly cooperative processes. The ultrasensitive nature of the input-output response is mainly determined by two parameters: the dimer dissociation constant and the repressor concentration. Because in vivo concentrations are tunable through a variety of mechanisms, molecular titration represents a flexible mechanism for generating ultrasensitivity. Using physiological parameters, we report how details of in vivo protein degradation affect the strength of the ultrasensitivity at steady state. Given that developmental systems often transduce signals into cell-fate decisions on timescales incompatible with steady state, we further examine whether molecular titration can produce ultrasensitive responses within physiologically relevant time intervals. Using Drosophila somatic sex determination as a developmental paradigm, we demonstrate that molecular titration can generate ultrasensitivity on timescales compatible with most cell-fate decisions. Gene duplication followed by loss-of-function mutations can create dominant negatives that titrate and compete with the original protein. Dominant negatives are abundant in gene regulatory circuits, and our results suggest that molecular titration might be generating an ultrasensitive response in these networks.}, number={5}, journal={Journal of Molecular Biology}, author={Buchler, N.E. and Louis, M.}, year={2008}, pages={1106–1119} }
 @article{fritz_buchler_hwa_gerland_2007, title={Designing sequential transcription logic: A simple genetic circuit for conditional memory}, volume={1}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-34548533820&partnerID=MN8TOARS}, DOI={10.1007/s11693-007-9006-8}, abstractNote={The ability to learn and respond to recurrent events depends on the capacity to remember transient biological signals received in the past. Moreover, it may be desirable to remember or ignore these transient signals conditioned upon other signals that are active at specific points in time or in unique environments. Here, we propose a simple genetic circuit in bacteria that is capable of conditionally memorizing a signal in the form of a transcription factor concentration. The circuit behaves similarly to a "data latch" in an electronic circuit, i.e. it reads and stores an input signal only when conditioned to do so by a "read command." Our circuit is of the same size as the well-known genetic toggle switch (an unconditional latch) which consists of two mutually repressing genes, but is complemented with a "regulatory front end" involving protein heterodimerization as a simple way to implement conditional control. Deterministic and stochastic analysis of the circuit dynamics indicate that an experimental implementation is feasible based on well-characterized genes and proteins. It is not known, to which extent molecular networks are able to conditionally store information in natural contexts for bacteria. However, our results suggest that such sequential logic elements may be readily implemented by cells through the combination of existing protein-protein interactions and simple transcriptional regulation.}, number={2}, journal={Systems and Synthetic Biology}, author={Fritz, G. and Buchler, N.E. and Hwa, T. and Gerland, U.}, year={2007}, pages={89–98} }
 @article{buchler_gerland_hwa_2005, title={Nonlinear protein degradation and the function of genetic circuits}, volume={102}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-22144443131&partnerID=MN8TOARS}, DOI={10.1073/pnas.0409553102}, abstractNote={The functions of most genetic circuits require a sufficient degree of cooperativity in the circuit components. Although mechanisms of cooperativity have been studied most extensively in the context of transcriptional initiation control, cooperativity from other processes involved in the operation of the circuits can also play important roles. In this work, we examine a simple kinetic source of cooperativity stemming from the nonlinear degradation of multimeric proteins. Ample experimental evidence suggests that protein subunits can degrade less rapidly when associated in multimeric complexes, an effect we refer to as "cooperative stability." For dimeric transcription factors, this effect leads to a concentration-dependence in the degradation rate because monomers, which are predominant at low concentrations, will be more rapidly degraded. Thus, cooperative stability can effectively widen the accessible range of protein levels in vivo. Through theoretical analysis of two exemplary genetic circuits in bacteria, we show that such an increased range is important for the robust operation of genetic circuits as well as their evolvability. Our calculations demonstrate that a few-fold difference between the degradation rate of monomers and dimers can already enhance the function of these circuits substantially. We discuss molecular mechanisms of cooperative stability and their occurrence in natural or engineered systems. Our results suggest that cooperative stability needs to be considered explicitly and characterized quantitatively in any systematic experimental or theoretical study of gene circuits.}, number={27}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Buchler, N.E. and Gerland, U. and Hwa, T.}, year={2005}, pages={9559–9564} }
 @article{bintu_buchler_garcia_gerland_hwa_kondev_kuhlman_phillips_2005, title={Transcriptional regulation by the numbers: Applications}, volume={15}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-15744387380&partnerID=MN8TOARS}, DOI={10.1016/j.gde.2005.02.006}, abstractNote={With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to their respective context. Thermodynamic models provide a useful framework for the quantitative analysis of bacterial transcription regulation. This framework can facilitate the quantification of vastly different forms of gene expression from several well-characterized bacterial promoters that are regulated by one or two species of transcription factors; it is useful because it requires only a few parameters. As such, it provides a compact description useful for higher-level studies (e.g. of genetic networks) without the need to invoke the biochemical details of every component. Moreover, it can be used to generate hypotheses on the likely mechanisms of transcriptional control.}, number={2}, journal={Current Opinion in Genetics and Development}, author={Bintu, L. and Buchler, N.E. and Garcia, H.G. and Gerland, U. and Hwa, T. and Kondev, J. and Kuhlman, T. and Phillips, R.}, year={2005}, pages={125–135} }
 @article{bintu_buchler_garcia_gerland_hwa_kondev_phillips_2005, title={Transcriptional regulation by the numbers: Models}, volume={15}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-15744394192&partnerID=MN8TOARS}, DOI={10.1016/j.gde.2005.02.007}, abstractNote={The expression of genes is regularly characterized with respect to how much, how fast, when and where. Such quantitative data demands quantitative models. Thermodynamic models are based on the assumption that the level of gene expression is proportional to the equilibrium probability that RNA polymerase (RNAP) is bound to the promoter of interest. Statistical mechanics provides a framework for computing these probabilities. Within this framework, interactions of activators, repressors, helper molecules and RNAP are described by a single function, the "regulation factor". This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell.}, number={2}, journal={Current Opinion in Genetics and Development}, author={Bintu, L. and Buchler, N.E. and Garcia, H.G. and Gerland, U. and Hwa, T. and Kondev, J. and Phillips, R.}, year={2005}, pages={116–124} }
 @article{archambault_buchler_wilmes_jacobson_cross_2005, title={Two-faced cyclins with eyes on the targets}, volume={4}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-14844287697&partnerID=MN8TOARS}, number={1}, journal={Cell Cycle}, author={Archambault, V. and Buchler, N.E. and Wilmes, G.M. and Jacobson, M.D. and Cross, F.R.}, year={2005}, pages={125–130} }
 @article{buchler_gerland_hwa_2003, title={On schemes of combinatorial transcription logic}, volume={100}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0037965981&partnerID=MN8TOARS}, DOI={10.1073/pnas.0930314100}, abstractNote={Cells receive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate specific genetic responses. Here we explore theoretically the potentials and limitations of combinatorial signal integration at the level of cis-regulatory transcription control. Our analysis suggests that many complex transcription-control functions of the type encountered in higher eukaryotes are already implementable within the much simpler bacterial transcription system. Using a quantitative model of bacterial transcription and invoking only specific protein–DNA interaction and weak glue-like interaction between regulatory proteins, we show explicit schemes to implement regulatory logic functions of increasing complexity by appropriately selecting the strengths and arranging the relative positions of the relevant protein-binding DNA sequences in the cis-regulatory region. The architectures that emerge are naturally modular and evolvable. Our results suggest that the transcription regulatory apparatus is a “programmable” computing machine, belonging formally to the class of Boltzmann machines. Crucial to our results is the ability to regulate gene expression at a distance. In bacteria, this can be achieved for isolated genes via DNA looping controlled by the dimerization of DNA-bound proteins. However, if adopted extensively in the genome, long-distance interaction can cause unintentional intergenic cross talk, a detrimental side effect difficult to overcome by the known bacterial transcription-regulation systems. This may be a key factor limiting the genome-wide adoption of complex transcription control in bacteria. Implications of our findings for combinatorial transcription control in eukaryotes are discussed.}, number={9}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Buchler, N.E. and Gerland, U. and Hwa, T.}, year={2003}, pages={5136–5141} }
 @article{surveying determinants of protein structure designability across different energy models and amino-acid alphabets: a consensus_2000, url={https://publons.com/publon/2047266/}, DOI={10.1063/1.480893}, abstractNote={A variety of analytical and computational models have been proposed to answer the question of why some protein structures are more “designable” (i.e., have more sequences folding into them) than others. One class of analytical and statistical-mechanical models has approached the designability problem from a thermodynamic viewpoint. These models highlighted specific structural features important for increased designability. Furthermore, designability was shown to be inherently related to thermodynamically relevant energetic measures of protein folding, such as the foldability F and energy gap Δ10. However, many of these models have been done within a very narrow focus: Namely, pair–contact interactions and two-letter amino-acid alphabets. Recently, two-letter amino-acid alphabets for pair–contact models have been shown to contain designability artifacts which disappear for larger-letter amino-acid alphabets. In addition, a solvation model was demonstrated to give identical designability results to previous...}, journal={The Journal of Chemical Physics}, year={2000} }
 @article{buchler_goldstein_1999, title={Effect of alphabet size and foldability requirements on protein structure designability}, volume={34}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032939920&partnerID=MN8TOARS}, DOI={10.1002/(SICI)1097-0134(19990101)34:1<113::AID-PROT9>3.0.CO;2-J}, abstractNote={A number of investigators have addressed the issue of why certain protein structures are especially common by considering structure designability, defined as the number of sequences that would successfully fold into any particular native structure. One such approach, based on foldability, suggested that structures could be classified according to their maximum possible foldability and that this optimal foldability would be highly correlated with structure designability. Other approaches have focused on computing the designability of lattice proteins written with reduced two‐letter amino acid alphabets. These different approaches suggested contrasting characteristics of the most designable structures. This report compares the designability of lattice proteins over a wide range of amino acid alphabets and foldability requirements. While all alphabets have a wide distribution of protein designabilities, the form of the distribution depends on how protein “viability” is defined. Furthermore, under increasing foldability requirements, the change in designabilities for all alphabets are in good agreement with the previous conclusions of the foldability approach. Most importantly, it was noticed that those structures that were highly designable for the two‐letter amino acid alphabets are not especially designable with higher‐letter alphabets. Proteins 1999;34:113–124. © 1999 Wiley‐Liss, Inc.}, number={1}, journal={Proteins: Structure, Function and Genetics}, author={Buchler, N.E.G. and Goldstein, R.A.}, year={1999}, pages={113–124} }
 @article{universal correlation between energy gap and foldability for the random energy model and lattice proteins_1999, url={https://publons.com/publon/2047267/}, DOI={10.1063/1.479951}, abstractNote={The random energy model, originally used to analyze the physics of spin glasses, has been employed to explore what makes a protein a good folder versus a bad folder. In earlier work, the ratio of the folding temperature over the glass–transition temperature was related to a statistical measure of protein energy landscapes denoted as the foldability F. It was posited and subsequently established by simulation that good folders had larger foldabilities, on average, than bad folders. An alternative hypothesis, equally verified by protein folding simulations, was that it is the energy gap Δ between the native state and the next highest energy that distinguishes good folders from bad folders. This duality of measures has led to some controversy and confusion with little done to reconcile the two. In this paper, we revisit the random energy model to derive the statistical distributions of the various energy gaps and foldability. The resulting joint distribution allows us to explicitly demonstrate the positive c...}, journal={The Journal of Chemical Physics}, year={1999} }
 @article{buchler_zuiderweg_wang_goldstein_1997, title={Protein Heteronuclear NMR Assignments Using Mean-Field Simulated Annealing}, volume={125}, url={https://publons.com/publon/2047265/}, DOI={10.1006/JMRE.1997.1106}, abstractNote={A computational method for the assignment of the NMR spectra of larger (21 kDa) proteins using a set of six of the most sensitive heteronuclear multidimensional nuclear magnetic resonance experiments is described. Connectivity data obtained from HNC alpha, HN(CO)C alpha, HN(C alpha)H alpha, and H alpha (C alpha CO)NH and spin-system identification data obtained from CP-(H)CCH-TOCSY and CP-(H)C(C alpha CO)NH-TOCSY were used to perform sequence-specific assignments using a mean-field formalism and simulated annealing. This mean-field method reports the resonance assignments in a probabilistic fashion, displaying the certainty of assignments in an unambiguous and quantitative manner. This technique was applied to the NMR data of the 172-residue peptide-binding domain of the E. coli heat-shock protein, DnaK. The method is demonstrated to be robust to significant amounts of missing, spurious, noisy, extraneous, and erroneous data.}, number={1}, journal={Journal of Magnetic Resonance}, author={Buchler, N.E.G. and Zuiderweg, E.R.P. and Wang, H. and Goldstein, R.A.}, year={1997}, pages={34–42} }
 @article{buchler_zuiderweg_wang_goldstein_1997, title={Protein Heteronuclear NMR Assignments Using Mean-Field Simulated Annealing}, volume={125}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0031083526&partnerID=MN8TOARS}, number={1}, journal={Journal of Magnetic Resonance}, author={Buchler, N.E.G. and Zuiderweg, E.R.P. and Wang, H. and Goldstein, R.A.}, year={1997}, pages={34–42} }
 @article{bl herculis model pulsations .3. livermore opacities_1994, url={https://publons.com/publon/51431452/}, journal={Astronomy & Astrophysics}, year={1994} }