1
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Kodan N, Hussaini R, Weber SC, Kondev J, Mohapatra L. Transcription templated assembly of the nucleolus in the C. elegans embryo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597440. [PMID: 38895351 PMCID: PMC11185672 DOI: 10.1101/2024.06.06.597440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The nucleolus is a multicomponent structure made of RNA and proteins that serves as the site of ribosome biogenesis within the nucleus. It has been extensively studied as a prototype of a biomolecular condensate whose assembly is driven by phase separation. While the steady-state size of the nucleolus is quantitatively accounted for by the thermodynamics of phase separation, we show that experimental measurements of the assembly dynamics are inconsistent with a simple model of a phase-separating system relaxing to its equilibrium state. Instead, we show that the dynamics are well described by a model in which the transcription of ribosomal RNA actively drives nucleolar assembly. We find that our model of active transcription-templated assembly quantitatively accounts for the rapid kinetics observed in early embryos at different developmental stages, and for different RNAi perturbations of embryo size. Our model predicts a scaling of the time to assembly with the volume of the nucleus to the one-third power, which is confirmed by experimental data. Our study highlights the role of active processes such as transcription in controlling the placement and timing of assembly of membraneless organelles.
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Affiliation(s)
- Nishant Kodan
- School of Physics and Astronomy, College of Science, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Rabeya Hussaini
- Department of Physics, New York University, New York, NY 10003, USA
| | - Stephanie C Weber
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Lishibanya Mohapatra
- School of Physics and Astronomy, College of Science, Rochester Institute of Technology, Rochester, NY 14623, USA
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2
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Syed S, Duan Y, Lim B. Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos. eLife 2023; 12:e85997. [PMID: 37934571 PMCID: PMC10629816 DOI: 10.7554/elife.85997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023] Open
Abstract
It is well known that enhancers regulate the spatiotemporal expression of their target genes by recruiting transcription factors (TFs) to the cognate binding sites in the region. However, the role of multiple binding sites for the same TFs and their specific spatial arrangement in determining the overall competency of the enhancer has yet to be fully understood. In this study, we utilized the MS2-MCP live imaging technique to quantitatively analyze the regulatory logic of the snail distal enhancer in early Drosophila embryos. Through systematic modulation of Dorsal and Twist binding motifs in this enhancer, we found that a mutation in any one of these binding sites causes a drastic reduction in transcriptional amplitude, resulting in a reduction in mRNA production of the target gene. We provide evidence of synergy, such that multiple binding sites with moderate affinities cooperatively recruit more TFs to drive stronger transcriptional activity than a single site. Moreover, a Hidden Markov-based stochastic model of transcription reveals that embryos with mutated binding sites have a higher probability of returning to the inactive promoter state. We propose that TF-DNA binding regulates spatial and temporal gene expression and drives robust pattern formation by modulating transcriptional kinetics and tuning bursting rates.
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Affiliation(s)
- Sahla Syed
- Department of Chemical and Biomolecular Engineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Yifei Duan
- Department of Chemical and Biomolecular Engineering, University of PennsylvaniaPhiladelphiaUnited States
- Master of Biotechnology Program, University of PennsylvaniaPhiladelphiaUnited States
| | - Bomyi Lim
- Department of Chemical and Biomolecular Engineering, University of PennsylvaniaPhiladelphiaUnited States
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3
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Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023; 58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
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Affiliation(s)
- Kaelan J Brennan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA
| | - Hsiao-Yun Liu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
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4
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Afzal Z, Lange JJ, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter BD, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023; 150:dev201259. [PMID: 37102683 PMCID: PMC10233718 DOI: 10.1242/dev.201259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/19/2023] [Indexed: 04/28/2023]
Abstract
Signaling pathways regulate the patterns of Hox gene expression that underlie their functions in the specification of axial identity. Little is known about the properties of cis-regulatory elements and underlying transcriptional mechanisms that integrate graded signaling inputs to coordinately control Hox expression. Here, we optimized a single molecule fluorescent in situ hybridization (smFISH) technique with probes spanning introns to evaluate how three shared retinoic acid response element (RARE)-dependent enhancers in the Hoxb cluster regulate patterns of nascent transcription in vivo at the level of single cells in wild-type and mutant embryos. We predominately detect nascent transcription of only a single Hoxb gene in each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets of genes. Single and/or compound RARE mutations indicate that each enhancer differentially impacts global and local patterns of nascent transcription, suggesting that selectivity and competitive interactions between these enhancers is important to robustly maintain the proper levels and patterns of nascent Hoxb transcription. This implies that rapid and dynamic regulatory interactions potentiate transcription of genes through combined inputs from these enhancers in coordinating the retinoic acid response.
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Affiliation(s)
- Zainab Afzal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Jeffrey J. Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christof Nolte
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ariel Paulson
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Anatomy and Cell Biology Department, Kansas University Medical Center, Kansas City, KS 66160, USA
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5
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Brouwer I, Kerklingh E, van Leeuwen F, Lenstra TL. Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting. Nat Struct Mol Biol 2023; 30:692-702. [PMID: 37127821 DOI: 10.1038/s41594-023-00981-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Abstract
Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by the remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in Saccharomyces cerevisiae to measure how bursting changes upon combined perturbations of chromatin remodelers, the transcription factor Gal4 and preinitiation complex components. Using dynamic epistasis analysis, we reveal how the remodeling of different nucleosomes regulates transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC and Gal4 binding synergistically facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. At canonical TATA boxes, the nucleosomes are displaced by TBP binding to allow for transcription activation even in the absence of remodelers. Overall, our results reveal how promoter nucleosome remodeling together with Gal4 and preinitiation complex binding regulates transcriptional bursting.
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Affiliation(s)
- Ineke Brouwer
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Emma Kerklingh
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands.
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6
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Harden TT, Vincent BJ, DePace AH. Transcriptional activators in the early Drosophila embryo perform different kinetic roles. Cell Syst 2023; 14:258-272.e4. [PMID: 37080162 PMCID: PMC10473017 DOI: 10.1016/j.cels.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/26/2022] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Combinatorial regulation of gene expression by transcription factors (TFs) may in part arise from kinetic synergy-wherein TFs regulate different steps in the transcription cycle. Kinetic synergy requires that TFs play distinguishable kinetic roles. Here, we used live imaging to determine the kinetic roles of three TFs that activate transcription in the Drosophila embryo-Zelda, Bicoid, and Stat92E-by introducing their binding sites into the even-skipped stripe 2 enhancer. These TFs influence different sets of kinetic parameters, and their influence can change over time. All three TFs increased the fraction of transcriptionally active nuclei; Zelda also shortened the first-passage time into transcription and regulated the interval between transcription events. Stat92E also increased the lifetimes of active transcription. Different TFs can therefore play distinct kinetic roles in activating the transcription. This has consequences for understanding the composition and flexibility of regulatory DNA sequences and the biochemical function of TFs. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Timothy T Harden
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ben J Vincent
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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7
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Li W, Liu Z, Wang P, Di R, Wang X, Liu Y, Chu M. The transcription factor RUNX1 affects the maturation of porcine oocytes via the BMP15/TGF-β signaling pathway. Int J Biol Macromol 2023; 238:124026. [PMID: 36933589 DOI: 10.1016/j.ijbiomac.2023.124026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
Bone morphogenetic protein 15 (BMP15) is specifically expressed in oocytes in pigs at all stages from early stages to ovulation and has an important role in oocyte maturation. However, there are few reports on the molecular mechanisms by which BMP15 affects oocyte maturation. In this study, we identified the core promoter region of BMP15 using a dual luciferase activity assay and successfully predicted the DNA binding motif of the transcription factor RUNX1. The effect of BMP15 and RUNX1 on oocyte maturation was examined using the first polar body extrusion rate, a reactive oxygen species (ROS) assay and total glutathione (GSH) content at three time points of 12, 24 and 48 h of in vitro culture of porcine isolated oocytes. Subsequently, the effect of the transcription factor RUNX1 on the TGF-β signaling pathway (BMPR1B and ALK5) was further verified using RT-qPCR and Western blotting. We found that the overexpression of BMP15 significantly increased the first polar body extrusion rate (P < 0.01) and total glutathione content of oocytes cultured in vitro for 24 h and decreased reactive oxygen levels (P < 0.01), whereas interference with BMP15 decreased the first polar body extrusion rate (P < 0.01), increased reactive oxygen levels in oocytes cultured in vitro for 24 h (P < 0.01), and decreased glutathione content (P < 0.01). The dual luciferase activity assay and online software prediction showed that RUNX1 is a potential transcription factor binding to the core promoter region (-1203/-1423 bp) of BMP15. Overexpression of RUNX1 significantly increased the expression of BMP15 and oocyte maturation rate, while inhibition of RUNX1 decreased the expression of BMP15 and the oocyte maturation rate. Moreover, the expression of BMPR1B and ALK5 in the TGF-β signaling pathway increased significantly after overexpression of RUNX1, whereas their expression decreased after inhibition of RUNX1. Overall, our results suggest that the transcription factor RUNX1 positively regulates the expression of BMP15 and influences oocyte maturation through the TGF-β signaling pathway. This study provides a theoretical basis for further complementing the BMP15/TGF-β signaling pathway to regulate mammalian oocyte maturation.
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Affiliation(s)
- Wentao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ziyi Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Peng Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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8
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Alamos S, Reimer A, Westrum C, Turner MA, Talledo P, Zhao J, Luu E, Garcia HG. Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient. Cell Syst 2023; 14:220-236.e3. [PMID: 36696901 PMCID: PMC10125799 DOI: 10.1016/j.cels.2022.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/03/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023]
Abstract
How enhancers interpret morphogen gradients to generate gene expression patterns is a central question in developmental biology. Recent studies have proposed that enhancers can dictate whether, when, and at what rate promoters engage in transcription, but the complexity of endogenous enhancers calls for theoretical models with too many free parameters to quantitatively dissect these regulatory strategies. To overcome this limitation, we established a minimal promoter-proximal synthetic enhancer in embryos of Drosophila melanogaster. Here, a gradient of the Dorsal activator is read by a single Dorsal DNA binding site. Using live imaging to quantify transcriptional activity, we found that a single binding site can regulate whether promoters engage in transcription in a concentration-dependent manner. By modulating the binding-site affinity, we determined that a gene's decision to transcribe and its transcriptional onset time can be explained by a simple model where the promoter traverses multiple kinetic barriers before transcription can ensue.
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Affiliation(s)
- Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Armando Reimer
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
| | - Clay Westrum
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Meghan A Turner
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Paul Talledo
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Emma Luu
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA; Department of Physics, University of California at Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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9
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Competing constraints shape the nonequilibrium limits of cellular decision-making. Proc Natl Acad Sci U S A 2023; 120:e2211203120. [PMID: 36862689 PMCID: PMC10013869 DOI: 10.1073/pnas.2211203120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Gene regulation is central to cellular function. Yet, despite decades of work, we lack quantitative models that can predict how transcriptional control emerges from molecular interactions at the gene locus. Thermodynamic models of transcription, which assume that gene circuits operate at equilibrium, have previously been employed with considerable success in the context of bacterial systems. However, the presence of ATP-dependent processes within the eukaryotic transcriptional cycle suggests that equilibrium models may be insufficient to capture how eukaryotic gene circuits sense and respond to input transcription factor concentrations. Here, we employ simple kinetic models of transcription to investigate how energy dissipation within the transcriptional cycle impacts the rate at which genes transmit information and drive cellular decisions. We find that biologically plausible levels of energy input can lead to significant gains in how rapidly gene loci transmit information but discover that the regulatory mechanisms underlying these gains change depending on the level of interference from noncognate activator binding. When interference is low, information is maximized by harnessing energy to push the sensitivity of the transcriptional response to input transcription factors beyond its equilibrium limits. Conversely, when interference is high, conditions favor genes that harness energy to increase transcriptional specificity by proofreading activator identity. Our analysis further reveals that equilibrium gene regulatory mechanisms break down as transcriptional interference increases, suggesting that energy dissipation may be indispensable in systems where noncognate factor interference is sufficiently large.
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10
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Kim YJ, Rhee K, Liu J, Jeammet S, Turner MA, Small SJ, Garcia HG. Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer. eLife 2022; 11:73395. [PMID: 36503705 PMCID: PMC9836395 DOI: 10.7554/elife.73395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
A challenge in quantitative biology is to predict output patterns of gene expression from knowledge of input transcription factor patterns and from the arrangement of binding sites for these transcription factors on regulatory DNA. We tested whether widespread thermodynamic models could be used to infer parameters describing simple regulatory architectures that inform parameter-free predictions of more complex enhancers in the context of transcriptional repression by Runt in the early fruit fly embryo. By modulating the number and placement of Runt binding sites within an enhancer, and quantifying the resulting transcriptional activity using live imaging, we discovered that thermodynamic models call for higher-order cooperativity between multiple molecular players. This higher-order cooperativity captures the combinatorial complexity underlying eukaryotic transcriptional regulation and cannot be determined from simpler regulatory architectures, highlighting the challenges in reaching a predictive understanding of transcriptional regulation in eukaryotes and calling for approaches that quantitatively dissect their molecular nature.
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Affiliation(s)
- Yang Joon Kim
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Kaitlin Rhee
- Department of Chemical Biology, University of California, Berkeley, Berkeley, United States
| | - Jonathan Liu
- Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Selene Jeammet
- Department of Biology, Ecole Polytechnique, Paris, France
| | - Meghan A Turner
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Stephen J Small
- Department of Biology, New York University, New York, United States
| | - Hernan G Garcia
- Chan Zuckerberg Biohub, San Francisco, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, United States
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11
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Kim ED, Dorrity MW, Fitzgerald BA, Seo H, Sepuru KM, Queitsch C, Mitsuda N, Han SK, Torii KU. Dynamic chromatin accessibility deploys heterotypic cis/trans-acting factors driving stomatal cell-fate commitment. NATURE PLANTS 2022; 8:1453-1466. [PMID: 36522450 PMCID: PMC9788986 DOI: 10.1038/s41477-022-01304-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/28/2022] [Indexed: 05/12/2023]
Abstract
Chromatin architecture and transcription factor (TF) binding underpin cell-fate specification during development, but their mutual regulatory relationships remain unclear. Here we report an atlas of dynamic chromatin landscapes during stomatal cell-lineage progression, in which sequential cell-state transitions are governed by lineage-specific bHLH TFs. Major reprogramming of chromatin accessibility occurs at the proliferation-to-differentiation transition. We discover novel co-cis regulatory elements (CREs) signifying the early precursor stage, BBR/BPC (GAGA) and bHLH (E-box) motifs, where master-regulatory bHLH TFs, SPEECHLESS and MUTE, consecutively bind to initiate and terminate the proliferative state, respectively. BPC TFs complex with MUTE to repress SPEECHLESS expression through a local deposition of repressive histone marks. We elucidate the mechanism by which cell-state-specific heterotypic TF complexes facilitate cell-fate commitment by recruiting chromatin modifiers via key co-CREs.
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Affiliation(s)
- Eun-Deok Kim
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Bridget A Fitzgerald
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hyemin Seo
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Krishna Mohan Sepuru
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Soon-Ki Han
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Keiko U Torii
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan.
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12
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“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation. Mol Cell 2022; 82:3970-3984. [DOI: 10.1016/j.molcel.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/19/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
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13
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How does an organism extract relevant information from transcription factor concentrations? Biochem Soc Trans 2022; 50:1365-1376. [DOI: 10.1042/bst20220333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022]
Abstract
How does an organism regulate its genes? The involved regulation typically occurs in terms of a signal processing chain: an externally applied stimulus or a maternally supplied transcription factor leads to the expression of some downstream genes, which, in turn, are transcription factors for further genes. Especially during development, these transcription factors are frequently expressed in amounts where noise is still important; yet, the signals that they provide must not be lost in the noise. Thus, the organism needs to extract exactly relevant information in the signal. New experimental approaches involving single-molecule measurements at high temporal precision as well as increased precision in manipulations directly on the genome are allowing us to tackle this question anew. These new experimental advances mean that also from the theoretical side, theoretical advances should be possible. In this review, I will describe, specifically on the example of fly embryo gene regulation, how theoretical approaches, especially from inference and information theory, can help in understanding gene regulation. To do so, I will first review some more traditional theoretical models for gene regulation, followed by a brief discussion of information-theoretical approaches and when they can be applied. I will then introduce early fly development as an exemplary system where such information-theoretical approaches have traditionally been applied and can be applied; I will specifically focus on how one such method, namely the information bottleneck approach, has recently been used to infer structural features of enhancer architecture.
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14
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Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? CURRENT OPINION IN SYSTEMS BIOLOGY 2022; 31:100435. [PMID: 36590072 PMCID: PMC9802646 DOI: 10.1016/j.coisb.2022.100435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory-theory that prescribes rather than just describes-in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.
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Affiliation(s)
- Benjamin Zoller
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA
- Department of Developmental and Stem Cell Biology UMR3738, Institut Pasteur, Paris, France
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA
- Department of Developmental and Stem Cell Biology UMR3738, Institut Pasteur, Paris, France
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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15
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Luzete-Monteiro E, Zaret KS. Structures and consequences of pioneer factor binding to nucleosomes. Curr Opin Struct Biol 2022; 75:102425. [PMID: 35863165 PMCID: PMC9976633 DOI: 10.1016/j.sbi.2022.102425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022]
Abstract
Pioneer transcription factors are able to bind a partially exposed motif on the surface of a nucleosome, enabling the proteins to target sites in silent regions of chromatin that have been compacted by linker histone. The targeting of nucleosomal DNA by pioneer factors has been observed in vitro and in vivo, where binding can promote local nucleosome exposure that allows other transcription factors, nucleosome remodelers, and histone modifiers to engage the chromatin and elicit gene activation or further repression. Pioneer factors thereby establish new gene expression programs during cell fate changes that occur during embryonic development, regeneration, and cancer. Here, we review recent biophysical studies that reveal the structural features and strategies used by pioneer factors to accomplish nucleosome binding and the consequential changes to nucleosomes that can lead to DNA accessibility.
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Affiliation(s)
- Edgar Luzete-Monteiro
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104-4544
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA
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16
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Wang J, Zhang S, Lu H, Xu H. Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction. Nat Commun 2022; 13:2714. [PMID: 35581264 PMCID: PMC9114328 DOI: 10.1038/s41467-022-30315-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Many eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the kinetic mechanisms of complex eukaryotic gene regulation. Alternative promoters differ in their expression patterns, whose mechanisms are not well understood. Here the authors show that alternative promoters of a Drosophila embryonic gene hunchback are regulated by different action modes of two enhancers.
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Affiliation(s)
- Jingyao Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Shihe Zhang
- Institute of Natural Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China. .,School of Physics and Astronomy, Shanghai Jiao Tong University, 200240, Shanghai, China.
| | - Hongfang Lu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Heng Xu
- Institute of Natural Sciences, Shanghai Jiao Tong University, 200240, Shanghai, China. .,School of Physics and Astronomy, Shanghai Jiao Tong University, 200240, Shanghai, China.
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17
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Fernandes G, Tran H, Andrieu M, Diaw Y, Perez Romero C, Fradin C, Coppey M, Walczak AM, Dostatni N. Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription. eLife 2022; 11:74509. [PMID: 35363606 PMCID: PMC8975551 DOI: 10.7554/elife.74509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/10/2022] [Indexed: 11/23/2022] Open
Abstract
For over 40 years, the Bicoid-hunchback (Bcd-hb) system in the fruit fly embryo has been used as a model to study how positional information in morphogen concentration gradients is robustly translated into step-like responses. A body of quantitative comparisons between theory and experiment have since questioned the initial paradigm that the sharp hb transcription pattern emerges solely from diffusive biochemical interactions between the Bicoid transcription factor and the gene promoter region. Several alternative mechanisms have been proposed, such as additional sources of positional information, positive feedback from Hb proteins or out-of-equilibrium transcription activation. By using the MS2-MCP RNA-tagging system and analysing in real time, the transcription dynamics of synthetic reporters for Bicoid and/or its two partners Zelda and Hunchback, we show that all the early hb expression pattern features and temporal dynamics are compatible with an equilibrium model with a short decay length Bicoid activity gradient as a sole source of positional information. Meanwhile, Bicoid’s partners speed-up the process by different means: Zelda lowers the Bicoid concentration threshold required for transcriptional activation while Hunchback reduces burstiness and increases the polymerase firing rate.
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Affiliation(s)
- Gonçalo Fernandes
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Huy Tran
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France.,Laboratoire de Physique de l'École Normale Supérieure, CNRS, Université PSL, Sorbonne Université and Université de Paris, Paris, France
| | - Maxime Andrieu
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Youssoupha Diaw
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Carmina Perez Romero
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Cécile Fradin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.,Department of Physics and Astronomy, McMaster University, Hamilton, Canada
| | - Mathieu Coppey
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'École Normale Supérieure, CNRS, Université PSL, Sorbonne Université and Université de Paris, Paris, France
| | - Nathalie Dostatni
- Institut Curie, Université PSL, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
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18
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Falo-Sanjuan J, Bray S. Notch-dependent and -independent transcription are modulated by tissue movements at gastrulation. eLife 2022; 11:73656. [PMID: 35583918 PMCID: PMC9183233 DOI: 10.7554/elife.73656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/27/2022] [Indexed: 12/30/2022] Open
Abstract
Cells sense and integrate external information from diverse sources that include mechanical cues. Shaping of tissues during development may thus require coordination between mechanical forces from morphogenesis and cell-cell signalling to confer appropriate changes in gene expression. By live-imaging Notch-induced transcription in real time, we have discovered that morphogenetic movements during Drosophila gastrulation bring about an increase in activity-levels of a Notch-responsive enhancer. Mutations that disrupt the timing of gastrulation resulted in concomitant delays in transcription up-regulation that correlated with the start of mesoderm invagination. As a similar gastrulation-induced effect was detected when transcription was elicited by the intracellular domain NICD, it cannot be attributed to forces exerted on Notch receptor activation. A Notch-independent vnd enhancer also exhibited a modest gastrulation-induced activity increase in the same stripe of cells. Together, these observations argue that gastrulation-associated forces act on the nucleus to modulate transcription levels. This regulation was uncoupled when the complex linking the nucleoskeleton and cytoskeleton (LINC) was disrupted, indicating a likely conduit. We propose that the coupling between tissue-level mechanics, arising from gastrulation, and enhancer activity represents a general mechanism for ensuring correct tissue specification during development and that Notch-dependent enhancers are highly sensitive to this regulation.
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Affiliation(s)
- Julia Falo-Sanjuan
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
| | - Sarah Bray
- Department of Physiology, Development and Neuroscience, University of CambridgeCambridgeUnited Kingdom
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19
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Dutta S, Patel AL, Keenan SE, Shvartsman SY. From complex datasets to predictive models of embryonic development. NATURE COMPUTATIONAL SCIENCE 2021; 1:516-520. [PMID: 38217248 DOI: 10.1038/s43588-021-00110-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/12/2021] [Indexed: 01/15/2024]
Abstract
Modern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these new tools requires systematic approaches for data-driven analysis of the underlying developmental processes. Here, we use data from our work on signal-dependent gene repression in the Drosophila embryo to illustrate how computational models can compactly summarize quantitative results of live imaging, chromatin immunoprecipitation and optogenetic perturbation experiments. The presented computational approach is ideally suited for integrating rapidly accumulating quantitative data and for guiding future studies of embryogenesis.
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Affiliation(s)
- Sayantan Dutta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Aleena L Patel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Shannon E Keenan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Stanislav Y Shvartsman
- Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Center of Computational Biology, Flatiron Institute, New York, NY, USA.
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20
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Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG. Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Comput Biol 2021; 17:e1008999. [PMID: 34003867 PMCID: PMC8162642 DOI: 10.1371/journal.pcbi.1008999] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/28/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022] Open
Abstract
The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.
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Affiliation(s)
- Jonathan Liu
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
| | - Donald Hansen
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Elizabeth Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Meghan Turner
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, United States of America
| | - Hernan G. Garcia
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, United States of America
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California, United States of America
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21
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Rothenberg EV. Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment. Biophys J 2021; 120:4162-4181. [PMID: 33838137 PMCID: PMC8516641 DOI: 10.1016/j.bpj.2021.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Transcription factors are the major agents that read the regulatory sequence information in the genome to initiate changes in expression of specific genes, both in development and in physiological activation responses. Their actions depend on site-specific DNA binding and are largely guided by their individual DNA target sequence specificities. However, their action is far more conditional in a real developmental context than would be expected for simple reading of local genomic DNA sequence, which is common to all cells in the organism. They are constrained by slow-changing chromatin states and by interactions with other transcription factors, which affect their occupancy patterns of potential sites across the genome. These mechanisms lead to emergent discontinuities in function even for transcription factors with minimally changing expression. This is well revealed by diverse lineages of blood cells developing throughout life from hematopoietic stem cells, which use overlapping combinations of transcription factors to drive strongly divergent gene regulation programs. Here, using development of T lymphocytes from hematopoietic multipotent progenitor cells as a focus, recent evidence is reviewed on how binding specificity and dynamics, transcription factor cooperativity, and chromatin state changes impact the effective regulatory functions of key transcription factors including PU.1, Runx1, Notch-RBPJ, and Bcl11b.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.
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22
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Gene Regulation and Cellular Metabolism: An Essential Partnership. Trends Genet 2021; 37:389-400. [PMID: 33092903 PMCID: PMC7969386 DOI: 10.1016/j.tig.2020.09.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 01/09/2023]
Abstract
It is recognized that cell metabolism is tightly connected to other cellular processes such as regulation of gene expression. Metabolic pathways not only provide the precursor molecules necessary for gene expression, but they also provide ATP, the primary fuel driving gene expression. However, metabolic conditions are highly variable since nutrient uptake is not a uniform process. Thus, cells must continually calibrate gene expression to their changing metabolite and energy budgets. This review discusses recent advances in understanding the molecular and biophysical mechanisms that connect metabolism and gene regulation as cells navigate their growth, proliferation, and differentiation. Particular focus is given to these mechanisms in the context of organismal development.
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23
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Eck E, Liu J, Kazemzadeh-Atoufi M, Ghoreishi S, Blythe SA, Garcia HG. Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility. eLife 2020; 9:e56429. [PMID: 33074101 PMCID: PMC7738189 DOI: 10.7554/elife.56429] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/16/2020] [Indexed: 12/28/2022] Open
Abstract
Thermodynamic models of gene regulation can predict transcriptional regulation in bacteria, but in eukaryotes, chromatin accessibility and energy expenditure may call for a different framework. Here, we systematically tested the predictive power of models of DNA accessibility based on the Monod-Wyman-Changeux (MWC) model of allostery, which posits that chromatin fluctuates between accessible and inaccessible states. We dissected the regulatory dynamics of hunchback by the activator Bicoid and the pioneer-like transcription factor Zelda in living Drosophila embryos and showed that no thermodynamic or non-equilibrium MWC model can recapitulate hunchback transcription. Therefore, we explored a model where DNA accessibility is not the result of thermal fluctuations but is catalyzed by Bicoid and Zelda, possibly through histone acetylation, and found that this model can predict hunchback dynamics. Thus, our theory-experiment dialogue uncovered potential molecular mechanisms of transcriptional regulatory dynamics, a key step toward reaching a predictive understanding of developmental decision-making.
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Affiliation(s)
- Elizabeth Eck
- Biophysics Graduate Group, University of California at BerkeleyBerkeleyUnited States
| | - Jonathan Liu
- Department of Physics, University of California at BerkeleyBerkeleyUnited States
| | | | - Sydney Ghoreishi
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at BerkeleyBerkeleyUnited States
- Department of Physics, University of California at BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California at BerkeleyBerkeleyUnited States
- Institute for Quantitative Biosciences-QB3, University of California at BerkeleyBerkeleyUnited States
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