1
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Gillis A, Berry S. Global control of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
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Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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2
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Stec N, Klosin A. Transcriptional bodies manage tight resources. Nat Cell Biol 2024; 26:512-513. [PMID: 38589532 DOI: 10.1038/s41556-024-01395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Affiliation(s)
- Natalia Stec
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Adam Klosin
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland.
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3
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Ugolini M, Kerlin MA, Kuznetsova K, Oda H, Kimura H, Vastenhouw NL. Transcription bodies regulate gene expression by sequestering CDK9. Nat Cell Biol 2024; 26:604-612. [PMID: 38589534 PMCID: PMC11021188 DOI: 10.1038/s41556-024-01389-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells. It remains unclear, however, if and how transcription bodies affect gene expression. Here we disrupted the formation of two prominent endogenous transcription bodies that mark the onset of zygotic transcription in zebrafish embryos and analysed the effect on gene expression using enriched SLAM-seq and live-cell imaging. We find that the disruption of transcription bodies results in the misregulation of hundreds of genes. Here we focus on genes that are upregulated. These genes have accessible chromatin and are poised to be transcribed in the presence of the two transcription bodies, but they do not go into elongation. Live-cell imaging shows that disruption of the two large transcription bodies enables these poised genes to be transcribed in ectopic transcription bodies, suggesting that the large transcription bodies sequester a pause release factor. Supporting this hypothesis, we find that CDK9-the kinase that releases paused polymerase II-is highly enriched in the two large transcription bodies. Overexpression of CDK9 in wild-type embryos results in the formation of ectopic transcription bodies and thus phenocopies the removal of the two large transcription bodies. Taken together, our results show that transcription bodies regulate transcription by sequestering machinery, thereby preventing genes elsewhere in the nucleus from being transcribed.
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Affiliation(s)
- Martino Ugolini
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Maciej A Kerlin
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland
| | - Ksenia Kuznetsova
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- Institute of Human Genetics, CNRS, Montpellier, France
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Nadine L Vastenhouw
- Center for Integrative Genomics (CIG), University of Lausanne (UNIL), Lausanne, Switzerland.
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
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4
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Lu F, Park BJ, Fujiwara R, Wilusz JE, Gilmour DS, Lehmann R, Lionnet T. Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.07.561364. [PMID: 37873455 PMCID: PMC10592978 DOI: 10.1101/2023.10.07.561364] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Numerous components of the transcription machinery, including RNA polymerase II (Pol II), accumulate in regions of high local concentration known as clusters, which are thought to facilitate transcription. Using the histone locus of Drosophila nurse cells as a model, we find that Pol II forms long-lived, transcriptionally poised clusters distinct from liquid droplets, which contain unbound and paused Pol II. Depletion of the Integrator complex endonuclease module, but not its phosphatase module or Pol II pausing factors disperses these Pol II clusters. Consequently, histone transcription fails to reach peak levels during S-phase and aberrantly continues throughout the cell cycle. We propose that Pol II clustering is a regulatory step occurring near promoters that limits rapid gene activation to defined times. One Sentence Summary Using the Drosophila histone locus as a model, we show that clustered RNA polymerase II is poised for synchronous activation.
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5
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O'Haren T, Aoki T, Rieder LE. Zelda is dispensable for Drosophila melanogaster histone gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572383. [PMID: 38187550 PMCID: PMC10769256 DOI: 10.1101/2023.12.19.572383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
To ensure that the embryo can package exponentially increasing amounts of DNA, replication-dependent histones are some of the earliest transcribed genes from the zygotic genome. However, how the histone genes are identified is not known. The pioneer factors Zelda and CLAMP collaborate at a subset of genes to regulate zygotic genome activation in Drosophila melanogaster and target early activated genes to induce transcription. CLAMP also regulates the embryonic histone genes and helps establish the histone locus body, a suite of factors that controls histone mRNA biosynthesis. The relationship between Zelda and CLAMP led us to hypothesize that Zelda helps identify histone genes for early embryonic expression. We found that Zelda targets the histone locus early during embryogenesis, prior to histone gene expression. However, depletion of zelda in the early embryo does not affect histone mRNA levels or histone locus body formation. While surprising, these results concur with other investigations into Zelda's role in the early embryo, suggesting the earliest factors responsible for specifying the zygotic histone genes remain undiscovered.
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Affiliation(s)
- Tommy O'Haren
- Emory University Department of Biology, Atlanta, GA 30322, USA
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540 USA
| | - Leila E Rieder
- Emory University Department of Biology, Atlanta, GA 30322, USA
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6
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Geisler MS, Kemp JP, Duronio RJ. Histone locus bodies: a paradigm for how nuclear biomolecular condensates control cell cycle regulated gene expression. Nucleus 2023; 14:2293604. [PMID: 38095604 PMCID: PMC10730174 DOI: 10.1080/19491034.2023.2293604] [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: 09/29/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Histone locus bodies (HLBs) are biomolecular condensates that assemble at replication-dependent (RD) histone genes in animal cells. These genes produce unique mRNAs that are not polyadenylated and instead end in a conserved 3' stem loop critical for coordinated production of histone proteins during S phase of the cell cycle. Several evolutionarily conserved factors necessary for synthesis of RD histone mRNAs concentrate only in the HLB. Moreover, because HLBs are present throughout the cell cycle even though RD histone genes are only expressed during S phase, changes in HLB composition during cell cycle progression drive much of the cell cycle regulation of RD histone gene expression. Thus, HLBs provide a powerful opportunity to determine the cause-and-effect relationships between nuclear body formation and cell cycle regulated gene expression. In this review, we focus on progress during the last five years that has advanced our understanding of HLB biology.
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Affiliation(s)
- Mark S. Geisler
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - James P. Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J. Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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7
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Gaskill MM, Soluri IV, Branks AE, Boka AP, Stadler MR, Vietor K, Huang HYS, Gibson TJ, Mukherjee A, Mir M, Blythe SA, Harrison MM. Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression. Dev Cell 2023; 58:1610-1624.e8. [PMID: 37478844 PMCID: PMC10528433 DOI: 10.1016/j.devcel.2023.06.010] [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: 11/15/2022] [Revised: 04/19/2023] [Accepted: 06/29/2023] [Indexed: 07/23/2023]
Abstract
The eukaryotic genome is organized to enable the precise regulation of gene expression. This organization is established as the embryo transitions from a fertilized gamete to a totipotent zygote. To understand the factors and processes that drive genomic organization, we focused on the pioneer factor GAGA factor (GAF) that is required for early development in Drosophila. GAF transcriptionally activates the zygotic genome and is localized to subnuclear foci. This non-uniform distribution is driven by binding to highly abundant GA repeats. At GA repeats, GAF is necessary to form heterochromatin and silence transcription. Thus, GAF is required to establish both active and silent regions. We propose that foci formation enables GAF to have opposing transcriptional roles within a single nucleus. Our data support a model in which the subnuclear concentration of transcription factors acts to organize the nucleus into functionally distinct domains essential for the robust regulation of gene expression.
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Affiliation(s)
- Marissa M Gaskill
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Isabella V Soluri
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Annemarie E Branks
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alan P Boka
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael R Stadler
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katherine Vietor
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hao-Yu S Huang
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Apratim Mukherjee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mustafa Mir
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Regenerative, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelby A Blythe
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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8
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Cho CY, O'Farrell PH. Stepwise modifications of transcriptional hubs link pioneer factor activity to a burst of transcription. Nat Commun 2023; 14:4848. [PMID: 37563108 PMCID: PMC10415302 DOI: 10.1038/s41467-023-40485-6] [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: 11/22/2022] [Accepted: 07/29/2023] [Indexed: 08/12/2023] Open
Abstract
Binding of transcription factors (TFs) promotes the subsequent recruitment of coactivators and preinitiation complexes to initiate eukaryotic transcription, but this time course is usually not visualized. It is commonly assumed that recruited factors eventually co-reside in a higher-order structure, allowing distantly bound TFs to activate transcription at core promoters. We use live imaging of endogenously tagged proteins, including the pioneer TF Zelda, the coactivator dBrd4, and RNA polymerase II (RNAPII), to define a cascade of events upstream of transcriptional initiation in early Drosophila embryos. These factors are sequentially and transiently recruited to discrete clusters during activation of non-histone genes. Zelda and the acetyltransferase dCBP nucleate dBrd4 clusters, which then trigger pre-transcriptional clustering of RNAPII. Subsequent transcriptional elongation disperses clusters of dBrd4 and RNAPII. Our results suggest that activation of transcription by eukaryotic TFs involves a succession of distinct biomolecular condensates that culminates in a self-limiting burst of transcription.
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Affiliation(s)
- Chun-Yi Cho
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Patrick H O'Farrell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA.
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9
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Theis A, Harrison MM. Reprogramming of three-dimensional chromatin organization in the early embryo. Curr Opin Struct Biol 2023; 81:102613. [PMID: 37224641 PMCID: PMC10524315 DOI: 10.1016/j.sbi.2023.102613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023]
Abstract
Chromatin organization within the three-dimensional (3D) nuclear space is important for proper gene expression and developmental programming. This organization is established during the dramatic reprogramming that occurs in early embryonic development. Thus, the early embryo is an ideal model for examining the formation and dynamics of 3D chromatin structure. Advances in high-resolution microscopy and single-nucleus genomic analyses have provided fundamental insights into the mechanisms driving genome organization in the early embryo. Here, we highlight recent findings describing the dynamics and driving mechanisms for establishing 3D chromatin organization and discuss the role such organization has on gene regulation in early embryonic development.
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Affiliation(s)
- Alexandra Theis
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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10
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Pownall ME, Miao L, Vejnar CE, M’Saad O, Sherrard A, Frederick MA, Benitez MD, Boswell CW, Zaret KS, Bewersdorf J, Giraldez AJ. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023; 381:92-100. [PMID: 37410825 PMCID: PMC10372697 DOI: 10.1126/science.ade5308] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
Nanoscale chromatin organization regulates gene expression. Although chromatin is notably reprogrammed during zygotic genome activation (ZGA), the organization of chromatin regulatory factors during this universal process remains unclear. In this work, we developed chromatin expansion microscopy (ChromExM) to visualize chromatin, transcription, and transcription factors in vivo. ChromExM of embryos during ZGA revealed how the pioneer factor Nanog interacts with nucleosomes and RNA polymerase II (Pol II), providing direct visualization of transcriptional elongation as string-like nanostructures. Blocking elongation led to more Pol II particles clustered around Nanog, with Pol II stalled at promoters and Nanog-bound enhancers. This led to a new model termed "kiss and kick", in which enhancer-promoter contacts are transient and released by transcriptional elongation. Our results demonstrate that ChromExM is broadly applicable to study nanoscale nuclear organization.
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Affiliation(s)
- Mark E. Pownall
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Liyun Miao
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Charles E. Vejnar
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Ons M’Saad
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
| | - Alice Sherrard
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Megan A. Frederick
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria D.J. Benitez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Curtis W. Boswell
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine; New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine; New Haven, CT 06510, USA
- Department of Biomedical Engineering, Yale University; New Haven, CT 06510, USA
- Department of Physics, Yale University; New Haven, CT 06510, USA
- Nanobiology Institute, Yale University; West Haven, CT 06477, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Cancer Center, Yale University School of Medicine; New Haven, CT 06510, USA
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11
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Hadzhiev Y, Wheatley L, Cooper L, Ansaloni F, Whalley C, Chen Z, Finaurini S, Gustincich S, Sanges R, Burgess S, Beggs A, Müller F. The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation. Dev Cell 2023; 58:155-170.e8. [PMID: 36693321 PMCID: PMC9904021 DOI: 10.1016/j.devcel.2022.12.007] [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: 08/11/2021] [Revised: 08/10/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023]
Abstract
In anamniote embryos, the major wave of zygotic genome activation starts during the mid-blastula transition. However, some genes escape global genome repression, are activated substantially earlier, and contribute to the minor wave of genome activation. The mechanisms underlying the minor wave of genome activation are little understood. We explored the genomic organization and cis-regulatory mechanisms of a transcription body, in which the minor wave of genome activation is first detected in zebrafish. We identified the miR-430 cluster as having excessive copy number and the highest density of Pol-II-transcribed promoters in the genome, and this is required for forming the transcription body. However, this transcription body is not essential for, nor does it encompasse, minor wave transcription globally. Instead, distinct minor-wave-specific promoter architecture suggests that promoter-autonomous mechanisms regulate the minor wave of genome activation. The minor-wave-specific features also suggest distinct transcription initiation mechanisms between the minor and major waves of genome activation.
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Affiliation(s)
- Yavor Hadzhiev
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Lucy Wheatley
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ledean Cooper
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Federico Ansaloni
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy; Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Celina Whalley
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Zhelin Chen
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Sara Finaurini
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Remo Sanges
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy; Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genoa, Italy
| | - Shawn Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Andrew Beggs
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ferenc Müller
- Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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12
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Kuznetsova K, Chabot NM, Ugolini M, Wu E, Lalit M, Oda H, Sato Y, Kimura H, Jug F, Vastenhouw NL. Nanog organizes transcription bodies. Curr Biol 2023; 33:164-173.e5. [PMID: 36476751 DOI: 10.1016/j.cub.2022.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/21/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
The localization of transcriptional activity in specialized transcription bodies is a hallmark of gene expression in eukaryotic cells.1-3 How proteins of the transcriptional machinery come together to form such bodies, however, is unclear. Here, we take advantage of two large, isolated, and long-lived transcription bodies that reproducibly form during early zebrafish embryogenesis to characterize the dynamics of transcription body formation. Once formed, these transcription bodies are enriched for initiating and elongating RNA polymerase II, as well as the transcription factors Nanog and Sox19b. Analyzing the events leading up to transcription, we find that Nanog and Sox19b cluster prior to transcription. The clustering of transcription factors is sequential; Nanog clusters first, and this is required for the clustering of Sox19b and the initiation of transcription. Mutant analysis revealed that both the DNA-binding domain as well as one of the two intrinsically disordered regions of Nanog are required to organize the two bodies of transcriptional activity. Taken together, our data suggest that the clustering of transcription factors dictates the formation of transcription bodies.
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Affiliation(s)
- Ksenia Kuznetsova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Noémie M Chabot
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Martino Ugolini
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Edlyn Wu
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Manan Lalit
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Haruka Oda
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Florian Jug
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Fondazione Human Technopole, Viale Rita Levi-Montalcini 1, Area MIND, 20157 Milano, Italy
| | - Nadine L Vastenhouw
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Integrative Genomics, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland.
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13
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Abstract
The control of gene expression in eukaryotes relies on how transcription factors and RNA polymerases manipulate the structure of chromatin. These interactions are especially important in development as gene expression programs change. Chromatin generally limits the accessibility of DNA, and thus exposing sequences at regulatory elements is critical for gene expression. However, it is challenging to understand how transcription factors manipulate chromatin structure and the sequence of regulatory events. The Drosophila embryo has provided a powerful setting to directly observe the establishment and elaboration of chromatin features and experimentally test the causality of transcriptional events that are shared among many metazoans. The large embryo is tractable by live imaging, and a variety of well-developed tools allow the manipulation of factors during early development. The early embryo develops as a syncytium with rapid nuclear divisions and no zygotic transcription, with largely featureless chromatin. Thus, studies in this system have revealed the progression of genome activation triggered by pioneer factors that initiate DNA exposure at regulatory elements and the establishment of chromatin domains, including heterochromatin, the nucleolus, and nuclear bodies. The de novo emergence of nuclear structures in the early embryo reveals features of chromatin dynamics that are likely to be central to transcriptional regulation in all cells.
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Affiliation(s)
- Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road Chevy Chase, MD 20815-6789, USA
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Unveiling dynamic enhancer–promoter interactions in Drosophila melanogaster. Biochem Soc Trans 2022; 50:1633-1642. [DOI: 10.1042/bst20220325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022]
Abstract
Proper enhancer–promoter interactions are essential to maintaining specific transcriptional patterns and preventing ectopic gene expression. Drosophila is an ideal model organism to study transcriptional regulation due to extensively characterized regulatory regions and the ease of implementing new genetic and molecular techniques for quantitative analysis. The mechanisms of enhancer–promoter interactions have been investigated over a range of length scales. At a DNA level, compositions of both enhancer and promoter sequences affect transcriptional dynamics, including duration, amplitude, and frequency of transcriptional bursting. 3D chromatin topology is also important for proper enhancer–promoter contacts. By working competitively or cooperatively with one another, multiple, simultaneous enhancer–enhancer, enhancer–promoter, and promoter–promoter interactions often occur to maintain appropriate levels of mRNAs. For some long-range enhancer–promoter interactions, extra regulatory elements like insulators and tethering elements are required to promote proper interactions while blocking aberrant ones. This review provides an overview of our current understanding of the mechanism of enhancer–promoter interactions and how perturbations of such interactions affect transcription and subsequent physiological outcomes.
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Bauer M. How does an organism extract relevant information from transcription factor concentrations? Biochem Soc Trans 2022; 50:1365-1376. [PMID: 36111776 PMCID: PMC9704516 DOI: 10.1042/bst20220333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 09/10/2024]
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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Affiliation(s)
- Marianne Bauer
- Bionanoscience Department, Delft University of Technology, van der Maasweg 9, 2629 Delft, The Netherlands
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, U.S.A
- Lewis–Sigler Institute for Integrative Genomics Princeton University, Princeton, NJ 08544, U.S.A
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Cho CY, Kemp JP, Duronio RJ, O'Farrell PH. Coordinating transcription and replication to mitigate their conflicts in early Drosophila embryos. Cell Rep 2022; 41:111507. [PMID: 36261005 PMCID: PMC9667882 DOI: 10.1016/j.celrep.2022.111507] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/30/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Collisions between transcribing RNA polymerases and DNA replication forks are disruptive. The threat of collisions is particularly acute during the rapid early embryonic cell cycles of Drosophila when S phase occupies the entirety of interphase. We hypothesize that collision-avoidance mechanisms safeguard this early transcription. Real-time imaging of endogenously tagged RNA polymerase II (RNAPII) and a reporter for nascent transcripts in unperturbed embryos shows clustering of RNAPII at around 2 min after mitotic exit, followed by progressive dispersal as associated nascent transcripts accumulate later in interphase. Abrupt inhibition of various steps in DNA replication, including origin licensing, origin firing, and polymerization, suppresses post-mitotic RNAPII clustering and transcription in nuclear cycles. We propose that replication dependency defers the onset of transcription so that RNAPII transcribes behind advancing replication forks. The resulting orderly progression can explain how early embryos circumvent transcription-replication conflicts to express essential developmental genes.
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Affiliation(s)
- Chun-Yi Cho
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James P Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biology, Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patrick H O'Farrell
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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