1
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Fajri N, Petryk N. Monitoring and quantifying replication fork dynamics with high-throughput methods. Commun Biol 2024; 7:729. [PMID: 38877080 PMCID: PMC11178896 DOI: 10.1038/s42003-024-06412-1] [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: 12/07/2023] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
Before each cell division, eukaryotic cells must replicate their chromosomes to ensure the accurate transmission of genetic information. Chromosome replication involves more than just DNA duplication; it also includes chromatin assembly, inheritance of epigenetic marks, and faithful resumption of all genomic functions after replication. Recent progress in quantitative technologies has revolutionized our understanding of the complexity and dynamics of DNA replication forks at both molecular and genomic scales. Here, we highlight the pivotal role of these novel methods in uncovering the principles and mechanisms of chromosome replication. These technologies have illuminated the regulation of genome replication programs, quantified the impact of DNA replication on genomic mutations and evolutionary processes, and elucidated the mechanisms of replication-coupled chromatin assembly and epigenome maintenance.
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Affiliation(s)
- Nora Fajri
- UMR9019 - CNRS, Intégrité du Génome et Cancers, Université Paris-Saclay, Gustave Roussy, Villejuif, France, 114 rue Edouard Vaillant, 94805, Villejuif, France
| | - Nataliya Petryk
- UMR9019 - CNRS, Intégrité du Génome et Cancers, Université Paris-Saclay, Gustave Roussy, Villejuif, France, 114 rue Edouard Vaillant, 94805, Villejuif, France.
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2
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Flury V, Groth A. Safeguarding the epigenome through the cell cycle: a multitasking game. Curr Opin Genet Dev 2024; 85:102161. [PMID: 38447236 DOI: 10.1016/j.gde.2024.102161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Sustaining cell identity and function across cell division is germane to human development, healthspan, and cancer avoidance. This relies significantly on propagation of chromatin organization between cell generations, as chromatin presents a barrier to cell fate and cell state conversions. Inheritance of chromatin states across the many cell divisions required for development and tissue homeostasis represents a major challenge, especially because chromatin is disrupted to allow passage of the DNA replication fork to synthesize the two daughter strands. This process also leads to a twofold dilution of epigenetic information in histones, which needs to be accurately restored for faithful propagation of chromatin states across cell divisions. Recent research has identified distinct multilayered mechanisms acting to propagate epigenetic information to daughter strands. Here, we summarize key principles of how epigenetic information in parental histones is transferred across DNA replication and how new histones robustly acquire the same information postreplication, representing a core component of epigenetic cell memory.
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Affiliation(s)
- Valentin Flury
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark. https://twitter.com/@ValeFlury
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark.
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3
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Dreyer J, Ricci G, van den Berg J, Bhardwaj V, Funk J, Armstrong C, van Batenburg V, Sine C, VanInsberghe MA, Marsman R, Mandemaker IK, di Sanzo S, Costantini J, Manzo SG, Biran A, Burny C, Völker-Albert M, Groth A, Spencer SL, van Oudenaarden A, Mattiroli F. Acute multi-level response to defective de novo chromatin assembly in S-phase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586291. [PMID: 38585916 PMCID: PMC10996472 DOI: 10.1101/2024.03.22.586291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Long-term perturbation of de novo chromatin assembly during DNA replication has profound effects on epigenome maintenance and cell fate. The early mechanistic origin of these defects is unknown. Here, we combine acute degradation of Chromatin Assembly Factor 1 (CAF-1), a key player in de novo chromatin assembly, with single-cell genomics, quantitative proteomics, and live-microscopy to uncover these initiating mechanisms in human cells. CAF-1 loss immediately slows down DNA replication speed and renders nascent DNA hyperaccessible. A rapid cellular response, distinct from canonical DNA damage signaling, is triggered and lowers histone mRNAs. As a result, histone variants usage and their modifications are altered, limiting transcriptional fidelity and delaying chromatin maturation within a single S-phase. This multi-level response induces a cell-cycle arrest after mitosis. Our work reveals the immediate consequences of defective de novo chromatin assembly during DNA replication, explaining how at later times the epigenome and cell fate can be altered.
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Affiliation(s)
- Jan Dreyer
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Giulia Ricci
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jeroen van den Berg
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Vivek Bhardwaj
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Janina Funk
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Claire Armstrong
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Vincent van Batenburg
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Chance Sine
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Michael A. VanInsberghe
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Richard Marsman
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Imke K. Mandemaker
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Simone di Sanzo
- MOLEQLAR Analytics GmbH, Rosenheimer Street 141 h, 81671 Munich, Germany
| | - Juliette Costantini
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Stefano G. Manzo
- Oncode Institute, The Netherlands
- Division of Gene Regulation, Netherlands Cancer Institute, The Netherlands
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Alva Biran
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Claire Burny
- MOLEQLAR Analytics GmbH, Rosenheimer Street 141 h, 81671 Munich, Germany
| | | | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sabrina L. Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alexander van Oudenaarden
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Oncode Institute, The Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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4
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Espinosa-Martínez M, Alcázar-Fabra M, Landeira D. The molecular basis of cell memory in mammals: The epigenetic cycle. SCIENCE ADVANCES 2024; 10:eadl3188. [PMID: 38416817 PMCID: PMC10901381 DOI: 10.1126/sciadv.adl3188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Cell memory refers to the capacity of cells to maintain their gene expression program once the initiating environmental signal has ceased. This exceptional feature is key during the formation of mammalian organisms, and it is believed to be in part mediated by epigenetic factors that can endorse cells with the landmarks required to maintain transcriptional programs upon cell duplication. Here, we review current literature analyzing the molecular basis of epigenetic memory in mammals, with a focus on the mechanisms by which transcriptionally repressive chromatin modifications such as methylation of DNA and histone H3 are propagated through mitotic cell divisions. The emerging picture suggests that cellular memory is supported by an epigenetic cycle in which reversible activities carried out by epigenetic regulators in coordination with cell cycle transition create a multiphasic system that can accommodate both maintenance of cell identity and cell differentiation in proliferating stem cell populations.
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Affiliation(s)
- Mencía Espinosa-Martínez
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - María Alcázar-Fabra
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - David Landeira
- Centre for Genomics and Oncological Research (GENYO), Avenue de la Ilustración 114, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
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5
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Bandau S, Alvarez V, Jiang H, Graff S, Sundaramoorthy R, Gierlinski M, Toman M, Owen-Hughes T, Sidoli S, Lamond A, Alabert C. RNA polymerase II promotes the organization of chromatin following DNA replication. EMBO Rep 2024; 25:1387-1414. [PMID: 38347224 PMCID: PMC10933433 DOI: 10.1038/s44319-024-00085-x] [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: 07/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.
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Affiliation(s)
- Susanne Bandau
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Vanesa Alvarez
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Sarah Graff
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | | | - Marek Gierlinski
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, UK
| | - Matt Toman
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Structure and Function, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Simone Sidoli
- Department of Biochemistry at the Albert Einstein College of Medicine, New York, NY, USA
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK
| | - Constance Alabert
- MCDB, School of Life Sciences, University of Dundee, DD15EH, Dundee, UK.
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6
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Fenstermaker TK, Petruk S, Mazo A. An emerging paradigm in epigenetic marking: coordination of transcription and replication. Transcription 2024; 15:22-37. [PMID: 38378467 DOI: 10.1080/21541264.2024.2316965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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7
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Werner M, Hamperl S. A quick restart: RNA polymerase jumping onto post-replicative chromatin. Mol Cell 2024; 84:186-188. [PMID: 38242096 DOI: 10.1016/j.molcel.2023.12.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024]
Abstract
Two recent studies in Molecular Cell1 and Nature2 show that evicted RNA polymerases reassociate rapidly with post-replicative chromatin and proceed into an unusual transcription cycle, bypassing regular controls and creating a temporary window for altered gene expression.
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Affiliation(s)
- Marcel Werner
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Feodor-Lynen-Strasse 21, 81377 München, Germany
| | - Stephan Hamperl
- Institute of Epigenetics and Stem Cells, Helmholtz Munich, Feodor-Lynen-Strasse 21, 81377 München, Germany.
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8
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Bruno F, Coronel-Guisado C, González-Aguilera C. Collisions of RNA polymerases behind the replication fork promote alternative RNA splicing in newly replicated chromatin. Mol Cell 2024; 84:221-233.e6. [PMID: 38151016 DOI: 10.1016/j.molcel.2023.11.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/23/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023]
Abstract
DNA replication produces a global disorganization of chromatin structure that takes hours to be restored. However, how these chromatin rearrangements affect the regulation of gene expression and the maintenance of cell identity is not clear. Here, we use ChOR-seq and ChrRNA-seq experiments to analyze RNA polymerase II (RNAPII) activity and nascent RNA synthesis during the first hours after chromatin replication in human cells. We observe that transcription elongation is rapidly reactivated in nascent chromatin but that RNAPII abundance and distribution are altered, producing heterogeneous changes in RNA synthesis. Moreover, this first wave of transcription results in RNAPII blockages behind the replication fork, leading to changes in alternative splicing. Altogether, our results deepen our understanding of how transcriptional programs are regulated during cell division and uncover molecular mechanisms that explain why chromatin replication is an important source of gene expression variability.
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Affiliation(s)
- Federica Bruno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, CSIC, Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Cristóbal Coronel-Guisado
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, CSIC, Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Cristina González-Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, CSIC, Universidad Pablo de Olavide, 41092, Seville, Spain; Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013, Seville, Spain.
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9
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Ahmad K, Brahma S, Henikoff S. Epigenetic pioneering by SWI/SNF family remodelers. Mol Cell 2024; 84:194-201. [PMID: 38016477 PMCID: PMC10842064 DOI: 10.1016/j.molcel.2023.10.045] [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: 07/06/2023] [Revised: 09/20/2023] [Accepted: 10/31/2023] [Indexed: 11/30/2023]
Abstract
In eukaryotic genomes, transcriptional machinery and nucleosomes compete for binding to DNA sequences; thus, a crucial aspect of gene regulatory element function is to modulate chromatin accessibility for transcription factor (TF) and RNA polymerase binding. Recent structural studies have revealed multiple modes of TF engagement with nucleosomes, but how initial "pioneering" results in steady-state DNA accessibility for further TF binding and RNA polymerase II (RNAPII) engagement has been unclear. Even less well understood is how distant sites of open chromatin interact with one another, such as when developmental enhancers activate promoters to release RNAPII for productive elongation. Here, we review evidence for the centrality of the conserved SWI/SNF family of nucleosome remodeling complexes, both in pioneering and in mediating enhancer-promoter contacts. Consideration of the nucleosome unwrapping and ATP hydrolysis activities of SWI/SNF complexes, together with their architectural features, may reconcile steady-state TF occupancy with rapid TF dynamics observed by live imaging.
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Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sandipan Brahma
- University of Nebraska Medical Center, Department of Genetics, Cell Biology & Anatomy, Omaha, NE, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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10
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Brahma S, Henikoff S. The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes. Nat Genet 2024; 56:100-111. [PMID: 38049663 PMCID: PMC10786724 DOI: 10.1038/s41588-023-01603-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023]
Abstract
Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent nucleosome remodeling, which is carried out by complexes such as Brahma-associated factor (BAF). However, the mechanistic links between transcription, nucleosome remodeling and chromatin accessibility are unclear. Here, we used a chemical-genetic approach coupled with time-resolved chromatin profiling to dissect the interplay between RNA Polymerase II (RNAPII), BAF and DNA-sequence-specific transcription factors in mouse embryonic stem cells. We show that BAF dynamically unwraps and evicts nucleosomes at accessible chromatin regions, while RNAPII promoter-proximal pausing stabilizes BAF chromatin occupancy and enhances ATP-dependent nucleosome eviction by BAF. We find that although RNAPII and BAF dynamically probe both transcriptionally active and Polycomb-repressed genomic regions, pluripotency transcription factor chromatin binding confers locus specificity for productive chromatin remodeling and nucleosome eviction by BAF. Our study suggests a paradigm for how functional synergy between dynamically acting chromatin factors regulates locus-specific nucleosome organization and chromatin accessibility.
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Affiliation(s)
- Sandipan Brahma
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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11
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Huang Y, Huo Y, Huang L, Zhang L, Zheng Y, Zhang N, Yang M. Super-enhancers: Implications in gastric cancer. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108489. [PMID: 38355091 DOI: 10.1016/j.mrrev.2024.108489] [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: 09/21/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Gastric cancer (GC) is the fifth most prevalent malignancy and the third leading cause of cancer-related mortality globally. Despite intensive efforts to enhance the efficiencies of various therapeutics (chemotherapy, surgical interventions, molecular-targeted therapies, immunotherapies), the prognosis for patients with GC remains poor. This might be predominantly due to the limited understanding of the complicated etiology of GC. Importantly, epigenetic modifications and alterations are crucial during GC development. Super-enhancers (SEs) are a large cluster of adjacent enhancers that greatly activate transcription. SEs sustain cell-specific identity by enhancing the transcription of specific oncogenes. In this review, we systematically summarize how SEs are involved in GC development, including the SE landscape in GC, the SE target genes in GC, and the interventions related to SE functions for treating GC.
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Affiliation(s)
- Yizhou Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Yanfei Huo
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Linying Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Long Zhang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Yanxiu Zheng
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong Province, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China.
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, Shandong Province, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China.
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12
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Chen B, MacAlpine HK, Hartemink AJ, MacAlpine DM. Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase. Genome Res 2023; 33:2108-2118. [PMID: 38081658 PMCID: PMC10760526 DOI: 10.1101/gr.278273.123] [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: 07/14/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023]
Abstract
Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2 tetramers as part of the replication-dependent chromatin assembly process. Loss of CAF-1 leads to a delay in chromatin maturation, albeit with minimal impact on steady-state chromatin structure. However, the mechanisms by which CAF-1 mediates the deposition of (H3-H4)2 tetramers and the phenotypic consequences of CAF-1-associated assembly defects are not well understood. We used nascent chromatin occupancy profiling to track the spatiotemporal kinetics of chromatin maturation in both wild-type (WT) and CAF-1 mutant yeast cells. Our results show that loss of CAF-1 leads to a heterogeneous rate of nucleosome assembly, with some nucleosomes maturing at near WT kinetics and others showing significantly slower maturation kinetics. The slow-to-mature nucleosomes are enriched in intergenic and poorly transcribed regions, suggesting that transcription-dependent assembly mechanisms can reset the slow-to-mature nucleosomes following replication. Nucleosomes with slow maturation kinetics are also associated with poly(dA:dT) sequences, which implies that CAF-1 deposits histones in a manner that counteracts resistance from the inflexible DNA sequence, promoting the formation of histone octamers as well as ordered nucleosome arrays. In addition, we show that the delay in chromatin maturation is accompanied by a transient and S-phase-specific loss of gene silencing and transcriptional regulation, revealing that the DNA replication program can directly shape the chromatin landscape and modulate gene expression through the process of chromatin maturation.
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Affiliation(s)
- Boning Chen
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA;
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13
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Wen Q, Zhou J, Tian C, Li X, Song G, Gao Y, Sun Y, Ma C, Yao S, Liang X, Kang X, Wang N, Yao Y, Wang H, Liang X, Tang J, Offer SM, Lei X, Yu C, Liu X, Liu Z, Wang Z, Gan H. Symmetric inheritance of parental histones contributes to safeguarding the fate of mouse embryonic stem cells during differentiation. Nat Genet 2023; 55:1555-1566. [PMID: 37666989 PMCID: PMC10777717 DOI: 10.1038/s41588-023-01477-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/17/2023] [Indexed: 09/06/2023]
Abstract
Parental histones, the carriers of posttranslational modifications, are deposited evenly onto the replicating DNA of sister chromatids in a process dependent on the Mcm2 subunit of DNA helicase and the Pole3 subunit of leading-strand DNA polymerase. The biological significance of parental histone propagation remains unclear. Here we show that Mcm2-mutated or Pole3-deleted mouse embryonic stem cells (ESCs) display aberrant histone landscapes and impaired neural differentiation. Mutation of the Mcm2 histone-binding domain causes defects in pre-implantation development and embryonic lethality. ESCs with biased parental histone transfer exhibit increased epigenetic heterogeneity, showing altered histone variant H3.3 and H3K27me3 patterning at genomic sites regulating differentiation genes. Our results indicate that the lagging strand pattern of H3.3 leads to the redistribution of H3K27me3 in Mcm2-2A ESCs. We demonstrate that symmetric parental histone deposition to sister chromatids contributes to cellular differentiation and development.
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Affiliation(s)
- Qing Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiaqi Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Congcong Tian
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xinran Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Guibing Song
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuan Gao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yaping Sun
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chiyuan Ma
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Sitong Yao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaoyan Liang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xing Kang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Nan Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuan Yao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohuan Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jialin Tang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
| | - Steven M Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Xiaohua Lei
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chuanhe Yu
- Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Xiangyu Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, China
- Department of Hematology, The Second People's Hospital of Shenzhen, Shenzhen, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin, China
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Haiyun Gan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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14
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Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM. Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1. Science 2023; 381:eadd8673. [PMID: 37616371 PMCID: PMC11186048 DOI: 10.1126/science.add8673] [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: 07/09/2022] [Accepted: 07/19/2023] [Indexed: 08/26/2023]
Abstract
Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly process is lacking. In this work, we report the crystal structure of human CAF-1 in the absence of histones and the cryo-electron microscopy structure of CAF-1 in complex with histones H3 and H4. One histone H3-H4 heterodimer is bound by one CAF-1 complex mainly through the p60 subunit and the acidic domain of the p150 subunit. We also observed a dimeric CAF-1-H3-H4 supercomplex in which two H3-H4 heterodimers are poised for tetramer assembly and discovered that CAF-1 facilitates right-handed DNA wrapping of H3-H4 tetramers. These findings signify the involvement of DNA in H3-H4 tetramer formation and suggest a right-handed nucleosome precursor in chromatin replication.
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Affiliation(s)
- Chao-Pei Liu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenyu Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Hu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Aoqun Song
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongbo Ding
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cong Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences; Hangzhou, Zhejiang 310024, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin 300353, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Juan Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peini Hou
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kangning Zeng
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenyu Li
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Bing Zhu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences; Hangzhou, Zhejiang 310024, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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15
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Barrientos-Moreno M, Maya-Miles D, Murillo-Pineda M, Fontalva S, Pérez-Alegre M, Andujar E, Prado F. Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects. Sci Rep 2023; 13:11397. [PMID: 37452085 PMCID: PMC10349138 DOI: 10.1038/s41598-023-38280-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Genome duplication occurs through the coordinated action of DNA replication and nucleosome assembly at replication forks. Defective nucleosome assembly causes DNA lesions by fork breakage that need to be repaired. In addition, it causes a loss of chromatin integrity. These chromatin alterations can be restored, even though the mechanisms are unknown. Here, we show that the process of chromatin restoration can deal with highly severe chromatin defects induced by the absence of the chaperones CAF1 and Rtt106 or a strong reduction in the pool of available histones, and that this process can be followed by analyzing the topoisomer distribution of the 2µ plasmid. Using this assay, we demonstrate that chromatin restoration is slow and independent of checkpoint activation, whereas it requires the action of transcription and the FACT complex. Therefore, cells are able to "repair" not only DNA lesions but also chromatin alterations associated with defective nucleosome assembly.
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Affiliation(s)
- Marta Barrientos-Moreno
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Douglas Maya-Miles
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Marina Murillo-Pineda
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Sara Fontalva
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Mónica Pérez-Alegre
- Genomic Unit, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Eloísa Andujar
- Genomic Unit, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain
| | - Félix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC‑University of Seville‑University Pablo de Olavide, Seville, Spain.
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16
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Liu C, Yu J, Song A, Wang M, Hu J, Chen P, Zhao J, Li G. Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction. Nat Commun 2023; 14:4081. [PMID: 37429872 DOI: 10.1038/s41467-023-39846-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/30/2023] [Indexed: 07/12/2023] Open
Abstract
During cell renewal, epigenetic information needs to be precisely restored to maintain cell identity and genome integrity following DNA replication. The histone mark H3K27me3 is essential for the formation of facultative heterochromatin and the repression of developmental genes in embryonic stem cells. However, how the restoration of H3K27me3 is precisely achieved following DNA replication is still poorly understood. Here we employ ChOR-seq (Chromatin Occupancy after Replication) to monitor the dynamic re-establishment of H3K27me3 on nascent DNA during DNA replication. We find that the restoration rate of H3K27me3 is highly correlated with dense chromatin states. In addition, we reveal that the linker histone H1 facilitates the rapid post-replication restoration of H3K27me3 on repressed genes and the restoration rate of H3K27me3 on nascent DNA is greatly compromised after partial depletion of H1. Finally, our in vitro biochemical experiments demonstrate that H1 facilitates the propagation of H3K27me3 by PRC2 through compacting chromatin. Collectively, our results indicate that H1-mediated chromatin compaction facilitates the propagation and restoration of H3K27me3 after DNA replication.
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Affiliation(s)
- Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Aoqun Song
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Min Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jiansen Hu
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Science, 100101, Beijing, China
| | - Ping Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory for Tumor Invasion and Metastasis, Capital Medical University, 100069, Beijing, China
| | - Jicheng Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, 430072, Wuhan, China.
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17
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Gaggioli V, Lo CSY, Reverón-Gómez N, Jasencakova Z, Domenech H, Nguyen H, Sidoli S, Tvardovskiy A, Uruci S, Slotman JA, Chai Y, Gonçalves JGSCS, Manolika EM, Jensen ON, Wheeler D, Sridharan S, Chakrabarty S, Demmers J, Kanaar R, Groth A, Taneja N. Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability. Nat Cell Biol 2023; 25:1017-1032. [PMID: 37414849 PMCID: PMC10344782 DOI: 10.1038/s41556-023-01167-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/16/2023] [Indexed: 07/08/2023]
Abstract
Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces chromatin compaction by accumulating the repressive modifications, H3K9me1/me2/me3, in the vicinity of stressed replication forks. This closed conformation is also favoured by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering single-stranded DNA gap formation and sensitizing cells towards chemotherapeutic drugs. These findings may help in explaining chemotherapy resistance and poor prognosis observed in patients with cancer displaying elevated levels of G9a/H3K9me3.
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Affiliation(s)
- Vincent Gaggioli
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zuzana Jasencakova
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heura Domenech
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hong Nguyen
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Simone Sidoli
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrey Tvardovskiy
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum Munchen, Neuherberg, Germany
| | - Sidrit Uruci
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Johan A Slotman
- Department of Pathology, Erasmus Optical Imaging Centre, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Yi Chai
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | | | - Eleni Maria Manolika
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sriram Sridharan
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Jeroen Demmers
- Proteomics Center and Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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18
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Tian C, Zhou J, Li X, Gao Y, Wen Q, Kang X, Wang N, Yao Y, Jiang J, Song G, Zhang T, Hu S, Liao J, Yu C, Wang Z, Liu X, Pei X, Chan K, Liu Z, Gan H. Impaired histone inheritance promotes tumor progression. Nat Commun 2023; 14:3429. [PMID: 37301892 PMCID: PMC10257670 DOI: 10.1038/s41467-023-39185-y] [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: 10/20/2022] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Faithful inheritance of parental histones is essential to maintain epigenetic information and cellular identity during cell division. Parental histones are evenly deposited onto the replicating DNA of sister chromatids in a process dependent on the MCM2 subunit of DNA helicase. However, the impact of aberrant parental histone partition on human disease such as cancer is largely unknown. In this study, we construct a model of impaired histone inheritance by introducing MCM2-2A mutation (defective in parental histone binding) in MCF-7 breast cancer cells. The resulting impaired histone inheritance reprograms the histone modification landscapes of progeny cells, especially the repressive histone mark H3K27me3. Lower H3K27me3 levels derepress the expression of genes associated with development, cell proliferation, and epithelial to mesenchymal transition. These epigenetic changes confer fitness advantages to some newly emerged subclones and consequently promote tumor growth and metastasis after orthotopic implantation. In summary, our results indicate that impaired inheritance of parental histones can drive tumor progression.
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Affiliation(s)
- Congcong Tian
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Jiaqi Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Xinran Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Yuan Gao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Qing Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Xing Kang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Nan Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Yuan Yao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Jiuhang Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, 510642, Guangzhou, Guangdong, China
| | - Guibing Song
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- College of Animal Science and Technology, Northwest A&F University, 712100, Shaanxi, Angling, China
| | - Tianjun Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Suili Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, 510642, Guangzhou, Guangdong, China
| | - JingYi Liao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Chuanhe Yu
- Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiangyu Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, 518060, Shenzhen, China
| | - Xinhai Pei
- Department of Anatomy and Histology, Shenzhen University Health Science Center, 518060, Shenzhen, China
| | - Kuiming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong Special Administration Region, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, 518172, Shenzhen, China
| | - Zichuan Liu
- School of Pharmaceutical Science and Technology, Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, 300072, Tianjin, China
| | - Haiyun Gan
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
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19
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Chen B, MacAlpine HK, Hartemink AJ, MacAlpine DM. Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.541209. [PMID: 37292814 PMCID: PMC10245875 DOI: 10.1101/2023.05.25.541209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2 tetramers as part of the replication-dependent chromatin assembly process. Loss of CAF-1 leads to a delay in chromatin maturation, albeit with minimal impact on steady-state chromatin structure. However, the mechanisms by which CAF-1 mediates the deposition of (H3-H4)2 tetramers and the phenotypic consequences of CAF-1-associated assembly defects are not well understood. We used nascent chromatin occupancy profiling to track the spatiotemporal kinetics of chromatin maturation in both wild-type (WT) and CAF-1 mutant yeast cells. Our results show that loss of CAF-1 leads to a heterogeneous rate of nucleosome assembly, with some nucleosomes maturing at near WT kinetics and others exhibiting significantly slower maturation kinetics. The slow-to-mature nucleosomes are enriched in intergenic and poorly transcribed regions, suggesting that transcription-dependent assembly mechanisms can reset the slow-to-mature nucleosomes following replication. Nucleosomes with slow maturation kinetics are also associated with poly(dA:dT) sequences, which implies that CAF-1 deposits histones in a manner that counteracts resistance from the inflexible DNA sequence, promoting the formation of histone octamers as well as ordered nucleosome arrays. In addition, we demonstrate that the delay in chromatin maturation is accompanied by a transient and S-phase specific loss of gene silencing and transcriptional regulation, revealing that the DNA replication program can directly shape the chromatin landscape and modulate gene expression through the process of chromatin maturation.
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Affiliation(s)
- Boning Chen
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Heather K. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | | | - David M. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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20
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Flury V, Reverón-Gómez N, Alcaraz N, Stewart-Morgan KR, Wenger A, Klose RJ, Groth A. Recycling of modified H2A-H2B provides short-term memory of chromatin states. Cell 2023; 186:1050-1065.e19. [PMID: 36750094 PMCID: PMC9994263 DOI: 10.1016/j.cell.2023.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/11/2022] [Accepted: 01/06/2023] [Indexed: 02/08/2023]
Abstract
Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The histone H3-H4 modification landscape is restored by parental histone recycling and modification of new histones. How DNA replication impacts on histone H2A-H2B is currently unknown. Here, we measure H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. We show that H2AK119ub1, H2BK120ub1, and H2A.Z are recycled accurately during DNA replication. Modified H2A-H2B are segregated symmetrically to daughter strands via POLA1 on the lagging strand, but independent of H3-H4 recycling. Post-replication, H2A-H2B modification and variant landscapes are quickly restored, and H2AK119ub1 guides accurate restoration of H3K27me3. This work reveals epigenetic transmission of parental H2A-H2B during DNA replication and identifies cross talk between H3-H4 and H2A-H2B modifications in epigenome propagation. We propose that rapid short-term memory of recycled H2A-H2B modifications facilitates restoration of stable H3-H4 chromatin states.
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Affiliation(s)
- Valentin Flury
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nicolas Alcaraz
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kathleen R Stewart-Morgan
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alice Wenger
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark.
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21
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Stewart-Morgan KR, Groth A. Profiling Chromatin Accessibility on Replicated DNA with repli-ATAC-Seq. Methods Mol Biol 2023; 2611:71-84. [PMID: 36807065 DOI: 10.1007/978-1-0716-2899-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Open or accessible chromatin typifies euchromatic regions and helps define cell type-specific transcription programs. DNA replication massively disorders chromatin composition and structure, and how accessible regions are affected by and recover from this disruption has been unclear. Here, we present repli-ATAC-seq, a protocol to profile accessible chromatin genome-wide on replicated DNA starting from 100,000 cells. In this method, replicated DNA is labeled with a short 5-ethynyl-2'-deoxyuridine (EdU) pulse in cultured cells and isolated from a population of tagmented fragments for amplification and next-generation sequencing. Repli-ATAC-seq provides high-resolution information on chromatin dynamics after DNA replication and reveals new insights into the interplay between DNA replication, transcription, and the chromatin landscape.
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Affiliation(s)
- Kathleen R Stewart-Morgan
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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22
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Kwan EX, Alvino GM, Lynch KL, Levan PF, Amemiya HM, Wang XS, Johnson SA, Sanchez JC, Miller MA, Croy M, Lee SB, Naushab M, Bedalov A, Cuperus JT, Brewer BJ, Queitsch C, Raghuraman MK. Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast. Cell Rep 2023; 42:112161. [PMID: 36842087 PMCID: PMC10142053 DOI: 10.1016/j.celrep.2023.112161] [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: 05/31/2022] [Revised: 12/19/2022] [Accepted: 02/09/2023] [Indexed: 02/27/2023] Open
Abstract
Timely completion of genome replication is a prerequisite for mitosis, genome integrity, and cell survival. A challenge to this timely completion comes from the need to replicate the hundreds of untranscribed copies of rDNA that organisms maintain in addition to the copies required for ribosome biogenesis. Replication of these rDNA arrays is relegated to late S phase despite their large size, repetitive nature, and essentiality. Here, we show that, in Saccharomyces cerevisiae, reducing the number of rDNA repeats leads to early rDNA replication, which results in delaying replication elsewhere in the genome. Moreover, cells with early-replicating rDNA arrays and delayed genome-wide replication aberrantly release the mitotic phosphatase Cdc14 from the nucleolus and enter anaphase prematurely. We propose that rDNA copy number determines the replication time of the rDNA locus and that the release of Cdc14 upon completion of rDNA replication is a signal for cell cycle progression.
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Affiliation(s)
- Elizabeth X Kwan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Gina M Alvino
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kelsey L Lynch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Paula F Levan
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Haley M Amemiya
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Xiaobin S Wang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sarah A Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joseph C Sanchez
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Madison A Miller
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Mackenzie Croy
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Seung-Been Lee
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Maria Naushab
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Antonio Bedalov
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Bonita J Brewer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - M K Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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23
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Mühlen D, Li X, Dovgusha O, Jäckle H, Günesdogan U. Recycling of parental histones preserves the epigenetic landscape during embryonic development. SCIENCE ADVANCES 2023; 9:eadd6440. [PMID: 36724233 PMCID: PMC9891698 DOI: 10.1126/sciadv.add6440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 12/27/2022] [Indexed: 06/16/2023]
Abstract
Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onward. Lack of new histone synthesis leads to more accessible chromatin and reduced nucleosome occupancy, since only parental histones are available. This leads to up-regulated and spurious transcription, whereas the control of the developmental transcriptional program is partially maintained. The genomic positions of modified parental histone H2A, H2B, and H3 are largely restored during DNA replication. However, parental histones with active marks become more dispersed within gene bodies, which is linked to transcription. Together, the results suggest that parental histones are recycled to preserve the epigenetic landscape during DNA replication in vivo.
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Affiliation(s)
- Dominik Mühlen
- University of Göttingen, Göttingen Center for Molecular Biosciences, Department of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Department for Molecular Developmental Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Xiaojuan Li
- University of Göttingen, Göttingen Center for Molecular Biosciences, Department of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Oleksandr Dovgusha
- University of Göttingen, Göttingen Center for Molecular Biosciences, Department of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Herbert Jäckle
- Max Planck Institute for Multidisciplinary Sciences, Department for Molecular Developmental Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ufuk Günesdogan
- University of Göttingen, Göttingen Center for Molecular Biosciences, Department of Developmental Biology, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Department for Molecular Developmental Biology, Am Fassberg 11, 37077 Göttingen, Germany
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24
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Alvarez V, Bandau S, Jiang H, Rios-Szwed D, Hukelmann J, Garcia-Wilson E, Wiechens N, Griesser E, Ten Have S, Owen-Hughes T, Lamond A, Alabert C. Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication. Cell Rep 2023; 42:111996. [PMID: 36680776 DOI: 10.1016/j.celrep.2023.111996] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/12/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Chromatin organization must be maintained during cell proliferation to preserve cellular identity and genome integrity. However, DNA replication results in transient displacement of DNA-bound proteins, and it is unclear how they regain access to newly replicated DNA. Using quantitative proteomics coupled to Nascent Chromatin Capture or isolation of Proteins on Nascent DNA, we provide time-resolved binding kinetics for thousands of proteins behind replisomes within euchromatin and heterochromatin in human cells. This shows that most proteins regain access within minutes to newly replicated DNA. In contrast, 25% of the identified proteins do not, and this delay cannot be inferred from their known function or nuclear abundance. Instead, chromatin organization and G1 phase entry affect their reassociation. Finally, DNA replication not only disrupts but also promotes recruitment of transcription factors and chromatin remodelers, providing a significant advance in understanding how DNA replication could contribute to programmed changes of cell memory.
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Affiliation(s)
- Vanesa Alvarez
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Susanne Bandau
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Hao Jiang
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Diana Rios-Szwed
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Jens Hukelmann
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Elisa Garcia-Wilson
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nicola Wiechens
- Laboratory of Chromatin Remodelling and Cancer Epigenetics, Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Eva Griesser
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sara Ten Have
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Tom Owen-Hughes
- Laboratory of Chromatin Remodelling and Cancer Epigenetics, Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Angus Lamond
- Laboratory of Quantitative Proteomics, Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Constance Alabert
- Division of Molecular, Cell, and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.
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25
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Brahma S, Henikoff S. RNA Polymerase II, the BAF remodeler and transcription factors synergize to evict nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525083. [PMID: 36711459 PMCID: PMC9882304 DOI: 10.1101/2023.01.22.525083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chromatin accessibility is a hallmark of active transcription and requires ATP-dependent nucleosome remodeling by Brahma-Associated Factor (BAF). However, the mechanistic link between transcription, nucleosome remodeling, and chromatin accessibility is unclear. Here, we used a chemical-genetic approach to dissect the interplay between RNA Polymerase II (RNAPII), BAF, and DNA-sequence-specific transcription factors (TFs) in mouse embryonic stem cells. By time-resolved chromatin profiling with acute transcription block at distinct stages, we show that RNAPII promoter-proximal pausing stabilizes BAF chromatin occupancy and enhances nucleosome eviction by BAF. We find that RNAPII and BAF probe both transcriptionally active and Polycomb-repressed genomic regions and provide evidence that TFs capture transient site exposure due to nucleosome unwrapping by BAF to confer locus specificity for persistent chromatin remodeling. Our study reveals the mechanistic basis of cell-type-specific chromatin accessibility. We propose a new paradigm for how functional synergy between dynamically acting chromatin factors regulates nucleosome organization.
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Affiliation(s)
- Sandipan Brahma
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave North, Seattle, WA, 98109
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave North, Seattle, WA, 98109
- Howard Hughes Medical Institute, USA
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26
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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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27
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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28
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Du W, Shi G, Shan CM, Li Z, Zhu B, Jia S, Li Q, Zhang Z. Mechanisms of chromatin-based epigenetic inheritance. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2162-2190. [PMID: 35792957 DOI: 10.1007/s11427-022-2120-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Multi-cellular organisms such as humans contain hundreds of cell types that share the same genetic information (DNA sequences), and yet have different cellular traits and functions. While how genetic information is passed through generations has been extensively characterized, it remains largely obscure how epigenetic information encoded by chromatin regulates the passage of certain traits, gene expression states and cell identity during mitotic cell divisions, and even through meiosis. In this review, we will summarize the recent advances on molecular mechanisms of epigenetic inheritance, discuss the potential impacts of epigenetic inheritance during normal development and in some disease conditions, and outline future research directions for this challenging, but exciting field.
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Affiliation(s)
- Wenlong Du
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guojun Shi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chun-Min Shan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiming Li
- Institutes of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Zhiguo Zhang
- Institutes of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
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29
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Santos MM, Johnson MC, Fiedler L, Zegerman P. Global early replication disrupts gene expression and chromatin conformation in a single cell cycle. Genome Biol 2022; 23:217. [PMID: 36253803 PMCID: PMC9575230 DOI: 10.1186/s13059-022-02788-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/10/2022] [Indexed: 12/03/2022] Open
Abstract
Background The early embryonic divisions of many organisms, including fish, flies, and frogs, are characterized by a very rapid S-phase caused by high rates of replication initiation. In somatic cells, S-phase is much longer due to both a reduction in the total number of initiation events and the imposition of a temporal order of origin activation. The physiological importance of changes in the rate and timing of replication initiation in S-phase remains unclear. Results Here we assess the importance of the temporal control of replication initiation using a conditional system in budding yeast to drive the early replication of the majority of origins in a single cell cycle. We show that global early replication disrupts the expression of over a quarter of all genes. By deleting individual origins, we show that delaying replication is sufficient to restore normal gene expression, directly implicating origin firing control in this regulation. Global early replication disrupts nucleosome positioning and transcription factor binding during S-phase, suggesting that the rate of S-phase is important to regulate the chromatin landscape. Conclusions Together, these data provide new insight into the role of the temporal control of origin firing during S-phase for coordinating replication, gene expression, and chromatin establishment as occurs in the early embryo. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02788-7.
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Affiliation(s)
- Miguel M Santos
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Mark C Johnson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Lukáš Fiedler
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Philip Zegerman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. .,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
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30
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Rao S, Han AL, Zukowski A, Kopin E, Sartorius CA, Kabos P, Ramachandran S. Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer. SCIENCE ADVANCES 2022; 8:eabm4358. [PMID: 36001652 PMCID: PMC9401618 DOI: 10.1126/sciadv.abm4358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/12/2022] [Indexed: 06/09/2023]
Abstract
Genome-wide binding profiles of estrogen receptor (ER) and FOXA1 reflect cancer state in ER+ breast cancer. However, routine profiling of tumor transcription factor (TF) binding is impractical in the clinic. Here, we show that plasma cell-free DNA (cfDNA) contains high-resolution ER and FOXA1 tumor binding profiles for breast cancer. Enrichment of TF footprints in plasma reflects the binding strength of the TF in originating tissue. We defined pure in vivo tumor TF signatures in plasma using ER+ breast cancer xenografts, which can distinguish xenografts with distinct ER states. Furthermore, state-specific ER-binding signatures can partition human breast tumors into groups with significantly different ER expression and mortality. Last, TF footprints in human plasma samples can identify the presence of ER+ breast cancer. Thus, plasma TF footprints enable minimally invasive mapping of the regulatory landscape of breast cancer in humans and open vast possibilities for clinical applications across multiple tumor types.
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Affiliation(s)
- Satyanarayan Rao
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Amy L. Han
- Department of Medicine/Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Alexis Zukowski
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Etana Kopin
- Department of Medicine/Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Carol A. Sartorius
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Peter Kabos
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Medicine/Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
- University of Colorado Cancer Center, Aurora, CO, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
- University of Colorado Cancer Center, Aurora, CO, USA
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31
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Bughio FJ, Maggert KA. Live analysis of position-effect variegation in Drosophila reveals different modes of action for HP1a and Su(var)3-9. Proc Natl Acad Sci U S A 2022; 119:e2118796119. [PMID: 35704756 PMCID: PMC9231485 DOI: 10.1073/pnas.2118796119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Position-effect variegation (PEV) results from the juxtaposition of euchromatic and heterochromatic components of eukaryotic genomes, silencing genes near the new euchromatin/heterochromatin junctions. Silencing is itself heritable through S phase, giving rise to distinctive random patterns of cell clones expressing the genes intermixed with clones in which the genes are silenced. Much of what we know about epigenetic inheritance in the soma stems from work on PEV aimed at identifying the components of the silencing machinery and its mechanism of inheritance. The roles of two central gene activities-the Su(var)3-9-encoded histone H3-lysine-9 methyltransferase and the Su(var)205-encoded methyl-H3-lysine-9 binding protein heterochromatin protein 1 (HP1a)-have been inferred from terminal phenotypes, leaving considerable gaps in understanding of how PEV behaves through development. Here, we investigate the PEV phenotypes of Su(var)3-9 and Su(var)205 mutations in live developing tissues. We discovered that mutation in Su(var)205 compromises the initial establishment of PEV in early embryogenesis. Later gains of heterochromatin-induced gene silencing are possible but are unstable and lost rapidly. In contrast, a strain with mutation in Su(var)3-9 exhibits robust silencing early in development but fails to maintain it through subsequent cell divisions. Our analyses show that, while the terminal phenotypes of these mutations may appear identical, they have arrived at them through different developmental trajectories. We discuss how our findings expand and clarify existing models for epigenetic inheritance of heterochromatin-induced gene silencing.
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Affiliation(s)
- Farah J. Bughio
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724
| | - Keith A. Maggert
- Department of Cellular and Molecular Medicine, University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724
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32
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Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq. Stem Cell Reports 2022; 17:1730-1742. [PMID: 35750045 PMCID: PMC9287678 DOI: 10.1016/j.stemcr.2022.05.020] [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: 03/23/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) can reprogram terminally differentiated somatic cells into totipotent embryos, but with multiple defects. The nucleosome positioning, as an important epigenetic regulator for gene expression, is largely unexplored during SCNT embryonic development. Here, we mapped genome-wide nucleosome profiles in mouse SCNT embryos using ultra-low-input MNase-seq (ULI-MNase-seq). We found that the nucleosome-depleted regions (NDRs) around promoters underwent dramatic reestablishment, which is consistent with the cell cycle. Dynamics of nucleosome position in SCNT embryos were delayed compared to fertilized embryos. Subsequently, we found that the aberrant gene expression levels in inner cell mass (ICM) were positively correlated with promoter NDRs in donor cells, which indicated that the memory of nucleosome occupancy in donor cells was a potential barrier for SCNT-mediated reprogramming. We further confirmed that the histone acetylation level of donor cells was associated with the memory of promoter NDRs. Our study provides insight into nucleosome reconfiguration during SCNT preimplantation embryonic development.
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33
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López-Jiménez E, González-Aguilera C. Role of Chromatin Replication in Transcriptional Plasticity, Cell Differentiation and Disease. Genes (Basel) 2022; 13:genes13061002. [PMID: 35741764 PMCID: PMC9222293 DOI: 10.3390/genes13061002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Chromatin organization is essential to maintain a correct regulation of gene expression and establish cell identity. However, during cell division, the replication of the genetic material produces a global disorganization of chromatin structure. In this paper, we describe the new scientific breakthroughs that have revealed the nature of the post-replicative chromatin and the mechanisms that facilitate its restoration. Moreover, we highlight the implications of these chromatin alterations in gene expression control and their impact on key biological processes, such as cell differentiation, cell reprogramming or human diseases linked to cell proliferation, such as cancer.
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Affiliation(s)
- Elena López-Jiménez
- Faculty of Medicine, National Heart and Lung Institute, Margaret Turner Warwick Centre for Fibrosing Lung Disease, Royal Brompton Campus, Imperial College London, London SW3 6LY, UK;
| | - Cristina González-Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
- Correspondence:
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34
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Ranjan R, Snedeker J, Wooten M, Chu C, Bracero S, Mouton T, Chen X. Differential condensation of sister chromatids acts with Cdc6 to ensure asynchronous S-phase entry in Drosophila male germline stem cell lineage. Dev Cell 2022; 57:1102-1118.e7. [PMID: 35483360 PMCID: PMC9134767 DOI: 10.1016/j.devcel.2022.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/16/2022] [Accepted: 04/05/2022] [Indexed: 01/06/2023]
Abstract
During Drosophila melanogaster male germline stem cell (GSC) asymmetric division, preexisting old versus newly synthesized histones H3 and H4 are asymmetrically inherited. However, the biological outcomes of this phenomenon have remained unclear. Here, we tracked old and new histones throughout the GSC cell cycle through the use of high spatial and temporal resolution microscopy. We found unique features that differ between old and new histone-enriched sister chromatids, including differences in nucleosome density, chromosomal condensation, and H3 Ser10 phosphorylation. These distinct chromosomal features lead to their differential association with Cdc6, a pre-replication complex component, and subsequent asynchronous DNA replication initiation in the resulting daughter cells. Disruption of asymmetric histone inheritance abolishes differential Cdc6 association and asynchronous S-phase entry, demonstrating that histone asymmetry acts upstream of these critical cell-cycle progression events. Furthermore, disruption of these GSC-specific chromatin features leads to GSC defects, indicating a connection between histone inheritance, cell-cycle progression, and cell fate determination.
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Affiliation(s)
- Rajesh Ranjan
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Carolina Chu
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sabrina Bracero
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Taylar Mouton
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xin Chen
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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35
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Janssens DH, Otto DJ, Meers MP, Setty M, Ahmad K, Henikoff S. CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells. Genome Biol 2022; 23:81. [PMID: 35300717 PMCID: PMC8928696 DOI: 10.1186/s13059-022-02642-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022] Open
Abstract
Cleavage Under Targets and Tagmentation (CUT&Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling in small samples and single cells. We describe a modified CUT&Tag protocol using a mixture of an antibody to the initiation form of RNA polymerase II (Pol2 Serine-5 phosphate) and an antibody to repressive Polycomb domains (H3K27me3) followed by computational signal deconvolution to produce high-resolution maps of both the active and repressive regulomes in single cells. The ability to seamlessly map active promoters, enhancers, and repressive regulatory elements using a single workflow provides a complete regulome profiling strategy suitable for high-throughput single-cell platforms.
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Affiliation(s)
- Derek H. Janssens
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Dominik J. Otto
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA ,grid.270240.30000 0001 2180 1622Translational Data Science IRC, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Michael P. Meers
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Manu Setty
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA ,grid.270240.30000 0001 2180 1622Translational Data Science IRC, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Kami Ahmad
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA
| | - Steven Henikoff
- grid.270240.30000 0001 2180 1622Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA 98109 USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Chevy Chase, MD USA
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36
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Ahmad K, Henikoff S, Ramachandran S. Managing the Steady State Chromatin Landscape by Nucleosome Dynamics. Annu Rev Biochem 2022; 91:183-195. [PMID: 35303789 DOI: 10.1146/annurev-biochem-032620-104508] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene regulation arises out of dynamic competition between nucleosomes, transcription factors, and other chromatin proteins for the opportunity to bind genomic DNA. The timescales of nucleosome assembly and binding of factors to DNA determine the outcomes of this competition at any given locus. Here, we review how these properties of chromatin proteins and the interplay between the dynamics of different factors are critical for gene regulation. We discuss how molecular structures of large chromatin-associated complexes, kinetic measurements, and high resolution mapping of protein-DNA complexes in vivo set the boundary conditions for chromatin dynamics, leading to models of how the steady state behaviors of regulatory elements arise. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; .,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics and RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
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37
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Thiriet C. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2536-2548. [PMID: 35137186 PMCID: PMC8934661 DOI: 10.1093/nar/gkac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
DNA replication occurring in S-phase is critical for the maintenance of the cell fate from one generation to the next, and requires the duplication of epigenetic information. The integrity of the epigenome is, in part, insured by the recycling of parental histones and de novo deposition of newly synthesized histones. While the histone variants have revealed important functions in epigenetic regulations, the deposition in chromatin during S-phase of newly synthesized histone variants remains unclear. The identification of histone variants of H3 and unique features of Physarum polycephalum provides a powerful system for investigating de novo deposition of newly synthesized histones by tracking the incorporation of exogenous histones within cells. The analyses revealed that the rate of deposition of H3.1 and H3.3 is anticorrelated as S-phase progresses, H3.3 is predominately produced and utilized in early S and dropped throughout S-phase, while H3.1 behaved in the opposite way. Disturbing the expression of H3 variants by siRNAs revealed mutual compensation of histone transcripts. Interestingly, the incorporation of pre-formed constrained histone complexes showed that tetramers of H3/H4 are more efficiently utilized by the cell than dimers. These results support the model whereby the histone variant distribution is established upon replication and new histone deposition.
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38
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Petryk N, Reverón-Gómez N, González-Aguilera C, Dalby M, Andersson R, Groth A. Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq. Nat Protoc 2021; 16:4446-4493. [PMID: 34363071 DOI: 10.1038/s41596-021-00585-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/07/2021] [Indexed: 11/09/2022]
Abstract
Elucidating the mechanisms underlying chromatin maintenance upon genome replication is critical for the understanding of how gene expression programs and cell identity are preserved across cell divisions. Here, we describe two recently developed techniques, chromatin occupancy after replication (ChOR)-seq and sister chromatids after replication (SCAR)-seq, that profile chromatin occupancy on newly replicated DNA in mammalian cells in 5 d of bench work. Both techniques share a common strategy that includes pulse labeling of newly synthesized DNA and chromatin immunoprecipitation (ChIP), followed by purification and high-throughput sequencing. Whereas ChOR-seq quantitatively profiles the post-replicative abundance of histone modifications and chromatin-associated proteins, SCAR-seq distinguishes chromatin occupancy between nascent sister chromatids. Together, these two complementary techniques have unraveled key mechanisms controlling the inheritance of modified histones during replication and revealed locus-specific dynamics of histone modifications across the cell cycle. Here, we provide the experimental protocols and bioinformatic pipelines for these methods.
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Affiliation(s)
- Nataliya Petryk
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cristina González-Aguilera
- Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), University of Seville-CSIC-University Pablo de Olavide, Andalusian Government, Seville, Spain.,Department of Cellular Biology, University of Seville, Seville, Spain
| | - Maria Dalby
- The Bioinformatics Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.,H. Lundbeck A/S, Valby, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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39
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Barnes T, Korber P. The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo. Int J Mol Sci 2021; 22:ijms22158233. [PMID: 34360997 PMCID: PMC8347975 DOI: 10.3390/ijms22158233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022] Open
Abstract
Poly(dA:dT) tracts cause nucleosome depletion in many species, e.g., at promoters and replication origins. Their intrinsic biophysical sequence properties make them stiff and unfavorable for nucleosome assembly, as probed by in vitro nucleosome reconstitution. The mere correlation between nucleosome depletion over poly(dA:dT) tracts in in vitro reconstituted and in in vivo chromatin inspired an intrinsic nucleosome exclusion mechanism in vivo that is based only on DNA and histone properties. However, we compile here published and new evidence that this correlation does not reflect mechanistic causation. (1) Nucleosome depletion over poly(dA:dT) in vivo is not universal, e.g., very weak in S. pombe. (2) The energy penalty for incorporating poly(dA:dT) tracts into nucleosomes is modest (<10%) relative to ATP hydrolysis energy abundantly invested by chromatin remodelers. (3) Nucleosome depletion over poly(dA:dT) is much stronger in vivo than in vitro if monitored without MNase and (4) actively maintained in vivo. (5) S. cerevisiae promoters evolved a strand-biased poly(dA) versus poly(dT) distribution. (6) Nucleosome depletion over poly(dA) is directional in vivo. (7) The ATP dependent chromatin remodeler RSC preferentially and directionally displaces nucleosomes towards 5′ of poly(dA). Especially distribution strand bias and displacement directionality would not be expected for an intrinsic mechanism. Together, this argues for an in vivo mechanism where active and species-specific read out of intrinsic sequence properties, e.g., by remodelers, shapes nucleosome organization.
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40
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Mitra S, Zhong J, Tran TQ, MacAlpine DM, Hartemink AJ. RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. Nucleic Acids Res 2021; 49:7925-7938. [PMID: 34255854 PMCID: PMC8373080 DOI: 10.1093/nar/gkab553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/28/2021] [Accepted: 07/08/2021] [Indexed: 01/25/2023] Open
Abstract
Chromatin is a tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and occupancy levels of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. In contrast, epigenomic accessibility data like MNase-seq, DNase-seq, and ATAC-seq provide insight into the chromatin landscape of all factors bound along the genome, but with little insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin accessibility data with nucleotide sequence to jointly compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors. We apply RoboCOP to MNase-seq and ATAC-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome, and show that our model makes better predictions than existing methods. We also compute a chromatin occupancy profile of the yeast genome under cadmium stress, revealing chromatin dynamics associated with transcriptional regulation.
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Affiliation(s)
- Sneha Mitra
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Jianling Zhong
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Trung Q Tran
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - David M MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC 27708, USA.,Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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41
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Li Z, Hua X, Serra-Cardona A, Xu X, Zhang Z. Efficient and strand-specific profiling of replicating chromatin with enrichment and sequencing of protein-associated nascent DNA in mammalian cells. Nat Protoc 2021; 16:2698-2721. [PMID: 33911256 PMCID: PMC9261918 DOI: 10.1038/s41596-021-00520-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/26/2021] [Indexed: 02/02/2023]
Abstract
Faithful duplication of both genetic and epigenetic information is essential for all eukaryotic cells. DNA replication initiates from replication origins and proceeds bidirectionally but asymmetrically, with the leading strand being synthesized continuously and the lagging strand discontinuously as Okazaki fragments by distinct DNA polymerases. Unraveling the underlying mechanisms of chromatin replication at both strands is crucial to better understand DNA replication and its coupled processes, including nucleosome assembly, sister chromatid cohesion and DNA mismatch repair. Here we describe the enrichment and sequencing of protein-associated nascent DNA (eSPAN) method to analyze the enrichment of proteins of interest, including histones and their modifications at replicating chromatin in a strand-specific manner in mammalian cells. Briefly, cells are pulsed with the thymidine analog bromodeoxyuridine to label newly synthesized DNA. After cell permeabilization, the target proteins are sequentially bound by antibodies and protein A-fused transposase, which digests and tags genomic DNA of interest once activated by magnesium. The strand specificity is preserved through oligo-replacement. Finally, the resulting double-strand DNA is denatured and immunoprecipitated with antibodies against bromodeoxyuridine to enrich nascent DNA associated with proteins of interest. After PCR amplification and next-generation sequencing, the mapped reads are used to calculate the relative enrichment of the target proteins around replication origins. Compared with alternative methods, the eSPAN protocol is simple, cost-effective and sensitive, even in a relatively small number of mammalian cells. The whole procedures from cell collection to generation of sequencing-ready libraries can be completed in 2 days.
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Affiliation(s)
- Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Xiaowei Xu
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
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42
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Bar-Ziv R, Brodsky S, Chapal M, Barkai N. Transcription Factor Binding to Replicated DNA. Cell Rep 2021; 30:3989-3995.e4. [PMID: 32209462 DOI: 10.1016/j.celrep.2020.02.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/13/2020] [Accepted: 02/27/2020] [Indexed: 11/17/2022] Open
Abstract
Genome replication perturbs the DNA regulatory environment by displacing DNA-bound proteins, replacing nucleosomes, and introducing dosage imbalance between regions replicating at different S-phase stages. Recently, we showed that these effects are integrated to maintain transcription homeostasis: replicated genes increase in dosage, but their expression remains stable due to replication-dependent epigenetic changes that suppress transcription. Here, we examine whether reduced transcription from replicated DNA results from limited accessibility to regulatory factors by measuring the time-resolved binding of RNA polymerase II (Pol II) and specific transcription factors (TFs) to DNA during S phase in budding yeast. We show that the Pol II binding pattern is largely insensitive to DNA dosage, indicating limited binding to replicated DNA. In contrast, binding of three TFs (Reb1, Abf1, and Rap1) to DNA increases with the increasing DNA dosage. We conclude that the replication-specific chromatin environment remains accessible to regulatory factors but suppresses RNA polymerase recruitment.
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Affiliation(s)
- Raz Bar-Ziv
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Chapal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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43
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Rao S, Ahmad K, Ramachandran S. Cooperative binding between distant transcription factors is a hallmark of active enhancers. Mol Cell 2021; 81:1651-1665.e4. [PMID: 33705711 DOI: 10.1016/j.molcel.2021.02.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/22/2022]
Abstract
Enhancers harbor binding motifs that recruit transcription factors (TFs) for gene activation. While cooperative binding of TFs at enhancers is known to be critical for transcriptional activation of a handful of developmental enhancers, the extent of TF cooperativity genome-wide is unknown. Here, we couple high-resolution nuclease footprinting with single-molecule methylation profiling to characterize TF cooperativity at active enhancers in the Drosophila genome. Enrichment of short micrococcal nuclease (MNase)-protected DNA segments indicates that the majority of enhancers harbor two or more TF-binding sites, and we uncover protected fragments that correspond to co-bound sites in thousands of enhancers. From the analysis of co-binding, we find that cooperativity dominates TF binding in vivo at the majority of active enhancers. Cooperativity is highest between sites spaced 50 bp apart, indicating that cooperativity occurs without apparent protein-protein interactions. Our findings suggest nucleosomes promoting cooperativity because co-binding may effectively clear nucleosomes and promote enhancer function.
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Affiliation(s)
- Satyanarayan Rao
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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44
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Biernat E, Kinney J, Dunlap K, Rizza C, Govind CK. The RSC complex remodels nucleosomes in transcribed coding sequences and promotes transcription in Saccharomyces cerevisiae. Genetics 2021; 217:6133232. [PMID: 33857307 PMCID: PMC8049546 DOI: 10.1093/genetics/iyab021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/05/2021] [Indexed: 01/06/2023] Open
Abstract
RSC (Remodels the Structure of Chromatin) is a conserved ATP-dependent chromatin remodeling complex that regulates many biological processes, including transcription by RNA polymerase II (Pol II). We report that RSC contributes in generating accessible nucleosomes in transcribed coding sequences (CDSs). RSC MNase ChIP-seq data revealed that RSC-bound nucleosome fragments were very heterogenous (∼80 bp to 180 bp) compared to a sharper profile displayed by the MNase inputs (140 bp to 160 bp), supporting the idea that RSC promotes accessibility of nucleosomal DNA. Notably, RSC binding to +1 nucleosomes and CDSs, but not with -1 nucleosomes, strongly correlated with Pol II occupancies, suggesting that RSC enrichment in CDSs is linked to transcription. We also observed that Pol II associates with nucleosomes throughout transcribed CDSs, and similar to RSC, Pol II-protected fragments were highly heterogenous, consistent with the idea that Pol II interacts with remodeled nucleosomes in CDSs. This idea is supported by the observation that the genes harboring high-levels of Pol II in their CDSs were the most strongly affected by ablating RSC function. Additionally, rapid nuclear depletion of Sth1 decreases nucleosome accessibility and results in accumulation of Pol II in highly transcribed CDSs. This is consistent with a slower clearance of elongating Pol II in cells with reduced RSC function, and is distinct from the effect of RSC depletion on PIC assembly. Altogether, our data provide evidence in support of the role of RSC in promoting Pol II elongation, in addition to its role in regulating transcription initiation.
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Affiliation(s)
- Emily Biernat
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Jeena Kinney
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Kyle Dunlap
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Christian Rizza
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Chhabi K Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
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45
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Duc C, Thiriet C. Replication-Coupled Chromatin Remodeling: An Overview of Disassembly and Assembly of Chromatin during Replication. Int J Mol Sci 2021; 22:1113. [PMID: 33498649 PMCID: PMC7865951 DOI: 10.3390/ijms22031113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks. The present review focuses on the eviction of nucleosomes in front of the replication forks to facilitate the passage of replication machinery and the mechanism of replication-coupled chromatin assembly behind the replication forks. The recycling of parental histones as well as the nuclear import and the assembly of newly synthesized histones are also discussed with regard to the epigenetic inheritance.
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Affiliation(s)
| | - Christophe Thiriet
- UFIP UMR-CNRS 6286, Épigénétique et Dynamique de la Chromatine, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France;
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46
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Ming X, Zhu B, Li Y. Mitotic inheritance of DNA methylation: more than just copy and paste. J Genet Genomics 2021; 48:1-13. [PMID: 33771455 DOI: 10.1016/j.jgg.2021.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Decades of investigation on DNA methylation have led to deeper insights into its metabolic mechanisms and biological functions. This understanding was fueled by the recent development of genome editing tools and our improved capacity for analyzing the global DNA methylome in mammalian cells. This review focuses on the maintenance of DNA methylation patterns during mitotic cell division. We discuss the latest discoveries of the mechanisms for the inheritance of DNA methylation as a stable epigenetic memory. We also highlight recent evidence showing the rapid turnover of DNA methylation as a dynamic gene regulatory mechanism. A body of work has shown that altered DNA methylomes are common features in aging and disease. We discuss the potential links between methylation maintenance mechanisms and disease-associated methylation changes.
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Affiliation(s)
- Xuan Ming
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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47
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Chen H, Liang H. A High-Resolution Map of Human Enhancer RNA Loci Characterizes Super-enhancer Activities in Cancer. Cancer Cell 2020; 38:701-715.e5. [PMID: 33007258 PMCID: PMC7658066 DOI: 10.1016/j.ccell.2020.08.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/21/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Although enhancers play critical roles in cancer, quantifying enhancer activities in clinical samples remains challenging, especially for super-enhancers. Enhancer activities can be inferred from enhancer RNA (eRNA) signals, which requires enhancer transcription loci definition. Only a small proportion of human eRNA loci has been precisely identified, limiting investigations of enhancer-mediated oncogenic mechanisms. Here, we characterize super-enhancer regions using aggregated RNA sequencing (RNA-seq) data from large cohorts. Super-enhancers usually contain discrete loci featuring sharp eRNA expression peaks. We identify >300,000 eRNA loci in ∼377 Mb super-enhancer regions that are regulated by evolutionarily conserved, well-positioned nucleosomes and are frequently dysregulated in cancer. The eRNAs provide explanatory power for cancer phenotypes beyond that provided by mRNA expression through resolving intratumoral heterogeneity with enhancer cell-type specificity. Our study provides a high-resolution map of eRNA loci through which super-enhancer activities can be quantified by RNA-seq and a user-friendly data portal, enabling a broad range of biomedical investigations.
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Affiliation(s)
- Han Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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48
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Francis NJ, Sihou D. Inheritance of Histone (H3/H4): A Binary Choice? Trends Biochem Sci 2020; 46:5-14. [PMID: 32917507 DOI: 10.1016/j.tibs.2020.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/09/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Histones carry information in the form of post-translational modifications (PTMs). For this information to be propagated through cell cycles, parental histones and their PTMs need to be maintained at the same genomic locations. Yet, during DNA replication, every nucleosome in the genome is disrupted to allow passage of the replisome. Recent data have identified histone chaperone activities that are intrinsic components of the replisome and implicate them in maintaining parental histones during DNA replication. We propose that structural and kinetic coordination between DNA replication and replisome-associated histone chaperone activities ensures positional inheritance of histones and their PTMs. When this coordination is perturbed, histones may instead be recycled to random genomic locations by alternative histone chaperones.
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Affiliation(s)
- Nicole J Francis
- Institut de Recherche Clinique de Montréal, 110 Avenue des Pins, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada; Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada.
| | - Djamouna Sihou
- Institut de Recherche Clinique de Montréal, 110 Avenue des Pins, Montréal, QC H2W 1R7, Canada; Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
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49
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Wen Z, Zhang L, Ruan H, Li G. Histone variant H2A.Z regulates nucleosome unwrapping and CTCF binding in mouse ES cells. Nucleic Acids Res 2020; 48:5939-5952. [PMID: 32392318 PMCID: PMC7293034 DOI: 10.1093/nar/gkaa360] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 03/27/2020] [Accepted: 04/29/2020] [Indexed: 01/28/2023] Open
Abstract
Nucleosome is the basic structural unit of chromatin, and its dynamics plays critical roles in the regulation of genome functions. However, how the nucleosome structure is regulated by histone variants in vivo is still largely uncharacterized. Here, by employing Micrococcal nuclease (MNase) digestion of crosslinked chromatin followed by chromatin immunoprecipitation (ChIP) and paired-end sequencing (MNase-X-ChIP-seq), we mapped unwrapping states of nucleosomes containing histone variant H2A.Z in mouse embryonic stem (ES) cells. We found that H2A.Z nucleosomes are more enriched with unwrapping states compared with canonical nucleosomes. Interestingly, +1 H2A.Z nucleosomes with 30–80 bp DNA is correlated with less active genes compared with +1 H2A.Z nucleosomes with 120–140 bp DNA. We confirmed the unwrapping of H2A.Z nucleosomes under native condition by re-ChIP of H2A.Z and H2A after CTCF CUT&RUN in mouse ES cells. Importantly, we found that depletion of H2A.Z results in decreased unwrapping of H3.3 nucleosomes and increased CTCF binding. Taken together, through MNase-X-ChIP-seq, we showed that histone variant H2A.Z regulates nucleosome unwrapping in vivo and that its function in regulating transcription or CTCF binding is correlated with unwrapping states of H2A.Z nucleosomes.
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Affiliation(s)
- Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Haihe Ruan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing, China
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50
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Parmar JJ, Padinhateeri R. Nucleosome positioning and chromatin organization. Curr Opin Struct Biol 2020; 64:111-118. [PMID: 32731156 DOI: 10.1016/j.sbi.2020.06.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/31/2020] [Accepted: 06/23/2020] [Indexed: 11/24/2022]
Abstract
In our cells, DNA is folded and packed with the help of many proteins into chromatin whose basic unit is a nucleosome-DNA wrapped around octamer of histone proteins. The chain of nucleosomes is further folded and arranged into many layers and has a dynamic organization. How does the complex chromatin organization emerge from interactions among DNA, histones, and non-histone proteins have been a question of great interest. Here we review recent literature that investigated how nucleosome positioning and nucleosome-mediated interactions drive chromatin organization. Unlike our earlier understanding, chromatin is organized into 3D domains of various sizes having irregularly organized nucleosomes. These domains emerge due to heterogeneous nucleosome positioning and diverse inter-nucleosome interactions that vary in space and time.
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Affiliation(s)
- Jyotsana J Parmar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, India.
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