1
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Shi G, Yang C, Wu J, Lei Y, Hu J, Feng J, Li Q. DNA polymerase δ subunit Pol32 binds histone H3-H4 and couples nucleosome assembly with Okazaki fragment processing. SCIENCE ADVANCES 2024; 10:eado1739. [PMID: 39121223 PMCID: PMC11313866 DOI: 10.1126/sciadv.ado1739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/05/2024] [Indexed: 08/11/2024]
Abstract
During lagging strand chromatin replication, multiple Okazaki fragments (OFs) require processing and nucleosome assembly, but the mechanisms linking these processes remain unclear. Here, using transmission electron microscopy and rapid degradation of DNA ligase Cdc9, we observed flap structures accumulated on lagging strands, controlled by both Pol δ's strand displacement activity and Fen1's nuclease digestion. The distance between neighboring flap structures exhibits a regular pattern, indicative of matured OF length. While fen1Δ or enhanced strand displacement activities by polymerase δ (Pol δ; pol3exo-) minimally affect inter-flap distance, mutants affecting replication-coupled nucleosome assembly, such as cac1Δ and mcm2-3A, do significantly alter it. Deletion of Pol32, a subunit of DNA Pol δ, significantly increases this distance. Mechanistically, Pol32 binds to histone H3-H4 and is critical for nucleosome assembly on the lagging strand. Together, we propose that Pol32 establishes a connection between nucleosome assembly and the processing of OFs on lagging strands.
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Affiliation(s)
- 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
| | - Chaoqi Yang
- 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
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jiale Wu
- 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
| | - Yang Lei
- 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
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Genome Editing Research Center, Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jianxun Feng
- 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
| | - 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
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2
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Karagyozova T, Almouzni G. Replicating chromatin in the nucleus: A histone variant perspective. Curr Opin Cell Biol 2024; 89:102397. [PMID: 38981199 DOI: 10.1016/j.ceb.2024.102397] [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: 04/12/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
In eukaryotes, chromatin and DNA replication are intimately linked, whereby chromatin impacts DNA replication control while genome duplication involves recovery of chromatin organisation. Here, we review recent advances in this area using a histone variant lens. We highlight how nucleosomal features interplay with origin definition and how the order of origin firing links with chromatin states in early mammalian development. We next discuss histone recycling and de novo deposition at the fork to finally open on the post-replicative recovery of the chromatin landscape to promote maintenance of cell identity.
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Affiliation(s)
- Tina Karagyozova
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue Contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue Contre le Cancer, 26 rue d'Ulm, 75005 Paris, France.
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3
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Yu J, Zhang Y, Fang Y, Paulo JA, Yaghoubi D, Hua X, Shipkovenska G, Toda T, Zhang Z, Gygi SP, Jia S, Li Q, Moazed D. A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance. Cell 2024:S0092-8674(24)00766-9. [PMID: 39094570 DOI: 10.1016/j.cell.2024.07.006] [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: 08/17/2023] [Revised: 03/17/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024]
Abstract
Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. Mrc1 contains a conserved histone-binding domain that forms a brace around the H3-H4 tetramer mimicking nucleosomal DNA and H2A-H2B histones, is required for heterochromatin inheritance, and promotes parental histone recycling during replication. We further identify binding sites for the FACT histone chaperone in Swi1/TIMELESS and DNA polymerase α that are required for heterochromatin inheritance. We propose that Mrc1, in concert with FACT acting as a mobile co-chaperone, coordinates the distribution of parental histones to newly replicated DNA.
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Affiliation(s)
- Juntao Yu
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Yujie Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yimeng Fang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Dadmehr Yaghoubi
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Xu Hua
- Institute for Cancer Genetics, Department of Pediatrics, and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gergana Shipkovenska
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - 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
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - 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, China.
| | - Danesh Moazed
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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4
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Serra-Cardona A, Hua X, McNutt SW, Zhou H, Toda T, Jia S, Chu F, Zhang Z. The PCNA-Pol δ complex couples lagging strand DNA synthesis to parental histone transfer for epigenetic inheritance. SCIENCE ADVANCES 2024; 10:eadn5175. [PMID: 38838138 PMCID: PMC11152121 DOI: 10.1126/sciadv.adn5175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Inheritance of epigenetic information is critical for maintaining cell identity. The transfer of parental histone H3-H4 tetramers, the primary carrier of epigenetic modifications on histone proteins, represents a crucial yet poorly understood step in the inheritance of epigenetic information. Here, we show the lagging strand DNA polymerase, Pol δ, interacts directly with H3-H4 and that the interaction between Pol δ and the sliding clamp PCNA regulates parental histone transfer to lagging strands, most likely independent of their roles in DNA synthesis. When combined, mutations at Pol δ and Mcm2 that compromise parental histone transfer result in a greater reduction in nucleosome occupancy at nascent chromatin than mutations in either alone. Last, PCNA contributes to nucleosome positioning on nascent chromatin. On the basis of these results, we suggest that the PCNA-Pol δ complex couples lagging strand DNA synthesis to parental H3-H4 transfer, facilitating epigenetic inheritance.
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Affiliation(s)
- Albert Serra-Cardona
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Xu Hua
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
| | - Takenori Toda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10019, USA
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5
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Chen R, Zhao MJ, Li YM, Liu AH, Wang RX, Mei YC, Chen X, Du HN. Di- and tri-methylation of histone H3K36 play distinct roles in DNA double-strand break repair. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1089-1105. [PMID: 38842635 DOI: 10.1007/s11427-024-2543-9] [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: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 06/07/2024]
Abstract
Histone H3 Lys36 (H3K36) methylation and its associated modifiers are crucial for DNA double-strand break (DSB) repair, but the mechanism governing whether and how different H3K36 methylation forms impact repair pathways is unclear. Here, we unveil the distinct roles of H3K36 dimethylation (H3K36me2) and H3K36 trimethylation (H3K36me3) in DSB repair via non-homologous end joining (NHEJ) or homologous recombination (HR). Yeast cells lacking H3K36me2 or H3K36me3 exhibit reduced NHEJ or HR efficiency. yKu70 and Rfa1 bind H3K36me2- or H3K36me3-modified peptides and chromatin, respectively. Disrupting these interactions impairs yKu70 and Rfa1 recruitment to damaged H3K36me2- or H3K36me3-rich loci, increasing DNA damage sensitivity and decreasing repair efficiency. Conversely, H3K36me2-enriched intergenic regions and H3K36me3-enriched gene bodies independently recruit yKu70 or Rfa1 under DSB stress. Importantly, human KU70 and RPA1, the homologs of yKu70 and Rfa1, exclusively associate with H3K36me2 and H3K36me3 in a conserved manner. These findings provide valuable insights into how H3K36me2 and H3K36me3 regulate distinct DSB repair pathways, highlighting H3K36 methylation as a critical element in the choice of DSB repair pathway.
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Affiliation(s)
- Runfa Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Meng-Jie Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Yu-Min Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Ao-Hui Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Ru-Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Yu-Chao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China.
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6
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Li N, Gao N. A commentary of "Initial DNA melting in human DNA replication initiation": Top 10 Scientific Advances of 2023, China. FUNDAMENTAL RESEARCH 2024; 4:701-703. [PMID: 38933211 PMCID: PMC11197563 DOI: 10.1016/j.fmre.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/20/2024] [Indexed: 06/28/2024] Open
Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
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7
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Snedeker J, Davis BEM, Ranjan R, Wooten M, Blundon J, Chen X. Reduced Levels of Lagging Strand Polymerases Shape Stem Cell Chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591383. [PMID: 38746451 PMCID: PMC11092439 DOI: 10.1101/2024.04.26.591383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Stem cells display asymmetric histone inheritance while non-stem progenitor cells exhibit symmetric patterns in the Drosophila male germline lineage. Here, we report that components involved in lagging strand synthesis, such as DNA polymerase α and δ (Polα and Polδ), have significantly reduced levels in stem cells compared to progenitor cells. Compromising Polα genetically induces the replication-coupled histone incorporation pattern in progenitor cells to be indistinguishable from that in stem cells, which can be recapitulated using a Polα inhibitor in a concentration-dependent manner. Furthermore, stem cell-derived chromatin fibers display a higher degree of old histone recycling by the leading strand compared to progenitor cell-derived chromatin fibers. However, upon reducing Polα levels in progenitor cells, the chromatin fibers now display asymmetric old histone recycling just like GSC-derived fibers. The old versus new histone asymmetry is comparable between stem cells and progenitor cells at both S-phase and M-phase. Together, these results indicate that developmentally programmed expression of key DNA replication components is important to shape stem cell chromatin. Furthermore, manipulating one crucial DNA replication component can induce replication-coupled histone dynamics in non-stem cells in a manner similar to that in stem cells.
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Affiliation(s)
- Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Brendon E. M. Davis
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Current address: Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Joshua Blundon
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD 21218, USA
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8
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Chen P, Li G, Li W. Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions. JACS AU 2024; 4:866-876. [PMID: 38559720 PMCID: PMC10976579 DOI: 10.1021/jacsau.3c00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024]
Abstract
Nucleosome, the building block of chromatin, plays pivotal roles in all DNA-related processes. While cryogenic-electron microscopy (cryo-EM) has significantly advanced our understanding of nucleosome structures, the emerging field of single-molecule force spectroscopy is illuminating their dynamic properties. This technique is crucial for revealing how nucleosome behavior is influenced by chaperones, remodelers, histone variants, and post-translational modifications, particularly in their folding and unfolding mechanisms under tension. Such insights are vital for deciphering the complex interplay in nucleosome assembly and structural regulation, highlighting the nucleosome's versatility in response to DNA activities. In this Perspective, we aim to consolidate the latest advancements in nucleosome dynamics, with a special focus on the revelations brought forth by single-molecule manipulation. Our objective is to highlight the insights gained from studying nucleosome dynamics through this innovative approach, emphasizing the transformative impact of single-molecule manipulation techniques in the field of chromatin research.
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Affiliation(s)
- Ping Chen
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Department
of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory
for Tumor Invasion and Metastasis, Capital
Medical University, Beijing 100069, P. R. China
| | - Guohong Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wei Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
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9
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Fousek-Schuller VJ, Borgstahl GEO. The Intriguing Mystery of RPA Phosphorylation in DNA Double-Strand Break Repair. Genes (Basel) 2024; 15:167. [PMID: 38397158 PMCID: PMC10888239 DOI: 10.3390/genes15020167] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Human Replication Protein A (RPA) was historically discovered as one of the six components needed to reconstitute simian virus 40 DNA replication from purified components. RPA is now known to be involved in all DNA metabolism pathways that involve single-stranded DNA (ssDNA). Heterotrimeric RPA comprises several domains connected by flexible linkers and is heavily regulated by post-translational modifications (PTMs). The structure of RPA has been challenging to obtain. Various structural methods have been applied, but a complete understanding of RPA's flexible structure, its function, and how it is regulated by PTMs has yet to be obtained. This review will summarize recent literature concerning how RPA is phosphorylated in the cell cycle, the structural analysis of RPA, DNA and protein interactions involving RPA, and how PTMs regulate RPA activity and complex formation in double-strand break repair. There are many holes in our understanding of this research area. We will conclude with perspectives for future research on how RPA PTMs control double-strand break repair in the cell cycle.
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Affiliation(s)
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer & Allied Diseases, UNMC, Omaha, NE 68198-6805, USA
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10
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Wang X, Tang Y, Xu J, Leng H, Shi G, Hu Z, Wu J, Xiu Y, Feng J, Li Q. The N-terminus of Spt16 anchors FACT to MCM2-7 for parental histone recycling. Nucleic Acids Res 2023; 51:11549-11567. [PMID: 37850662 PMCID: PMC10681723 DOI: 10.1093/nar/gkad846] [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: 02/11/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Parental histone recycling is vital for maintaining chromatin-based epigenetic information during replication, yet its underlying mechanisms remain unclear. Here, we uncover an unexpected role of histone chaperone FACT and its N-terminus of the Spt16 subunit during parental histone recycling and transfer in budding yeast. Depletion of Spt16 and mutations at its middle domain that impair histone binding compromise parental histone recycling on both the leading and lagging strands of DNA replication forks. Intriguingly, deletion of the Spt16-N domain impairs parental histone recycling, with a more pronounced defect observed on the lagging strand. Mechanistically, the Spt16-N domain interacts with the replicative helicase MCM2-7 and facilitates the formation of a ternary complex involving FACT, histone H3/H4 and Mcm2 histone binding domain, critical for the recycling and transfer of parental histones to lagging strands. Lack of the Spt16-N domain weakens the FACT-MCM interaction and reduces parental histone recycling. We propose that the Spt16-N domain acts as a protein-protein interaction module, enabling FACT to function as a shuttle chaperone in collaboration with Mcm2 and potentially other replisome components for efficient local parental histone recycling and inheritance.
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Affiliation(s)
- Xuezheng Wang
- 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
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yuantao Tang
- 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
| | - Jiawei Xu
- 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
| | - He Leng
- 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
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, 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
| | - Zaifeng Hu
- 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
| | - Jiale Wu
- 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
| | - Yuwen Xiu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jianxun Feng
- 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
| | - 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
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
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11
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Ghaddar N, Luciano P, Géli V, Corda Y. Chromatin assembly factor-1 preserves genome stability in ctf4Δ cells by promoting sister chromatid cohesion. Cell Stress 2023; 7:69-89. [PMID: 37662646 PMCID: PMC10468696 DOI: 10.15698/cst2023.09.289] [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: 02/23/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
Chromatin assembly and the establishment of sister chromatid cohesion are intimately connected to the progression of DNA replication forks. Here we examined the genetic interaction between the heterotrimeric chromatin assembly factor-1 (CAF-1), a central component of chromatin assembly during replication, and the core replisome component Ctf4. We find that CAF-1 deficient cells as well as cells affected in newly-synthesized H3-H4 histones deposition during DNA replication exhibit a severe negative growth with ctf4Δ mutant. We dissected the role of CAF-1 in the maintenance of genome stability in ctf4Δ yeast cells. In the absence of CTF4, CAF-1 is essential for viability in cells experiencing replication problems, in cells lacking functional S-phase checkpoint or functional spindle checkpoint, and in cells lacking DNA repair pathways involving homologous recombination. We present evidence that CAF-1 affects cohesin association to chromatin in a DNA-damage-dependent manner and is essential to maintain cohesion in the absence of CTF4. We also show that Eco1-catalyzed Smc3 acetylation is reduced in absence of CAF-1. Furthermore, we describe genetic interactions between CAF-1 and essential genes involved in cohesin loading, cohesin stabilization, and cohesin component indicating that CAF-1 is crucial for viability when sister chromatid cohesion is affected. Finally, our data indicate that the CAF-1-dependent pathway required for cohesion is functionally distinct from the Rtt101-Mms1-Mms22 pathway which functions in replicated chromatin assembly. Collectively, our results suggest that the deposition by CAF-1 of newly-synthesized H3-H4 histones during DNA replication creates a chromatin environment that favors sister chromatid cohesion and maintains genome integrity.
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Affiliation(s)
- Nagham Ghaddar
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix Marseille Univ, Institut Paoli-Calmettes, Marseille, France. Ligue Nationale Contre le Cancer (Labeled Equip)
| | - Pierre Luciano
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix Marseille Univ, Institut Paoli-Calmettes, Marseille, France. Ligue Nationale Contre le Cancer (Labeled Equip)
| | - Vincent Géli
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix Marseille Univ, Institut Paoli-Calmettes, Marseille, France. Ligue Nationale Contre le Cancer (Labeled Equip)
| | - Yves Corda
- Marseille Cancer Research Centre (CRCM), U1068 INSERM, UMR7258 CNRS, UM105 Aix Marseille Univ, Institut Paoli-Calmettes, Marseille, France. Ligue Nationale Contre le Cancer (Labeled Equip)
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12
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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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13
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Gan X, Zhang Y, Jiang D, Shi J, Zhao H, Xie C, Wang Y, Xu J, Zhang X, Cai G, Wang H, Huang J, Chen X. Proper RPA acetylation promotes accurate DNA replication and repair. Nucleic Acids Res 2023; 51:5565-5583. [PMID: 37140030 PMCID: PMC10287905 DOI: 10.1093/nar/gkad291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
The single-stranded DNA (ssDNA) binding protein complex RPA plays a critical role in promoting DNA replication and multiple DNA repair pathways. However, how RPA is regulated to achieve its functions precisely in these processes remains elusive. Here, we found that proper acetylation and deacetylation of RPA are required to regulate RPA function in promoting high-fidelity DNA replication and repair. We show that yeast RPA is acetylated on multiple conserved lysines by the acetyltransferase NuA4 upon DNA damage. Mimicking constitutive RPA acetylation or blocking its acetylation causes spontaneous mutations with the signature of micro-homology-mediated large deletions or insertions. In parallel, improper RPA acetylation/deacetylation impairs DNA double-strand break (DSB) repair by the accurate gene conversion or break-induced replication while increasing the error-prone repair by single-strand annealing or alternative end joining. Mechanistically, we show that proper acetylation and deacetylation of RPA ensure its normal nuclear localization and ssDNA binding ability. Importantly, mutation of the equivalent residues in human RPA1 also impairs RPA binding on ssDNA, leading to attenuated RAD51 loading and homologous recombination repair. Thus, timely RPA acetylation and deacetylation likely represent a conserved mechanism promoting high-fidelity replication and repair while discriminating the error-prone repair mechanisms in eukaryotes.
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Affiliation(s)
- Xiaoli Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yueyue Zhang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Donghao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyao Shi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Han Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Chengyu Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanyan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Cai
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
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14
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Zou Y, Pei J, Long H, Lan L, Dong K, Wang T, Li M, Zhao Z, Zhu L, Zhang G, Jin X, Wang Y, Wen Z, Wei M, Feng Y. H4S47 O-GlcNAcylation regulates the activation of mammalian replication origins. Nat Struct Mol Biol 2023:10.1038/s41594-023-00998-6. [PMID: 37202474 DOI: 10.1038/s41594-023-00998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 04/12/2023] [Indexed: 05/20/2023]
Abstract
The transmission and maintenance of genetic information in eukaryotic cells relies on the faithful duplication of the entire genome. In each round of division, excessive replication origins are licensed, with only a fraction activated to give rise to bi-directional replication forks in the context of chromatin. However, it remains elusive how eukaryotic replication origins are selectively activated. Here we demonstrate that O-GlcNAc transferase (OGT) enhances replication initiation by catalyzing H4S47 O-GlcNAcylation. Mutation of H4S47 impairs DBF4-dependent protein kinase (DDK) recruitment on chromatin, causing reduced phosphorylation of the replicative helicase mini-chromosome maintenance (MCM) complex and compromised DNA unwinding. Our short nascent-strand sequencing results further confirm the importance of H4S47 O-GlcNAcylation in origin activation. We propose that H4S47 O-GlcNAcylation directs origin activation through facilitating MCM phosphorylation, and this may shed light on the control of replication efficiency by chromatin environment.
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Affiliation(s)
- Yingying Zou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Jiayao Pei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Haizhen Long
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Liting Lan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kejian Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Tingting Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Ming Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Zhexuan Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Lirun Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Gangxuan Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Xin Jin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Yang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Zengqi Wen
- School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Min Wei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Yunpeng Feng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China.
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15
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Shan Z, Zhang Y, Bu J, Li H, Zhang Z, Xiong J, Zhu B. The patterns and participants of parental histone recycling during DNA replication in Saccharomyces cerevisiae. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2267-6. [PMID: 36914923 DOI: 10.1007/s11427-022-2267-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/27/2022] [Indexed: 03/14/2023]
Abstract
Epigenetic information carried by histone modifications not only reflects the state of gene expression, but also participates in the maintenance of chromatin states and the regulation of gene expression. Recycling of parental histones to daughter chromatin after DNA replication is vital to mitotic inheritance of epigenetic information and the maintenance of cell identity, because the locus-specific modifications of the parental histones need to be maintained. To assess the precision of parental histone recycling, we developed a synthetic local label-chasing system in budding yeast Saccharomyces cerevisiae. Using this system, we observed that parental histone H3 can be recycled to their original position, thereby recovering their position information after DNA replication at all tested loci, including heterochromatin boundary, non-transcribed region, and actively transcribed regions. Moreover, the recycling rate appears to be affected by local chromatin environment. We surveyed a number of potential regulatory factors and observed that histone H3-H4 chaperon Asf1 contributed to parental histone recycling, while the eukaryotic replisome-associated components Mcm2 and Dpb3 displayed compounding effects in this process. In addition, the FACT complex also plays a role in the recycling of parental histones and helps to stabilize the nucleosomes.
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Affiliation(s)
- Zhongqing Shan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiachen Bu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huizhi Li
- 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
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - 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.
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16
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Zhang Y, Zhang Q, Zhang Y, Han J. The Role of Histone Modification in DNA Replication-Coupled Nucleosome Assembly and Cancer. Int J Mol Sci 2023; 24:ijms24054939. [PMID: 36902370 PMCID: PMC10003558 DOI: 10.3390/ijms24054939] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 03/08/2023] Open
Abstract
Histone modification regulates replication-coupled nucleosome assembly, DNA damage repair, and gene transcription. Changes or mutations in factors involved in nucleosome assembly are closely related to the development and pathogenesis of cancer and other human diseases and are essential for maintaining genomic stability and epigenetic information transmission. In this review, we discuss the role of different types of histone posttranslational modifications in DNA replication-coupled nucleosome assembly and disease. In recent years, histone modification has been found to affect the deposition of newly synthesized histones and the repair of DNA damage, further affecting the assembly process of DNA replication-coupled nucleosomes. We summarize the role of histone modification in the nucleosome assembly process. At the same time, we review the mechanism of histone modification in cancer development and briefly describe the application of histone modification small molecule inhibitors in cancer therapy.
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17
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Zhao X, Wang J, Jin D, Cheng J, Chen H, Li Z, Wang Y, Lou H, Zhu JK, Du X, Gong Z. AtMCM10 promotes DNA replication-coupled nucleosome assembly in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:203-222. [PMID: 36541721 DOI: 10.1111/jipb.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Minichromosome Maintenance protein 10 (MCM10) is essential for DNA replication initiation and DNA elongation in yeasts and animals. Although the functions of MCM10 in DNA replication and repair have been well documented, the detailed mechanisms for MCM10 in these processes are not well known. Here, we identified AtMCM10 gene through a forward genetic screening for releasing a silenced marker gene. Although plant MCM10 possesses a similar crystal structure as animal MCM10, AtMCM10 is not essential for plant growth or development in Arabidopsis. AtMCM10 can directly bind to histone H3-H4 and promotes nucleosome assembly in vitro. The nucleosome density is decreased in Atmcm10, and most of the nucleosome density decreased regions in Atmcm10 are also regulated by newly synthesized histone chaperone Chromatin Assembly Factor-1 (CAF-1). Loss of both AtMCM10 and CAF-1 is embryo lethal, indicating that AtMCM10 and CAF-1 are indispensable for replication-coupled nucleosome assembly. AtMCM10 interacts with both new and parental histones. Atmcm10 mutants have lower H3.1 abundance and reduced H3K27me1/3 levels with releasing some silenced transposons. We propose that AtMCM10 deposits new and parental histones during nucleosome assembly, maintaining proper epigenetic modifications and genome stability during DNA replication.
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Affiliation(s)
- Xinjie Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dan Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hui Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jian-Kang Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Science, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
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18
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Li X, Wang L, Liu X, Zheng Z, Kong D. Cellular regulation and stability of DNA replication forks in eukaryotic cells. DNA Repair (Amst) 2022; 120:103418. [DOI: 10.1016/j.dnarep.2022.103418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/03/2022]
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19
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Urban JA, Ranjan R, Chen X. Asymmetric Histone Inheritance: Establishment, Recognition, and Execution. Annu Rev Genet 2022; 56:113-143. [PMID: 35905975 PMCID: PMC10054593 DOI: 10.1146/annurev-genet-072920-125226] [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: 11/09/2022]
Abstract
The discovery of biased histone inheritance in asymmetrically dividing Drosophila melanogaster male germline stem cells demonstrates one means to produce two distinct daughter cells with identical genetic material. This inspired further studies in different systems, which revealed that this phenomenon may be a widespread mechanism to introduce cellular diversity. While the extent of asymmetric histone inheritance could vary among systems, this phenomenon is proposed to occur in three steps: first, establishment of histone asymmetry between sister chromatids during DNA replication; second, recognition of sister chromatids carrying asymmetric histone information during mitosis; and third, execution of this asymmetry in the resulting daughter cells. By compiling the current knowledge from diverse eukaryotic systems, this review comprehensively details and compares known chromatin factors, mitotic machinery components, and cell cycle regulators that may contribute to each of these three steps. Also discussed are potential mechanisms that introduce and regulate variable histone inheritance modes and how these different modes may contribute to cell fate decisions in multicellular organisms.
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Affiliation(s)
- Jennifer A Urban
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA;
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
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20
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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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21
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Cimbalo A, Frangiamone M, Lozano M, Escrivá L, Vila-Donat P, Manyes L. Protective role of fermented whey and pumpkin extract against aflatoxin B 1 and ochratoxin A toxicity in Jurkat T-cells. WORLD MYCOTOXIN J 2022. [DOI: 10.3920/wmj2022.2780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The beneficial effect of fermented whey and pumpkin extract rich in carotenoids was evaluated in Jurkat cells against aflatoxin B1 (AFB1) and ochratoxin A (OTA) cytotoxicity through a proteomic approach. The functional ingredients were added into mycotoxin contaminated bread formulation, which were digested in vitro in order to simulate human intestinal absorption. Cell cultures were exposed during 7 days to these mycotoxins dissolved in: (a) 0.1% organic solvent (DMSO), (b) an intestinal digest of bread with pumpkin individually (PID) and (c) an intestinal digest of bread with pumpkin mixed with fermented whey (PID+WF). Extracted proteins were subjected to reduction and alkylation and subsequently a tryptic digestion in order to be analysed by liquid chromatography coupled with quadrupole time of flight (LC/MS-Q-TOF). Results obtained highlighted the beneficial role of functional ingredients employed through the identification of proteins involved in several biological processes and metabolic pathways, mainly antioxidant activity, nucleosome assembly and secretory senescence phenotype. Among proteins involved in antioxidant activity, peroxiredoxin 1 and 2 stand out. Comparing the different conditions investigated, a remarkable change was observed in their expression, ranging from a repression using the standard (DMSO 0.1%), to an overexpression when treated with the functional ingredients. Similarly, after PID and PID+WF treatment, histones’ expression implicated in the metabolic pathway of nucleosome assembly, such as H2A, H2B, H2C, H3 and H4, was increased. Furthermore, the expression of protein cyclin A2, which downregulation is involved in limiting carcinogenic cells growth, was lower in presence of both functional ingredients. Based on these findings, functional ingredients can act as protectors against genomic stress caused by mycotoxins, preventing the loss of vital cell functions and paralysing the growth of carcinogenic cells.
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Affiliation(s)
- A. Cimbalo
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - M. Frangiamone
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - M. Lozano
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - L. Escrivá
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - P. Vila-Donat
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
| | - L. Manyes
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Av. Vicent Andrés Estellés s/n., 46100 Burjassot, Spain
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22
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Zhang X, Li W, Liu Y, Li Y, Li Y, Yang W, Chen X, Pi L, Yang H. Replication protein RPA2A regulates floral transition by cooperating with PRC2 in Arabidopsis. THE NEW PHYTOLOGIST 2022; 235:2439-2453. [PMID: 35633113 DOI: 10.1111/nph.18279] [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: 01/22/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
RPA2A is a subunit of the conserved heterotrimeric replication protein A (RPA) in Arabidopsis, which is an essential replisome component that binds to single-stranded DNA during DNA replication. RPA2A controls a set of developmental processes, but the underlying mechanism is largely unknown. Here we show that RPA2A represses key flowering genes including FLOWERING LOCUS T (FT), AGAMOUS (AG) and AGAMOUS LIKE 71 (AGL71) to suppress floral transition by cooperating with the PRC2 complex. RPA2A is vigorously expressed in dividing cells and required for correct DNA replication. Mutation of RPA2A leads to early flowering, which is dependent on ectopic expression of key flowering genes including FT molecularly and genetically. RPA2A and PRC2 have common target genes including FT, AG and AGL71 supported using genetic analysis, transcriptome profiling and H3K27me3 ChIP-seq analysis. Furthermore, RPA2A physically interacts with PRC2 components CLF, EMF2 and MSI1, which recruits CLF to the chromatin loci of FT, AG and AGL71. Together, our results show that the replication protein RPA2A recruits PRC2 to key flowering genes through physical protein interaction, thereby repressing the expression of these genes to suppress floral transition in Arabidopsis.
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Affiliation(s)
- Xiaoling Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Wenjuan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Yue Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Yanzhuo Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Yang Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Wandong Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Limin Pi
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, 430072, China
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
- RNA Institute, Wuhan University, Wuhan, 430072, China
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23
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RPA1 controls chromatin architecture and maintains lipid metabolic homeostasis. Cell Rep 2022; 40:111071. [PMID: 35830798 DOI: 10.1016/j.celrep.2022.111071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/24/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease, with a prevalence of 25% worldwide. However, the underlying molecular mechanism involved in the development and progression of the NAFLD spectrum remains unclear. Single-stranded DNA-binding protein replication protein A1 (RPA1) participates in DNA replication, recombination, and damage repair. Here, we show that Rpa1+/- mice develop fatty liver disease during aging and in response to a high-fat diet. Liver-specific deletion of Rpa1 results in downregulation of genes related to fatty acid oxidation and impaired fatty acid oxidation, which leads to hepatic steatosis and hepatocellular carcinoma. Mechanistically, RPA1 binds gene regulatory regions, chromatin-remodeling factors, and HNF4A and remodels chromatin architecture, through which RPA1 promotes HNF4A transcriptional activity and fatty acid β oxidation. Collectively, our data demonstrate that RPA1 is an important regulator of NAFLD through controlling chromatin accessibility.
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24
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Yadav RN, Hossain MF, Das A, Srivastava AK, Banik BK. Organocatalysis: A recent development on stereoselective synthesis of o-glycosides. CATALYSIS REVIEWS 2022. [DOI: 10.1080/01614940.2022.2041303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ram Naresh Yadav
- Department of Chemistry, Faculty of Engineering & Technology, Veer Bahadur Singh Purvanchal University, Jaunpur, India
| | - Md. Firoj Hossain
- Department of Chemistry, University of North Bengal, Darjeeling, India
| | - Aparna Das
- Department of Mathematics and Natural Sciences, College of Sciences and Human Studies, Prince Mohammad Bin Fahd University, Khobar, Saudi Arabia
| | - Ashok Kumar Srivastava
- Department of Chemistry, Faculty of Engineering & Technology, Veer Bahadur Singh Purvanchal University, Jaunpur, India
| | - Bimal Krishna Banik
- Department of Mathematics and Natural Sciences, College of Sciences and Human Studies, Prince Mohammad Bin Fahd University, Khobar, Saudi Arabia
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25
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Li L, Wang J, Yang Z, Zhao Y, Jiang H, Jiang L, Hou W, Ye R, He Q, Kupiec M, Luke B, Cao Q, Qi Z, Li Z, Lou H. Metabolic remodeling maintains a reducing environment for rapid activation of the yeast DNA replication checkpoint. EMBO J 2022; 41:e108290. [PMID: 35028974 PMCID: PMC8844976 DOI: 10.15252/embj.2021108290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 11/04/2021] [Accepted: 12/09/2021] [Indexed: 12/31/2022] Open
Abstract
Nucleotide metabolism fuels normal DNA replication and is also primarily targeted by the DNA replication checkpoint when replication stalls. To reveal a comprehensive interconnection between genome maintenance and metabolism, we analyzed the metabolomic changes upon replication stress in the budding yeast S. cerevisiae. We found that upon treatment of cells with hydroxyurea, glucose is rapidly diverted to the oxidative pentose phosphate pathway (PPP). This effect is mediated by the AMP-dependent kinase, SNF1, which phosphorylates the transcription factor Mig1, thereby relieving repression of the gene encoding the rate-limiting enzyme of the PPP. Surprisingly, NADPH produced by the PPP is required for efficient recruitment of replication protein A (RPA) to single-stranded DNA, providing the signal for the activation of the Mec1/ATR-Rad53/CHK1 checkpoint signaling kinase cascade. Thus, SNF1, best known as a central energy controller, determines a fast mode of replication checkpoint activation through a redox mechanism. These findings establish that SNF1 provides a hub with direct links to cellular metabolism, redox, and surveillance of DNA replication in eukaryotes.
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Affiliation(s)
- Lili Li
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jie Wang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zijia Yang
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yiling Zhao
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Hui Jiang
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Luguang Jiang
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Maize Improvement Center of ChinaCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Wenya Hou
- Shenzhen University General HospitalGuangdong Key Laboratory for Genome Stability and Disease PreventionShenzhen University School of MedicineShenzhenChina
| | - Risheng Ye
- Department of Medical EducationTexas Tech University Health Sciences Center Paul L. Foster School of MedicineEl PasoTXUSA
| | - Qun He
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer ResearchTel Aviv UniversityRamat AvivIsrael
| | - Brian Luke
- Institute of Molecular Biology (IMB)MainzGermany,Institute of Developmental Biology and Neurobiology (IDN)Johannes Gutenberg UniversitätMainzGermany
| | - Qinhong Cao
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhi Qi
- Center for Quantitative Biology and Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | - Zhen Li
- State Key Laboratory of Plant Physiology and BiochemistryCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Huiqiang Lou
- South China HospitalHealth Science CenterGuangdong Key Laboratory of Genome Instability and Disease PreventionShenzhen University School of MedicineShenzhenChina
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26
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Popova LV, Nagarajan P, Lovejoy CM, Sunkel B, Gardner M, Wang M, Freitas M, Stanton B, Parthun M. Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones. Nucleic Acids Res 2021; 49:12136-12151. [PMID: 34788845 PMCID: PMC8643632 DOI: 10.1093/nar/gkab1044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/20/2021] [Accepted: 10/14/2021] [Indexed: 12/15/2022] Open
Abstract
A central component of the epigenome is the pattern of histone post-translational modifications that play a critical role in the formation of specific chromatin states. Following DNA replication, nascent chromatin is a 1:1 mixture of parental and newly synthesized histones and the transfer of modification patterns from parental histones to new histones is a fundamental step in epigenetic inheritance. Here we report that loss of HAT1, which acetylates lysines 5 and 12 of newly synthesized histone H4 during replication-coupled chromatin assembly, results in the loss of accessibility of large domains of heterochromatin, termed HAT1-dependent Accessibility Domains (HADs). HADs are mega base-scale domains that comprise ∼10% of the mouse genome. HAT1 globally represses H3 K9 me3 levels and HADs correspond to the regions of the genome that display HAT1-dependent increases in H3 K9me3 peak density. HADs display a high degree of overlap with a subset of Lamin-Associated Domains (LADs). HAT1 is required to maintain nuclear structure and integrity. These results indicate that HAT1 and the acetylation of newly synthesized histones may be critical regulators of the epigenetic inheritance of heterochromatin and suggest a new mechanism for the epigenetic regulation of nuclear lamina-heterochromatin interactions.
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Affiliation(s)
- Liudmila V Popova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Prabakaran Nagarajan
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Callie M Lovejoy
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin D Sunkel
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Miranda L Gardner
- Campus Chemical Instrument Center, Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH 43210, USA
| | - Meng Wang
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Z Stanton
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
- Abigail Wexner Research Institute at Nationwide Children's, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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27
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Feng S, Manley JL. Replication protein A associates with nucleolar R loops and regulates rRNA transcription and nucleolar morphology. Genes Dev 2021; 35:1579-1594. [PMID: 34819354 PMCID: PMC8653787 DOI: 10.1101/gad.348858.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/22/2021] [Indexed: 11/24/2022]
Abstract
Here, Feng and Manley report novel functions of the DNA replication and repair factor replication protein A (RPA) in control of nucleolar homeostasis. Their findings both indicate new roles for RPA in nucleoli through pre-rRNA transcriptional control and also emphasize that RPA function in nucleolar homeostasis is linked to R-loop resolution under both physiological and pathological conditions. The nucleolus is an important cellular compartment in which ribosomal RNAs (rRNAs) are transcribed and where certain stress pathways that are crucial for cell growth are coordinated. Here we report novel functions of the DNA replication and repair factor replication protein A (RPA) in control of nucleolar homeostasis. We show that loss of the DNA:RNA helicase senataxin (SETX) promotes RPA nucleolar localization, and that this relocalization is dependent on the presence of R loops. Notably, this nucleolar RPA phenotype was also observed in the presence of camptothecin (CPT)-induced genotoxic stress, as well as in SETX-deficient AOA2 patient fibroblasts. Extending these results, we found that RPA is recruited to rDNA following CPT treatment, where RPA prevents R-loop-induced DNA double-strand breaks. Furthermore, we show that loss of RPA significantly decreased 47S pre-rRNA levels, which was accompanied by increased expression of both RNAP II-mediated “promoter and pre-rRNA antisense” RNA as well as RNAP I-transcribed intragenic spacer RNAs. Finally, and likely reflecting the above, we found that loss of RPA promoted nucleolar structural disorganization, characterized by the appearance of reduced size nucleoli. Our findings both indicate new roles for RPA in nucleoli through pre-rRNA transcriptional control and also emphasize that RPA function in nucleolar homeostasis is linked to R-loop resolution under both physiological and pathological conditions.
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Affiliation(s)
- Shuang Feng
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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28
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SETD2-mediated H3K14 trimethylation promotes ATR activation and stalled replication fork restart in response to DNA replication stress. Proc Natl Acad Sci U S A 2021; 118:2011278118. [PMID: 34074749 PMCID: PMC8201831 DOI: 10.1073/pnas.2011278118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ataxia telangiectasia and Rad3 related (ATR) activation after replication stress involves a cascade of reactions, including replication protein A (RPA) complex loading onto single-stranded DNA and ATR activator loading onto chromatin. The contribution of histone modifications to ATR activation, however, is unclear. Here, we report that H3K14 trimethylation responds to replication stress by enhancing ATR activation. First, we confirmed that H3K14 monomethylation, dimethylation, and trimethylation all exist in mammalian cells, and that both SUV39H1 and SETD2 methyltransferases can catalyze H3K14 trimethylation in vivo and in vitro. Interestingly, SETD2-mediated H3K14 trimethylation markedly increases in response to replication stress induced with hydroxyurea, a replication stress inducer. Under these conditions, SETD2-mediated H3K14me3 recruited the RPA complex to chromatin via a direct interaction with RPA70. The increase in H3K14me3 levels was abolished, and RPA loading was attenuated when SETD2 was depleted or H3K14 was mutated. Rather, the cells were sensitive to replication stress such that the replication forks failed to restart, and cell-cycle progression was delayed. These findings help us understand how H3K14 trimethylation links replication stress with ATR activation.
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29
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Hammond-Martel I, Verreault A, Wurtele H. Chromatin dynamics and DNA replication roadblocks. DNA Repair (Amst) 2021; 104:103140. [PMID: 34087728 DOI: 10.1016/j.dnarep.2021.103140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
A broad spectrum of spontaneous and genotoxin-induced DNA lesions impede replication fork progression. The DNA damage response that acts to promote completion of DNA replication is associated with dynamic changes in chromatin structure that include two distinct processes which operate genome-wide during S-phase. The first, often referred to as histone recycling or parental histone segregation, is characterized by the transfer of parental histones located ahead of replication forks onto nascent DNA. The second, known as de novo chromatin assembly, consists of the deposition of new histone molecules onto nascent DNA. Because these two processes occur at all replication forks, their potential to influence a multitude of DNA repair and DNA damage tolerance mechanisms is considerable. The purpose of this review is to provide a description of parental histone segregation and de novo chromatin assembly, and to illustrate how these processes influence cellular responses to DNA replication roadblocks.
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Affiliation(s)
- Ian Hammond-Martel
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montreal, H1T 2M4, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada; Département de Pathologie et Biologie Cellulaire, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, H3T 1J4, Canada
| | - Hugo Wurtele
- Centre de recherche de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montreal, H1T 2M4, Canada; Département de Médecine, Université de Montréal, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, H3T 1J4, Canada.
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30
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Caldwell CC, Spies M. Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. Crit Rev Biochem Mol Biol 2020; 55:482-507. [PMID: 32856505 PMCID: PMC7821911 DOI: 10.1080/10409238.2020.1813070] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023]
Abstract
The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.
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Affiliation(s)
- Colleen C. Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
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31
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Dueva R, Iliakis G. Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. NAR Cancer 2020; 2:zcaa022. [PMID: 34316690 PMCID: PMC8210275 DOI: 10.1093/narcan/zcaa022] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) forms continuously during DNA replication and is an important intermediate during recombination-mediated repair of damaged DNA. Replication protein A (RPA) is the major eukaryotic ssDNA-binding protein. As such, RPA protects the transiently formed ssDNA from nucleolytic degradation and serves as a physical platform for the recruitment of DNA damage response factors. Prominent and well-studied RPA-interacting partners are the tumor suppressor protein p53, the RAD51 recombinase and the ATR-interacting proteins ATRIP and ETAA1. RPA interactions are also documented with the helicases BLM, WRN and SMARCAL1/HARP, as well as the nucleotide excision repair proteins XPA, XPG and XPF–ERCC1. Besides its well-studied roles in DNA replication (restart) and repair, accumulating evidence shows that RPA is engaged in DNA activities in a broader biological context, including nucleosome assembly on nascent chromatin, regulation of gene expression, telomere maintenance and numerous other aspects of nucleic acid metabolism. In addition, novel RPA inhibitors show promising effects in cancer treatment, as single agents or in combination with chemotherapeutics. Since the biochemical properties of RPA and its roles in DNA repair have been extensively reviewed, here we focus on recent discoveries describing several non-canonical functions.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
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32
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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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33
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Measuring Genome-Wide Nascent Nucleosome Assembly Using ReIN-Map. Methods Mol Biol 2020; 2196:117-141. [PMID: 32889717 DOI: 10.1007/978-1-0716-0868-5_10] [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: 04/05/2023]
Abstract
The successful assembly of nucleosomes following DNA replication is critically important for both the inheritance of epigenetic information and the maintenance of genome integrity. This process, termed DNA replication-coupled (RC) nucleosome assembly, requires that DNA replication and nucleosome assembly function in a highly coordinated fashion to transmit both genetic and epigenetic information. In this chapter, we describe a genome-wide method for measuring nucleosome occupancy patterns on nascent strands, which we have termed Replication-Intermediate Nucleosome Mapping (ReIN-Map), to monitor the RC nucleosome assembly level genome-wide in vivo. This method takes advantage of next-generation sequencing and in vivo labeling of newly synthesized DNA using a thymidine analogue, 5-bromo-2'-deoxyuridine (BrdU), and involves parallel analyses of the nucleosome formation using micrococcal nuclease (MNase) digestion of chromatin (MNase-seq) and of the newly synthesized DNA levels using sonication shearing of chromatin s (Sonication-seq). Replicated chromatin was enriched by immunoprecipitation using antibodies against BrdU (BrdU-IP), which is incorporated into DNA during DNA synthesis; the DNA is then subjected to strand-specific sequencing.
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34
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Grillone K, Riillo C, Scionti F, Rocca R, Tradigo G, Guzzi PH, Alcaro S, Di Martino MT, Tagliaferri P, Tassone P. Non-coding RNAs in cancer: platforms and strategies for investigating the genomic "dark matter". J Exp Clin Cancer Res 2020; 39:117. [PMID: 32563270 PMCID: PMC7305591 DOI: 10.1186/s13046-020-01622-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
The discovery of the role of non-coding RNAs (ncRNAs) in the onset and progression of malignancies is a promising frontier of cancer genetics. It is clear that ncRNAs are candidates for therapeutic intervention, since they may act as biomarkers or key regulators of cancer gene network. Recently, profiling and sequencing of ncRNAs disclosed deep deregulation in human cancers mostly due to aberrant mechanisms of ncRNAs biogenesis, such as amplification, deletion, abnormal epigenetic or transcriptional regulation. Although dysregulated ncRNAs may promote hallmarks of cancer as oncogenes or antagonize them as tumor suppressors, the mechanisms behind these events remain to be clarified. The development of new bioinformatic tools as well as novel molecular technologies is a challenging opportunity to disclose the role of the "dark matter" of the genome. In this review, we focus on currently available platforms, computational analyses and experimental strategies to investigate ncRNAs in cancer. We highlight the differences among experimental approaches aimed to dissect miRNAs and lncRNAs, which are the most studied ncRNAs. These two classes indeed need different investigation taking into account their intrinsic characteristics, such as length, structures and also the interacting molecules. Finally, we discuss the relevance of ncRNAs in clinical practice by considering promises and challenges behind the bench to bedside translation.
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Affiliation(s)
- Katia Grillone
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Caterina Riillo
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Francesca Scionti
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Roberta Rocca
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Net4science srl, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Giuseppe Tradigo
- Laboratory of Bioinformatics, Department of Medical and Surgical Sciences, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Pietro Hiram Guzzi
- Laboratory of Bioinformatics, Department of Medical and Surgical Sciences, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Net4science srl, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Department of Health Sciences, Magna Græcia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Maria Teresa Di Martino
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Pierfrancesco Tassone
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
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35
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Agudelo Garcia PA, Lovejoy CM, Nagarajan P, Park D, Popova LV, Freitas MA, Parthun MR. Histone acetyltransferase 1 is required for DNA replication fork function and stability. J Biol Chem 2020; 295:8363-8373. [PMID: 32366460 DOI: 10.1074/jbc.ra120.013496] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/28/2020] [Indexed: 01/20/2023] Open
Abstract
The replisome is a protein complex on the DNA replication fork and functions in a dynamic environment at the intersection of parental and nascent chromatin. Parental nucleosomes are disrupted in front of the replication fork. The daughter DNA duplexes are packaged with an equal amount of parental and newly synthesized histones in the wake of the replication fork through the activity of the replication-coupled chromatin assembly pathway. Histone acetyltransferase 1 (HAT1) is responsible for the cytosolic diacetylation of newly synthesized histone H4 on lysines 5 and 12, which accompanies replication-coupled chromatin assembly. Here, using proximity ligation assay-based chromatin assembly assays and DNA fiber analysis, we analyzed the role of murine HAT1 in replication-coupled chromatin assembly. We demonstrate that HAT1 physically associates with chromatin near DNA replication sites. We found that the association of HAT1 with newly replicated DNA is transient, but can be stabilized by replication fork stalling. The association of HAT1 with nascent chromatin may be functionally relevant, as HAT1 loss decreased replication fork progression and increased replication fork stalling. Moreover, in the absence of HAT1, stalled replication forks were unstable, and newly synthesized DNA became susceptible to MRE11-dependent degradation. These results suggest that HAT1 links replication fork function to the proper processing and assembly of newly synthesized histones.
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Affiliation(s)
- Paula A Agudelo Garcia
- Department of Biological Chemistry and Pharmacology, the Ohio State University, Columbus, Ohio, USA
| | - Callie M Lovejoy
- Department of Biological Chemistry and Pharmacology, the Ohio State University, Columbus, Ohio, USA
| | - Prabakaran Nagarajan
- Department of Biological Chemistry and Pharmacology, the Ohio State University, Columbus, Ohio, USA
| | - Dongju Park
- Department of Cancer Biology and Genetics, the Ohio State University, Columbus, Ohio, USA
| | - Liudmila V Popova
- Department of Biological Chemistry and Pharmacology, the Ohio State University, Columbus, Ohio, USA
| | - Michael A Freitas
- Department of Cancer Biology and Genetics, the Ohio State University, Columbus, Ohio, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, the Ohio State University, Columbus, Ohio, USA
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36
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Stewart-Morgan KR, Petryk N, Groth A. Chromatin replication and epigenetic cell memory. Nat Cell Biol 2020; 22:361-371. [PMID: 32231312 DOI: 10.1038/s41556-020-0487-y] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/18/2020] [Indexed: 02/07/2023]
Abstract
Propagation of the chromatin landscape across cell divisions is central to epigenetic cell memory. Mechanistic analysis of the interplay between DNA replication, the cell cycle, and the epigenome has provided insights into replication-coupled chromatin assembly and post-replicative chromatin maintenance. These breakthroughs are critical for defining how proliferation impacts the epigenome during cell identity changes in development and disease. Here we review these findings in the broader context of epigenetic inheritance across mitotic cell division.
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Affiliation(s)
- Kathleen R Stewart-Morgan
- The Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.,Epigenetics and Cell Fate, UMR7216 CNRS, University of Paris, Paris, France
| | - Anja Groth
- The Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
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37
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Zhang W, Feng J, Li Q. The replisome guides nucleosome assembly during DNA replication. Cell Biosci 2020; 10:37. [PMID: 32190287 PMCID: PMC7066812 DOI: 10.1186/s13578-020-00398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Nucleosome assembly during DNA replication is tightly coupled to ongoing DNA synthesis. This process, termed DNA replication-coupled (RC) nucleosome assembly, is essential for chromatin replication and has a great impact on both genome stability maintenance and epigenetic inheritance. This review discusses a set of recent findings regarding the role of replisome components contributing to RC nucleosome assembly. Starting with a brief introduction to the factors involved in nucleosome assembly and some aspects of the architecture of the eukaryotic replisome, we discuss studies from yeast to mammalian cells and the interactions of replisome components with histones and histone chaperones. We describe the proposed functions of replisome components during RC nucleosome assembly and discuss their impacts on histone segregation and implications for epigenetic inheritance.
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Affiliation(s)
- Wenshuo Zhang
- 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
| | - Jianxun Feng
- 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
| | - 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
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38
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Yu H, Bu C, Liu Y, Gong T, Liu X, Liu S, Peng X, Zhang W, Peng Y, Yang J, He L, Zhang Y, Yi X, Yang X, Sun L, Shang Y, Cheng Z, Liang J. Global crotonylome reveals CDYL-regulated RPA1 crotonylation in homologous recombination-mediated DNA repair. SCIENCE ADVANCES 2020; 6:eaay4697. [PMID: 32201722 PMCID: PMC7069697 DOI: 10.1126/sciadv.aay4697] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/17/2019] [Indexed: 05/15/2023]
Abstract
Previously, we reported that chromodomain Y-like (CDYL) acts as a crotonyl-coenzyme A hydratase and negatively regulates histone crotonylation (Kcr). However, the global CDYL-regulated crotonylome remains unclear. Here, we report a large-scale proteomics analysis for protein Kcr. We identify 14,311 Kcr sites across 3734 proteins in HeLa cells, providing by far the largest crotonylome dataset. We show that depletion of CDYL alters crotonylome landscape affecting diverse cellular pathways. Specifically, CDYL negatively regulated Kcr of RPA1, and mutation of the Kcr sites of RPA1 impaired its interaction with single-stranded DNA and/or with components of resection machinery, supporting a key role of RPA1 Kcr in homologous recombination DNA repair. Together, our study indicates that protein crotonylation has important implication in various pathophysiological processes.
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Affiliation(s)
- Huajing Yu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Yuncheng Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianyu Gong
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaoping Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shumeng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaojun Peng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Wenting Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yani Peng
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xia Yi
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaohan Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongfeng Shang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
- Corresponding author. (J.L.); (Z.C.)
| | - Jing Liang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Corresponding author. (J.L.); (Z.C.)
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Wooten M, Ranjan R, Chen X. Asymmetric Histone Inheritance in Asymmetrically Dividing Stem Cells. Trends Genet 2020; 36:30-43. [PMID: 31753528 PMCID: PMC6925335 DOI: 10.1016/j.tig.2019.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Abstract
Epigenetic mechanisms play essential roles in determining distinct cell fates during the development of multicellular organisms. Histone proteins represent crucial epigenetic components that help specify cell identities. Previous work has demonstrated that during the asymmetric cell division of Drosophila male germline stem cells (GSCs), histones H3 and H4 are asymmetrically inherited, such that pre-existing (old) histones are segregated towards the self-renewing GSC whereas newly synthesized (new) histones are enriched towards the differentiating daughter cell. In order to further understand the molecular mechanisms underlying this striking phenomenon, two key questions must be answered: when and how old and new histones are differentially incorporated by sister chromatids, and how epigenetically distinct sister chromatids are specifically recognized and segregated. Here, we discuss recent advances in our understanding of the molecular mechanisms and cellular bases underlying these fundamental and important biological processes responsible for generating two distinct cells through one cell division.
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Affiliation(s)
- Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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40
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Liu JQ, Li T. CRISPR-Cas9-mediated loss-of-function screens. FRONTIERS IN LIFE SCIENCE 2019. [DOI: 10.1080/21553769.2019.1670739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Jia-qing Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Tao Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
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41
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A quest for coordination among activities at the replisome. Biochem Soc Trans 2019; 47:1067-1075. [PMID: 31395754 DOI: 10.1042/bst20180402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022]
Abstract
Faithful DNA replication is required for transmission of the genetic material across generations. The basic mechanisms underlying this process are shared among all organisms: progressive unwinding of the long double-stranded DNA; synthesis of RNA primers; and synthesis of a new DNA chain. These activities are invariably performed by a multi-component machine called the replisome. A detailed description of this molecular machine has been achieved in prokaryotes and phages, with the replication processes in eukaryotes being comparatively less known. However, recent breakthroughs in the in vitro reconstitution of eukaryotic replisomes have resulted in valuable insight into their functions and mechanisms. In conjunction with the developments in eukaryotic replication, an emerging overall view of replisomes as dynamic protein ensembles is coming into fruition. The purpose of this review is to provide an overview of the recent insights into the dynamic nature of the bacterial replisome, revealed through single-molecule techniques, and to describe some aspects of the eukaryotic replisome under this framework. We primarily focus on Escherichia coli and Saccharomyces cerevisiae (budding yeast), since a significant amount of literature is available for these two model organisms. We end with a description of the methods of live-cell fluorescence microscopy for the characterization of replisome dynamics.
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Maya-Miles D, Andújar E, Pérez-Alegre M, Murillo-Pineda M, Barrientos-Moreno M, Cabello-Lobato MJ, Gómez-Marín E, Morillo-Huesca M, Prado F. Crosstalk between chromatin structure, cohesin activity and transcription. Epigenetics Chromatin 2019; 12:47. [PMID: 31331360 PMCID: PMC6647288 DOI: 10.1186/s13072-019-0293-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/10/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND A complex interplay between chromatin and topological machineries is critical for genome architecture and function. However, little is known about these reciprocal interactions, even for cohesin, despite its multiple roles in DNA metabolism. RESULTS We have used genome-wide analyses to address how cohesins and chromatin structure impact each other in yeast. Cohesin inactivation in scc1-73 mutants during the S and G2 phases causes specific changes in chromatin structure that preferentially take place at promoters; these changes include a significant increase in the occupancy of the - 1 and + 1 nucleosomes. In addition, cohesins play a major role in transcription regulation that is associated with specific promoter chromatin architecture. In scc1-73 cells, downregulated genes are enriched in promoters with short or no nucleosome-free region (NFR) and a fragile "nucleosome - 1/RSC complex" particle. These results, together with a preferential increase in the occupancy of nucleosome - 1 of these genes, suggest that cohesins promote transcription activation by helping RSC to form the NFR. In sharp contrast, the scc1-73 upregulated genes are enriched in promoters with an "open" chromatin structure and are mostly at cohesin-enriched regions, suggesting that a local accumulation of cohesins might help to inhibit transcription. On the other hand, a dramatic loss of chromatin integrity by histone depletion during DNA replication has a moderate effect on the accumulation and distribution of cohesin peaks along the genome. CONCLUSIONS Our analyses of the interplay between chromatin integrity and cohesin activity suggest that cohesins play a major role in transcription regulation, which is associated with specific chromatin architecture and cohesin-mediated nucleosome alterations of the regulated promoters. In contrast, chromatin integrity plays only a minor role in the binding and distribution of cohesins.
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Affiliation(s)
- Douglas Maya-Miles
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - Eloísa Andújar
- Genomic Unit, Andalusian Molecular Biology and Regenerative Medicine Center (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
| | - Marina Murillo-Pineda
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
- Present Address: Department of Biochemistry, University of Oxford, Oxford, UK
| | - Marta Barrientos-Moreno
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - María J. Cabello-Lobato
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
- Present Address: Division of Cancer Sciences, Manchester Cancer Research Center, University of Manchester, Manchester, UK
| | - Elena Gómez-Marín
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - Macarena Morillo-Huesca
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine (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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Zhang J, Peng W, Wang L. LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks. Bioinformatics 2019; 34:1705-1712. [PMID: 29329398 PMCID: PMC5946947 DOI: 10.1093/bioinformatics/bty003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 01/09/2018] [Indexed: 11/17/2022] Open
Abstract
Motivation Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome-wide nucleosome occupancy profiles and computational tools to the analysis on these data, the complex language of eukaryotic Nucleosome positioning remains incompletely understood. Results Here, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) to understand nucleosome positioning. We combined Inception-like networks with a gating mechanism for the response of multiple patterns and long term association in DNA sequences. We developed the open-source package LeNup based on the CNN to predict nucleosome positioning in Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster as well as Saccharomyces cerevisiae genomes. We trained LeNup on four benchmark datasets. LeNup achieved greater predictive accuracy than previously published methods. Availability and implementation LeNup is freely available as Python and Lua script source code under a BSD style license from https://github.com/biomedBit/LeNup. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juhua Zhang
- Department of Biomedical Engineering.,Key Laboratory of Convergence Medical Engineering System and Healthcare Technology of the Ministry of Industry and Information Technology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | | | - Lei Wang
- Department of Biomedical Engineering
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Yao G, He J, Kong Y, Zhai J, Xu Y, Yang G, Kong D, Dong F, Shi S, Yang Q, Sun Y. Transcriptional profiling of long noncoding RNAs and their target transcripts in ovarian cortical tissues from women with normal menstrual cycles and primary ovarian insufficiency. Mol Reprod Dev 2019; 86:847-861. [PMID: 31094033 DOI: 10.1002/mrd.23158] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 03/23/2019] [Accepted: 04/11/2019] [Indexed: 01/22/2023]
Abstract
Previous studies have shown that long noncoding RNAs (lncRNAs) show a highly tissue- and disease-specific expression pattern and that they regulate the expression of neighboring genes. Because lncRNAs have been shown to be secreted into the general circulation, they may be used as diagnostic tools for some diseases. Primary ovarian insufficiency (POI) is a disease in which women have menstrual cessation before the age of 40, accompanied by elevated follicle stimulating hormone and decreased estrogen levels. In this study, ovarian cortical tissues from five women with normal menstrual cycles and from five POI patients were used for next-generation RNA sequencing. We found 20 differentially expressed lncRNAs with 12 upregulated and eight downregulated lncRNAs in cortical tissues of POI ovaries, compared with normal controls (fold change ≥ 2 and false discovery rate[FDR] ≤ 0.05). We also found 52 differentially expressed messenger RNA transcripts, with 33 upregulated and 19 downregulated ones (foldchange ≥ 2 and FDR ≤ 0.05). Functional annotation showed that these differentially expressed transcripts were associated with follicular development and granulosa cell function. Thirteen differentially expressed lncRNAs and their targeted neighboring transcripts were coregulated in ovarian cortical tissues, including lnc-ADAMTS1-1:1/ADAMTS1, lnc-PHLDA3-3:2/CSRP1, lnc-COL1A1-5:1/COL1A1, lnc-SAMD14-5:3/COL1A1, and lnc-GULP1-2:1/COL3A1. Furthermore, serum levels of these lncRNAs in POI patients were significantly different from those in normal patients ( p < 0.05), and expression differences were consistent with those in ovarian cortical tissues. This study showed that key lncRNAs were differentially expressed in both ovarian cortical tissues and serum samples between women with normal menstrual cycles and POI patients. Further studies on the regulation of ovarian lncRNAs during follicular development are critical in understanding the etiologies of POI. Analyses of lncRNA expression in serum samples might provide a basis for early diagnosis and treatment of POI.
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Affiliation(s)
- Guidong Yao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiahuan He
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yue Kong
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Zhai
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yijiang Xu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guang Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Deqi Kong
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fangli Dong
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Senlin Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qingling Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingpu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Replication fork stalling elicits chromatin compaction for the stability of stalling replication forks. Proc Natl Acad Sci U S A 2019; 116:14563-14572. [PMID: 31262821 DOI: 10.1073/pnas.1821475116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA replication forks in eukaryotic cells stall at a variety of replication barriers. Stalling forks require strict cellular regulations to prevent fork collapse. However, the mechanism underlying these cellular regulations is poorly understood. In this study, a cellular mechanism was uncovered that regulates chromatin structures to stabilize stalling forks. When replication forks stall, H2BK33, a newly identified acetylation site, is deacetylated and H3K9 trimethylated in the nucleosomes surrounding stalling forks, which results in chromatin compaction around forks. Acetylation-mimic H2BK33Q and its deacetylase clr6-1 mutations compromise this fork stalling-induced chromatin compaction, cause physical separation of replicative helicase and DNA polymerases, and significantly increase the frequency of stalling fork collapse. Furthermore, this fork stalling-induced H2BK33 deacetylation is independent of checkpoint. In summary, these results suggest that eukaryotic cells have developed a cellular mechanism that stabilizes stalling forks by targeting nucleosomes and inducing chromatin compaction around stalling forks. This mechanism is named the "Chromsfork" control: Chromatin Compaction Stabilizes Stalling Replication Forks.
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Zhou Z, Wei W. Interrogating the noncoding genome in a high-throughput fashion. Natl Sci Rev 2019; 6:397-399. [PMID: 34691889 PMCID: PMC8291450 DOI: 10.1093/nsr/nwy138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhuo Zhou
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, China
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, China
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The histone chaperoning pathway: from ribosome to nucleosome. Essays Biochem 2019; 63:29-43. [PMID: 31015382 PMCID: PMC6484783 DOI: 10.1042/ebc20180055] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022]
Abstract
Nucleosomes represent the fundamental repeating unit of eukaryotic DNA, and comprise eight core histones around which DNA is wrapped in nearly two superhelical turns. Histones do not have the intrinsic ability to form nucleosomes; rather, they require an extensive repertoire of interacting proteins collectively known as ‘histone chaperones’. At a fundamental level, it is believed that histone chaperones guide the assembly of nucleosomes through preventing non-productive charge-based aggregates between the basic histones and acidic cellular components. At a broader level, histone chaperones influence almost all aspects of chromatin biology, regulating histone supply and demand, governing histone variant deposition, maintaining functional chromatin domains and being co-factors for histone post-translational modifications, to name a few. In this essay we review recent structural insights into histone-chaperone interactions, explore evidence for the existence of a histone chaperoning ‘pathway’ and reconcile how such histone-chaperone interactions may function thermodynamically to assemble nucleosomes and maintain chromatin homeostasis.
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Li S, Dong Z, Yang S, Feng J, Li Q. Chaperoning RPA during DNA metabolism. Curr Genet 2019; 65:857-864. [PMID: 30796471 DOI: 10.1007/s00294-019-00945-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/17/2022]
Abstract
Single-stranded DNA (ssDNA) is widely generated during DNA metabolisms including DNA replication, repair and recombination and is susceptible to digestion by nucleases and secondary structure formation. It is vital for DNA metabolism and genome stability that ssDNA is protected and stabilized, which are performed by the major ssDNA-binding protein, and replication protein A (RPA) in these processes. In addition, RPA-coated ssDNA also serves as a protein-protein-binding platform for coordinating multiple events during DNA metabolisms. However, little is known about whether and how the formation of RPA-ssDNA platform is regulated. Here we highlight our recent study of a novel RPA-binding protein, Regulator of Ty1 transposition 105 (Rtt105) in Saccharomyces cerevisiae, which regulates the RPA-ssDNA platform assembly at replication forks. We propose that Rtt105 functions as an "RPA chaperone" during DNA replication, likely also promoting the assembly of RPA-ssDNA platform in other processes in which RPA plays a critical role.
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Affiliation(s)
- Shuqi 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.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.,Laboratory of Host-Pathogen Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Ziqi Dong
- 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
| | - Shuangshuang Yang
- 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
| | - Jianxun Feng
- 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
| | - 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. .,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
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Fournier LA, Kumar A, Stirling PC. Chromatin as a Platform for Modulating the Replication Stress Response. Genes (Basel) 2018; 9:genes9120622. [PMID: 30544989 PMCID: PMC6316668 DOI: 10.3390/genes9120622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic DNA replication occurs in the context of chromatin. Recent years have seen major advances in our understanding of histone supply, histone recycling and nascent histone incorporation during replication. Furthermore, much is now known about the roles of histone remodellers and post-translational modifications in replication. It has also become clear that nucleosome dynamics during replication play critical roles in genome maintenance and that chromatin modifiers are important for preventing DNA replication stress. An understanding of how cells deploy specific nucleosome modifiers, chaperones and remodellers directly at sites of replication fork stalling has been building more slowly. Here we will specifically discuss recent advances in understanding how chromatin composition contribute to replication fork stability and restart.
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Affiliation(s)
| | - Arun Kumar
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 1L3, Canada.
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Zou T, Hashiya F, Wei Y, Yu Z, Pandian GN, Sugiyama H. Direct Observation of H3-H4 Octasome by High-Speed AFM. Chemistry 2018; 24:15998-16002. [DOI: 10.1002/chem.201804010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Tingting Zou
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Fumitaka Hashiya
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Yulei Wei
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Zutao Yu
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of Science; Graduate School of Science; Kyoto University, Sakyo; Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8501 Japan
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