1
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DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep 2022; 38:110555. [PMID: 35320711 PMCID: PMC9283007 DOI: 10.1016/j.celrep.2022.110555] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mutational signatures defined by single base substitution (SBS) patterns in cancer have elucidated potential mutagenic processes that contribute to malignancy. Two prevalent mutational patterns in human cancers are attributed to the APOBEC3 cytidine deaminase enzymes. Among the seven human APOBEC3 proteins, APOBEC3A is a potent deaminase and proposed driver of cancer mutagenesis. In this study, we prospectively examine genome-wide aberrations by expressing human APOBEC3A in avian DT40 cells. From whole-genome sequencing, we detect hundreds to thousands of base substitutions per genome. The APOBEC3A signature includes widespread cytidine mutations and a unique insertion-deletion (indel) signature consisting largely of cytidine deletions. This multi-dimensional APOBEC3A signature is prevalent in human cancer genomes. Our data further reveal replication-associated mutations, the rate of stem-loop and clustered mutations, and deamination of methylated cytidines. This comprehensive signature of APOBEC3A mutagenesis is a tool for future studies and a potential biomarker for APOBEC3 activity in cancer.
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Affiliation(s)
- Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nataliya Petryk
- Epigenetics & Cell Fate UMR7216, CNRS, University of Paris, 35 rue Hélène Brion, 75013 Paris, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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2
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Petryk N, Reverón-Gómez N, González-Aguilera C, Dalby M, Andersson R, Groth A. Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq. Nat Protoc 2021; 16:4446-4493. [PMID: 34363071 DOI: 10.1038/s41596-021-00585-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/07/2021] [Indexed: 11/09/2022]
Abstract
Elucidating the mechanisms underlying chromatin maintenance upon genome replication is critical for the understanding of how gene expression programs and cell identity are preserved across cell divisions. Here, we describe two recently developed techniques, chromatin occupancy after replication (ChOR)-seq and sister chromatids after replication (SCAR)-seq, that profile chromatin occupancy on newly replicated DNA in mammalian cells in 5 d of bench work. Both techniques share a common strategy that includes pulse labeling of newly synthesized DNA and chromatin immunoprecipitation (ChIP), followed by purification and high-throughput sequencing. Whereas ChOR-seq quantitatively profiles the post-replicative abundance of histone modifications and chromatin-associated proteins, SCAR-seq distinguishes chromatin occupancy between nascent sister chromatids. Together, these two complementary techniques have unraveled key mechanisms controlling the inheritance of modified histones during replication and revealed locus-specific dynamics of histone modifications across the cell cycle. Here, we provide the experimental protocols and bioinformatic pipelines for these methods.
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Affiliation(s)
- Nataliya Petryk
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cristina González-Aguilera
- Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), University of Seville-CSIC-University Pablo de Olavide, Andalusian Government, Seville, Spain.,Department of Cellular Biology, University of Seville, Seville, Spain
| | - Maria Dalby
- The Bioinformatics Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.,H. Lundbeck A/S, Valby, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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3
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Blin M, Lacroix L, Petryk N, Jaszczyszyn Y, Chen CL, Hyrien O, Le Tallec B. DNA molecular combing-based replication fork directionality profiling. Nucleic Acids Res 2021; 49:e69. [PMID: 33836085 PMCID: PMC8266662 DOI: 10.1093/nar/gkab219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/15/2021] [Accepted: 03/19/2021] [Indexed: 01/05/2023] Open
Abstract
The replication strategy of metazoan genomes is still unclear, mainly because definitive maps of replication origins are missing. High-throughput methods are based on population average and thus may exclusively identify efficient initiation sites, whereas inefficient origins go undetected. Single-molecule analyses of specific loci can detect both common and rare initiation events along the targeted regions. However, these usually concentrate on positioning individual events, which only gives an overview of the replication dynamics. Here, we computed the replication fork directionality (RFD) profiles of two large genes in different transcriptional states in chicken DT40 cells, namely untranscribed and transcribed DMD and CCSER1 expressed at WT levels or overexpressed, by aggregating hundreds of oriented replication tracks detected on individual DNA fibres stretched by molecular combing. These profiles reconstituted RFD domains composed of zones of initiation flanking a zone of termination originally observed in mammalian genomes and were highly consistent with independent population-averaging profiles generated by Okazaki fragment sequencing. Importantly, we demonstrate that inefficient origins do not appear as detectable RFD shifts, explaining why dispersed initiation has remained invisible to population-based assays. Our method can both generate quantitative profiles and identify discrete events, thereby constituting a comprehensive approach to study metazoan genome replication.
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Affiliation(s)
- Marion Blin
- Département de Gastro-entérologie, pôle MAD, Assistance Publique des Hôpitaux de Marseille, Centre Hospitalier Universitaire de Marseille, Marseille, France
| | - Laurent Lacroix
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, F-75005 Paris, France
| | - Nataliya Petryk
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, F-75005 Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), F-91198 Gif-sur-Yvette, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, F-75005 Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, F-75005 Paris, France
| | - Benoît Le Tallec
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, F-75005 Paris, France
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4
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Petryk N, Bultmann S, Bartke T, Defossez PA. Staying true to yourself: mechanisms of DNA methylation maintenance in mammals. Nucleic Acids Res 2021; 49:3020-3032. [PMID: 33300031 PMCID: PMC8034647 DOI: 10.1093/nar/gkaa1154] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022] Open
Abstract
DNA methylation is essential to development and cellular physiology in mammals. Faulty DNA methylation is frequently observed in human diseases like cancer and neurological disorders. Molecularly, this epigenetic mark is linked to other chromatin modifications and it regulates key genomic processes, including transcription and splicing. Each round of DNA replication generates two hemi-methylated copies of the genome. These must be converted back to symmetrically methylated DNA before the next S-phase, or the mark will fade away; therefore the maintenance of DNA methylation is essential. Mechanistically, the maintenance of this epigenetic modification takes place during and after DNA replication, and occurs within the very dynamic context of chromatin re-assembly. Here, we review recent discoveries and unresolved questions regarding the mechanisms, dynamics and fidelity of DNA methylation maintenance in mammals. We also discuss how it could be regulated in normal development and misregulated in disease.
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Affiliation(s)
- Nataliya Petryk
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, F-75013 Paris, France
| | - Sebastian Bultmann
- Department of Biology II, Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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5
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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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6
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Wu X, Kabalane H, Kahli M, Petryk N, Laperrousaz B, Jaszczyszyn Y, Drillon G, Nicolini FE, Perot G, Robert A, Fund C, Chibon F, Xia R, Wiels J, Argoul F, Maguer-Satta V, Arneodo A, Audit B, Hyrien O. Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions. Nucleic Acids Res 2019; 46:10157-10172. [PMID: 30189101 PMCID: PMC6212843 DOI: 10.1093/nar/gky797] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/24/2018] [Indexed: 01/08/2023] Open
Abstract
The spatiotemporal program of metazoan DNA replication is regulated during development and altered in cancers. We have generated novel OK-seq, Repli-seq and RNA-seq data to compare the DNA replication and gene expression programs of twelve cancer and non-cancer human cell types. Changes in replication fork directionality (RFD) determined by OK-seq are widespread but more frequent within GC-poor isochores and largely disconnected from transcription changes. Cancer cell RFD profiles cluster with non-cancer cells of similar developmental origin but not with different cancer types. Importantly, recurrent RFD changes are detected in specific tumour progression pathways. Using a model for establishment and early progression of chronic myeloid leukemia (CML), we identify 1027 replication initiation zones (IZs) that progressively change efficiency during long-term expression of the BCR-ABL1 oncogene, being twice more often downregulated than upregulated. Prolonged expression of BCR-ABL1 results in targeting of new IZs and accentuation of previous efficiency changes. Targeted IZs are predominantly located in GC-poor, late replicating gene deserts and frequently silenced in late CML. Prolonged expression of BCR-ABL1 results in massive deletion of GC-poor, late replicating DNA sequences enriched in origin silencing events. We conclude that BCR-ABL1 expression progressively affects replication and stability of GC-poor, late-replicating regions during CML progression.
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Affiliation(s)
- Xia Wu
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France.,Physics Department, East China Normal University, Shanghai, China
| | - Hadi Kabalane
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Malik Kahli
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Nataliya Petryk
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Bastien Laperrousaz
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342 Lyon, France.,CNRS UMR5286, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F- 69008 Lyon, France
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Guenola Drillon
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Frank-Emmanuel Nicolini
- CNRS UMR5286, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F- 69008 Lyon, France.,Centre Léon Bérard, F-69008 Lyon, France
| | - Gaëlle Perot
- INSERM U1218, Institut Bergonié, F-33000 Bordeaux, France
| | - Aude Robert
- UMR 8126, Université Paris-Sud Paris-Saclay, CNRS, Institut Gustave Roussy, Villejuif, France
| | - Cédric Fund
- École Normale Supérieure, PSL Research University, CNRS, Inserm, IBENS, Plateforme Génomique, 75005 Paris, France
| | | | - Ruohong Xia
- Physics Department, East China Normal University, Shanghai, China
| | - Joëlle Wiels
- UMR 8126, Université Paris-Sud Paris-Saclay, CNRS, Institut Gustave Roussy, Villejuif, France
| | - Françoise Argoul
- LOMA, Université de Bordeaux, CNRS, UMR 5798, F-33405 Talence, France
| | - Véronique Maguer-Satta
- CNRS UMR5286, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F- 69008 Lyon, France
| | - Alain Arneodo
- LOMA, Université de Bordeaux, CNRS, UMR 5798, F-33405 Talence, France
| | - Benjamin Audit
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Olivier Hyrien
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
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7
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Reverón-Gómez N, González-Aguilera C, Stewart-Morgan KR, Petryk N, Flury V, Graziano S, Johansen JV, Jakobsen JS, Alabert C, Groth A. Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication. Mol Cell 2018; 72:239-249.e5. [PMID: 30146316 PMCID: PMC6202308 DOI: 10.1016/j.molcel.2018.08.010] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/25/2018] [Accepted: 08/07/2018] [Indexed: 12/22/2022]
Abstract
Chromatin organization is disrupted genome-wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naive histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is faithfully copied during DNA replication or the epigenome is perturbed. Here we develop chromatin occupancy after replication (ChOR-seq) to determine histone PTM occupancy immediately after DNA replication and across the cell cycle. We show that H3K4me3, H3K36me3, H3K79me3, and H3K27me3 positional information is reproduced with high accuracy on newly synthesized DNA through histone recycling. Quantitative ChOR-seq reveals that de novo methylation to restore H3K4me3 and H3K27me3 levels occurs across the cell cycle with mark- and locus-specific kinetics. Collectively, this demonstrates that accurate parental histone recycling preserves positional information and allows PTM transmission to daughter cells while modification of new histones gives rise to complex epigenome fluctuations across the cell cycle that could underlie cell-to-cell heterogeneity.
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Affiliation(s)
- Nazaret Reverón-Gómez
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Cristina González-Aguilera
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kathleen R Stewart-Morgan
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Valentin Flury
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Simona Graziano
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Janus Schou Jakobsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Constance Alabert
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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8
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Wu X, Kabalane H, Kahli M, Petryk N, Laperrousaz B, Jaszczyszyn Y, Drillon G, Nicolini FE, Perot G, Robert A, Fund C, Chibon F, Xia R, Wiels J, Argoul F, Maguer-Satta V, Arneodo A, Audit B, Hyrien O. Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions. Nucleic Acids Res 2018; 46:10532. [PMID: 30212853 PMCID: PMC6212835 DOI: 10.1093/nar/gky849] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xia Wu
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France.,Physics Department, East China Normal University, Shanghai, China
| | - Hadi Kabalane
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Malik Kahli
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Nataliya Petryk
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Bastien Laperrousaz
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342 Lyon, France.,CNRS UMR5286, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F- 69008 Lyon, France
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Guenola Drillon
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Frank-Emmanuel Nicolini
- CNRS UMR5286, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F- 69008 Lyon, France.,Centre Léon Bérard, F-69008 Lyon, France
| | - Gaëlle Perot
- INSERM U1218, Institut Bergonié, F-33000 Bordeaux, France
| | - Aude Robert
- UMR 8126, Université Paris-Sud Paris-Saclay, CNRS, Institut Gustave Roussy, Villejuif, France
| | - Cédric Fund
- École Normale Supérieure, PSL Research University, CNRS, Inserm, IBENS, Plateforme Génomique, 75005 Paris, France
| | | | - Ruohong Xia
- Physics Department, East China Normal University, Shanghai, China
| | - Joëlle Wiels
- UMR 8126, Université Paris-Sud Paris-Saclay, CNRS, Institut Gustave Roussy, Villejuif, France
| | - Françoise Argoul
- LOMA, Université de Bordeaux, CNRS, UMR 5798, F-33405 Talence, France
| | - Véronique Maguer-Satta
- CNRS UMR5286, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, F- 69008 Lyon, France
| | - Alain Arneodo
- LOMA, Université de Bordeaux, CNRS, UMR 5798, F-33405 Talence, France
| | - Benjamin Audit
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Olivier Hyrien
- Institut de Biologie de l'École Normale Supérieure (IBENS), Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
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9
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Petryk N, Dalby M, Wenger A, Stromme CB, Strandsby A, Andersson R, Groth A. MCM2 promotes symmetric inheritance of modified histones during DNA replication. Science 2018; 361:1389-1392. [PMID: 30115746 DOI: 10.1126/science.aau0294] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/06/2018] [Indexed: 12/13/2022]
Abstract
During genome replication, parental histones are recycled to newly replicated DNA with their posttranslational modifications (PTMs). Whether sister chromatids inherit modified histones evenly remains unknown. We measured histone PTM partition to sister chromatids in embryonic stem cells. We found that parental histones H3-H4 segregate to both daughter DNA strands with a weak leading-strand bias, skewing partition at topologically associating domain (TAD) borders and enhancers proximal to replication initiation zones. Segregation of parental histones to the leading strand increased markedly in cells with histone-binding mutations in MCM2, part of the replicative helicase, exacerbating histone PTM sister chromatid asymmetry. This work reveals how histones are inherited to sister chromatids and identifies a mechanism by which the replication machinery ensures symmetric cell division.
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Affiliation(s)
- Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Maria Dalby
- The Bioinformatics Centre, Department of Biology, Faculty of Science, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alice Wenger
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Caroline B Stromme
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne Strandsby
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, Faculty of Science, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark. .,Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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10
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Petryk N, Kahli M, d'Aubenton-Carafa Y, Jaszczyszyn Y, Shen Y, Silvain M, Thermes C, Chen CL, Hyrien O. Replication landscape of the human genome. Nat Commun 2016; 7:10208. [PMID: 26751768 PMCID: PMC4729899 DOI: 10.1038/ncomms10208] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 11/13/2015] [Indexed: 12/21/2022] Open
Abstract
Despite intense investigation, human replication origins and termini remain elusive. Existing data have shown strong discrepancies. Here we sequenced highly purified Okazaki fragments from two cell types and, for the first time, quantitated replication fork directionality and delineated initiation and termination zones genome-wide. Replication initiates stochastically, primarily within non-transcribed, broad (up to 150 kb) zones that often abut transcribed genes, and terminates dispersively between them. Replication fork progression is significantly co-oriented with the transcription. Initiation and termination zones are frequently contiguous, sometimes separated by regions of unidirectional replication. Initiation zones are enriched in open chromatin and enhancer marks, even when not flanked by genes, and often border ‘topologically associating domains' (TADs). Initiation zones are enriched in origin recognition complex (ORC)-binding sites and better align to origins previously mapped using bubble-trap than λ-exonuclease. This novel panorama of replication reveals how chromatin and transcription modulate the initiation process to create cell-type-specific replication programs. The physical origin and termination sites of DNA replication in human cells have remained elusive. Here the authors use Okazaki fragment sequencing to reveal global replication patterns and show how chromatin and transcription modulate the process.
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Affiliation(s)
- Nataliya Petryk
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, 46 rue d'Ulm, Paris F-75005, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Malik Kahli
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, 46 rue d'Ulm, Paris F-75005, France
| | - Yves d'Aubenton-Carafa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Yan Jaszczyszyn
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Yimin Shen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Maud Silvain
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Claude Thermes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Chun-Long Chen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, UMR 9198, FRC 3115, Avenue de la Terrasse, Bâtiment 24, Gif-sur-Yvette, Paris F-91198, France
| | - Olivier Hyrien
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, 46 rue d'Ulm, Paris F-75005, France
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Petryk N, Zhou YF, Sybirna K, Mucchielli MH, Guiard B, Bao WG, Stasyk OV, Stasyk OG, Krasovska OS, Budin K, Reymond N, Imbeaud S, Coudouel S, Delacroix H, Sibirny A, Bolotin-Fukuhara M. Functional study of the Hap4-like genes suggests that the key regulators of carbon metabolism HAP4 and oxidative stress response YAP1 in yeast diverged from a common ancestor. PLoS One 2014; 9:e112263. [PMID: 25479159 PMCID: PMC4257542 DOI: 10.1371/journal.pone.0112263] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 10/06/2014] [Indexed: 12/05/2022] Open
Abstract
The transcriptional regulator HAP4, induced by respiratory substrates, is involved in the balance between fermentation and respiration in S. cerevisiae. We identified putative orthologues of the Hap4 protein in all ascomycetes, based only on a conserved sixteen amino acid-long motif. In addition to this motif, some of these proteins contain a DNA-binding motif of the bZIP type, while being nonetheless globally highly divergent. The genome of the yeast Hansenula polymorpha contains two HAP4-like genes encoding the protein HpHap4-A which, like ScHap4, is devoid of a bZIP motif, and HpHap4-B which contains it. This species has been chosen for a detailed examination of their respective properties. Based mostly on global gene expression studies performed in the S. cerevisiae HAP4 disruption mutant (ScΔhap4), we show here that HpHap4-A is functionally equivalent to ScHap4, whereas HpHap4-B is not. Moreover HpHAP4-B is able to complement the H2O2 hypersensitivity of the ScYap1 deletant, YAP1 being, in S. cerevisiae, the main regulator of oxidative stress. Finally, a transcriptomic analysis performed in the ScΔyap1 strain overexpressing HpHAP4-B shows that HpHap4-B acts both on oxidative stress response and carbohydrate metabolism in a manner different from both ScYap1 and ScHap4. Deletion of these two genes in their natural host, H. polymorpha, confirms that HpHAP4-A participates in the control of the fermentation/respiration balance, while HpHAP4-B is involved in oxidative stress since its deletion leads to hypersensitivity to H2O2. These data, placed in an evolutionary context, raise new questions concerning the evolution of the HAP4 transcriptional regulation function and suggest that Yap1 and Hap4 have diverged from a unique regulatory protein in the fungal ancestor.
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Affiliation(s)
- Nataliya Petryk
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
- Institute of Cell Biology, National Academy of Sciences, Lviv, Ukraine
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | - You-Fang Zhou
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
| | - Kateryna Sybirna
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
| | - Marie-Hélène Mucchielli
- Gif/Orsay DNA MicroArray Platform, Gif sur Yvette, France
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | - Bernard Guiard
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | - Wei-Guo Bao
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
| | - Oleh V. Stasyk
- Institute of Cell Biology, National Academy of Sciences, Lviv, Ukraine
| | - Olena G. Stasyk
- Institute of Cell Biology, National Academy of Sciences, Lviv, Ukraine
- Department of Biochemistry, Ivan Franko Lviv National University, Lviv, Ukraine
| | | | - Karine Budin
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
- Gif/Orsay DNA MicroArray Platform, Gif sur Yvette, France
| | - Nancie Reymond
- Gif/Orsay DNA MicroArray Platform, Gif sur Yvette, France
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | | | | | - Hervé Delacroix
- Gif/Orsay DNA MicroArray Platform, Gif sur Yvette, France
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, France
| | - Andriy Sibirny
- Institute of Cell Biology, National Academy of Sciences, Lviv, Ukraine
- University of Rzeszow, Rzeszow, Poland
| | - Monique Bolotin-Fukuhara
- Institut de Génétique et Microbiologie, IFR Génome 115, Université Paris-Sud and CNRS, Orsay, France
- * E-mail:
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Hyrien O, Rappailles A, Guilbaud G, Baker A, Chen CL, Goldar A, Petryk N, Kahli M, Ma E, d'Aubenton-Carafa Y, Audit B, Thermes C, Arneodo A. From simple bacterial and archaeal replicons to replication N/U-domains. J Mol Biol 2013; 425:4673-89. [PMID: 24095859 DOI: 10.1016/j.jmb.2013.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/15/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The Replicon Theory proposed 50 years ago has proven to apply for replicons of the three domains of life. Here, we review our knowledge of genome organization into single and multiple replicons in bacteria, archaea and eukarya. Bacterial and archaeal replicator/initiator systems are quite specific and efficient, whereas eukaryotic replicons show degenerate specificity and efficiency, allowing for complex regulation of origin firing time. We expand on recent evidence that ~50% of the human genome is organized as ~1,500 megabase-sized replication domains with a characteristic parabolic (U-shaped) replication timing profile and linear (N-shaped) gradient of replication fork polarity. These N/U-domains correspond to self-interacting segments of the chromatin fiber bordered by open chromatin zones and replicate by cascades of origin firing initiating at their borders and propagating to their center, possibly by fork-stimulated initiation. The conserved occurrence of this replication pattern in the germline of mammals has resulted over evolutionary times in the formation of megabase-sized domains with an N-shaped nucleotide compositional skew profile due to replication-associated mutational asymmetries. Overall, these results reveal an evolutionarily conserved but developmentally plastic organization of replication that is driving mammalian genome evolution.
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Affiliation(s)
- Olivier Hyrien
- Ecole Normale Supérieure, IBENS UMR8197 U1024, Paris 75005, France.
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Sybirna K, Petryk N, Zhou YF, Sibirny A, Bolotin-Fukuhara M. A novel Hansenula polymorpha transcriptional factor HpHAP4-B, able to functionally replace the S. cerevisiae HAP4 gene, contains an additional bZip motif. Yeast 2010; 27:941-54. [DOI: 10.1002/yea.1802] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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