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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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2
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Fenstermaker TK, Petruk S, Mazo A. An emerging paradigm in epigenetic marking: coordination of transcription and replication. Transcription 2024; 15:22-37. [PMID: 38378467 DOI: 10.1080/21541264.2024.2316965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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3
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Yakoub G, Luijsterburg MS. Transcription and replication: walking a genomic tightrope hand-in-hand. Trends Biochem Sci 2023; 48:1012-1013. [PMID: 37775422 DOI: 10.1016/j.tibs.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
A recent study by Fenstermaker et al. in Nature describes how transcriptionally active RNA polymerase II (Pol II) clings to the genomic tightrope during the passage of the replication fork and rapidly resumes transcription of immature RNA from both strands of nascent DNA, facilitated by protein-protein interactions between the replication and transcription machineries.
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Affiliation(s)
- George Yakoub
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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4
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Fenstermaker TK, Petruk S, Kovermann SK, Brock HW, Mazo A. RNA polymerase II associates with active genes during DNA replication. Nature 2023; 620:426-433. [PMID: 37468626 DOI: 10.1038/s41586-023-06341-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
The transcriptional machinery is thought to dissociate from DNA during replication. Certain proteins, termed epigenetic marks, must be transferred from parent to daughter DNA strands in order to maintain the memory of transcriptional states1,2. These proteins are believed to re-initiate rebuilding of chromatin structure, which ultimately recruits RNA polymerase II (Pol II) to the newly replicated daughter strands. It is believed that Pol II is recruited back to active genes only after chromatin is rebuilt3,4. However, there is little experimental evidence addressing the central questions of when and how Pol II is recruited back to the daughter strands and resumes transcription. Here we show that immediately after passage of the replication fork, Pol II in complex with other general transcription proteins and immature RNA re-associates with active genes on both leading and lagging strands of nascent DNA, and rapidly resumes transcription. This suggests that the transcriptionally active Pol II complex is retained in close proximity to DNA, with a Pol II-PCNA interaction potentially underlying this retention. These findings indicate that the Pol II machinery may not require epigenetic marks to be recruited to the newly synthesized DNA during the transition from DNA replication to resumption of transcription.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sina K Kovermann
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hugh W Brock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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5
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Wang L, Xue M, Zhang H, Ma L, Jiang D. TONSOKU is required for the maintenance of repressive chromatin modifications in Arabidopsis. Cell Rep 2023; 42:112738. [PMID: 37393621 DOI: 10.1016/j.celrep.2023.112738] [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: 04/13/2023] [Revised: 05/17/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023] Open
Abstract
The stability of eukaryotic genomes relies on the faithful transmission of DNA sequences and the maintenance of chromatin states through DNA replication. Plant TONSOKU (TSK) and its animal ortholog TONSOKU-like (TONSL) act as readers for newly synthesized histones and preserve DNA integrity via facilitating DNA repair at post-replicative chromatin. However, whether TSK/TONSL regulate the maintenance of chromatin states remains elusive. Here, we show that TSK is dispensable for global histone and nucleosome accumulation but necessary for maintaining repressive chromatin modifications, including H3K9me2, H2A.W, H3K27me3, and DNA methylation. TSK physically interacts with H3K9 methyltransferases and Polycomb proteins. Moreover, TSK mutation strongly enhances defects in Polycomb pathway mutants. TSK is intended to only associate with nascent chromatin until it starts to mature. We propose that TSK ensures the preservation of chromatin states by supporting the recruitment of chromatin modifiers to post-replicative chromatin in a critical short window of time following DNA replication.
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Affiliation(s)
- Lin Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mande Xue
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huairen Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijun Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Basta MD, Petruk S, Summer R, Rosenbloom J, Wermuth PJ, Macarak E, Levin AV, Mazo A, Walker JL. Changes in nascent chromatin structure regulate activation of the pro-fibrotic transcriptome and myofibroblast emergence in organ fibrosis. iScience 2023; 26:106570. [PMID: 37250334 PMCID: PMC10214303 DOI: 10.1016/j.isci.2023.106570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/03/2023] [Accepted: 03/29/2023] [Indexed: 05/31/2023] Open
Abstract
Cell reprogramming to a myofibroblast responsible for the pathological accumulation of extracellular matrix is fundamental to the onset of fibrosis. Here, we explored how condensed chromatin structure marked by H3K72me3 becomes modified to allow for activation of repressed genes to drive emergence of myofibroblasts. In the early stages of myofibroblast precursor cell differentiation, we discovered that H3K27me3 demethylase enzymes UTX/KDM6B creates a delay in the accumulation of H3K27me3 on nascent DNA revealing a period of decondensed chromatin structure. This period of decondensed nascent chromatin structure allows for binding of pro-fibrotic transcription factor, Myocardin-related transcription factor A (MRTF-A) to nascent DNA. Inhibition of UTX/KDM6B enzymatic activity condenses chromatin structure, prevents MRTF-A binding, blocks activation of the pro-fibrotic transcriptome, and results in an inhibition of fibrosis in lens and lung fibrosis models. Our work reveals UTX/KDM6B as central coordinators of fibrosis, highlighting the potential to target its demethylase activity to prevent organ fibrosis.
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Affiliation(s)
- Morgan D. Basta
- Department of Pathology and Genomic Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ross Summer
- Center for Translational Medicine, The Jane and Leonard Korman Respiratory Institute at the Sidney Kimmel Medial College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Joel Rosenbloom
- Department of Dermatology and Cutaneous Biology, The Joan and Joel Rosenbloom Research Center for Fibrotic Diseases, Sidney Kimmel Medical College Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Peter J. Wermuth
- Department of Dermatology and Cutaneous Biology, The Joan and Joel Rosenbloom Research Center for Fibrotic Diseases, Sidney Kimmel Medical College Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Edward Macarak
- Department of Dermatology and Cutaneous Biology, The Joan and Joel Rosenbloom Research Center for Fibrotic Diseases, Sidney Kimmel Medical College Thomas Jefferson University, Philadelphia, PA 19107, USA
| | | | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Janice L. Walker
- Department of Pathology and Genomic Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
- Department of Ophthalmology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
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7
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Lovejoy CM, Nagarajan P, Parthun MR. Dynamic Reassociation of the Nuclear Lamina with Newly Replicated DNA. RESEARCH SQUARE 2023:rs.3.rs-2846826. [PMID: 37215015 PMCID: PMC10197746 DOI: 10.21203/rs.3.rs-2846826/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The physical association of specific regions of chromatin with components of the nuclear lamina provides the framework for the 3-dimensionl architecture of the genome. The regulation of these interactions plays a critical role in the maintenance of gene expression patterns and cell identity. The breakdown and reassembly of the nuclear membrane as cells transit mitosis plays a central role in the regulation of the interactions between the genome and the nuclear lamina. However, other nuclear processes, such as transcription, have emerged as regulators of the association of DNA with the nuclear lamina. To determine whether DNA replication also has the potential to regulate DNA-nuclear lamina interactions, we adapted proximity ligation-based chromatin assembly assays to analyze the dynamics of nuclear lamina association with newly replicated DNA. We observe that lamin A/C and lamin B, as well as inner nuclear membrane proteins LBR and emerin, are found in proximity to newly replicated DNA. While core histones rapidly reassociate with DNA following passage of the replication fork, the complete reassociation of nuclear lamina components with newly replicated DNA occurs over a period of approximately 30 minutes. We propose models to describe the disassembly and reassembly of nascent chromatin with the nuclear lamina.
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8
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Moore CE, Yalcindag SE, Czeladko H, Ravindranathan R, Wijesekara Hanthi Y, Levy JC, Sannino V, Schindler D, Ciccia A, Costanzo V, Elia AE. RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks. J Cell Biol 2023; 222:e202106022. [PMID: 37036693 PMCID: PMC10097976 DOI: 10.1083/jcb.202106022] [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: 06/03/2021] [Revised: 09/05/2022] [Accepted: 01/30/2023] [Indexed: 04/11/2023] Open
Abstract
Replication fork reversal is an important mechanism to protect the stability of stalled forks and thereby preserve genomic integrity. While multiple enzymes have been identified that can remodel forks, their regulation remains poorly understood. Here, we demonstrate that the ubiquitin ligase RFWD3, whose mutation causes Fanconi Anemia, promotes recruitment of the DNA translocase ZRANB3 to stalled replication forks and ubiquitinated sites of DNA damage. Using electron microscopy, we show that RFWD3 stimulates fork remodeling in a ZRANB3-epistatic manner. Fork reversal is known to promote nascent DNA degradation in BRCA2-deficient cells. Consistent with a role for RFWD3 in fork reversal, inactivation of RFWD3 in these cells rescues fork degradation and collapse, analogous to ZRANB3 inactivation. RFWD3 loss impairs ZRANB3 localization to spontaneous nuclear foci induced by inhibition of the PCNA deubiquitinase USP1. We demonstrate that RFWD3 promotes PCNA ubiquitination and interaction with ZRANB3, providing a mechanism for RFWD3-dependent recruitment of ZRANB3. Together, these results uncover a new role for RFWD3 in regulating ZRANB3-dependent fork remodeling.
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Affiliation(s)
- Chandler E. Moore
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Selin E. Yalcindag
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hanna Czeladko
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ramya Ravindranathan
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yodhara Wijesekara Hanthi
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Juliana C. Levy
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vincenzo Sannino
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Detlev Schindler
- Department of Human Genetics, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Alberto Ciccia
- Department of Genetics and Development, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM ETS, The AIRC Institute for Molecular Oncology, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy
| | - Andrew E.H. Elia
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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9
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Lebdy R, Patouillard J, Larroque M, Urbach S, Abou Merhi R, Larroque C, Ribeyre C. The organizer of chromatin topology RIF1 ensures cellular resilience to DNA replication stress. Life Sci Alliance 2023; 6:e202101186. [PMID: 36746532 PMCID: PMC9906048 DOI: 10.26508/lsa.202101186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
Eukaryotic genomes are duplicated from thousands of replication origins that fire sequentially forming a defined spatiotemporal pattern of replication clusters. The temporal order of DNA replication is determined by chromatin architecture and, more specifically, by chromatin contacts that are stabilized by RIF1. Here, we show that RIF1 localizes near newly synthesized DNA. In cells exposed to the DNA replication inhibitor aphidicolin, suppression of RIF1 markedly decreased the efficacy of isolation of proteins on nascent DNA, suggesting that the isolation of proteins on nascent DNA procedure is biased by chromatin topology. RIF1 was required to limit the accumulation of DNA lesions induced by aphidicolin treatment and promoted the recruitment of cohesins in the vicinity of nascent DNA. Collectively, the data suggest that the stabilization of chromatin topology by RIF1 limits replication-associated genomic instability.
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Affiliation(s)
- Rana Lebdy
- Institut de Génétique Humaine, CNRS UMR9002, Université de Montpellier, Montpellier, France
- Doctoral School of Sciences and Technology-DSST, Rafic Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Julie Patouillard
- Institut de Génétique Humaine, CNRS UMR9002, Université de Montpellier, Montpellier, France
| | | | - Serge Urbach
- Institut de Génomique Fonctionnelle, CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Raghida Abou Merhi
- Doctoral School of Sciences and Technology-DSST, Rafic Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Christian Larroque
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
| | - Cyril Ribeyre
- Institut de Génétique Humaine, CNRS UMR9002, Université de Montpellier, Montpellier, France
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10
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Lambros M, Sella Y, Bergman A. Phenotypic pliancy and the breakdown of epigenetic polycomb mechanisms. PLoS Comput Biol 2023; 19:e1010889. [PMID: 36809239 PMCID: PMC9983867 DOI: 10.1371/journal.pcbi.1010889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 03/03/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023] Open
Abstract
Epigenetic regulatory mechanisms allow multicellular organisms to develop distinct specialized cell identities despite having the same total genome. Cell-fate choices are based on gene expression programs and environmental cues that cells experience during embryonic development, and are usually maintained throughout the life of the organism despite new environmental cues. The evolutionarily conserved Polycomb group (PcG) proteins form Polycomb Repressive Complexes that help orchestrate these developmental choices. Post-development, these complexes actively maintain the resulting cell fate, even in the face of environmental perturbations. Given the crucial role of these polycomb mechanisms in providing phenotypic fidelity (i.e. maintenance of cell fate), we hypothesize that their dysregulation after development will lead to decreased phenotypic fidelity allowing dysregulated cells to sustainably switch their phenotype in response to environmental changes. We call this abnormal phenotypic switching phenotypic pliancy. We introduce a general computational evolutionary model that allows us to test our systems-level phenotypic pliancy hypothesis in-silico and in a context-independent manner. We find that 1) phenotypic fidelity is an emergent systems-level property of PcG-like mechanism evolution, and 2) phenotypic pliancy is an emergent systems-level property resulting from this mechanism's dysregulation. Since there is evidence that metastatic cells behave in a phenotypically pliant manner, we hypothesize that progression to metastasis is driven by the emergence of phenotypic pliancy in cancer cells as a result of PcG mechanism dysregulation. We corroborate our hypothesis using single-cell RNA-sequencing data from metastatic cancers. We find that metastatic cancer cells are phenotypically pliant in the same manner as predicted by our model.
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Affiliation(s)
- Maryl Lambros
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yehonatan Sella
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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11
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Replication gap suppression depends on the double-strand DNA binding activity of BRCA2. Nat Commun 2023; 14:446. [PMID: 36707518 PMCID: PMC9883520 DOI: 10.1038/s41467-023-36149-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Replication stress (RS) is a major source of genomic instability and is intrinsic to cancer cells. RS is also the consequence of chemotherapeutic drugs for treating cancer. However, adaptation to RS is also a mechanism of resistance to chemotherapy. BRCA2 deficiency results in replication stress in human cells. BRCA2 protein's main functions include DNA repair by homologous recombination (HR) both at induced DNA double-strand breaks (DSB) and spontaneous replicative lesions. At stalled replication forks, BRCA2 protects the DNA from aberrant nucleolytic degradation and is thought to limit the appearance of ssDNA gaps by arresting replication and via post-replicative HR. However, whether and how BRCA2 acts to limit the formation of ssDNA gaps or mediate their repair, remains ill-defined. Here, we use breast cancer variants affecting different domains of BRCA2 to shed light on this function. We demonstrate that the N-terminal DNA binding domain (NTD), and specifically, its dsDNA binding activity, is required to prevent and repair/fill-in ssDNA gaps upon nucleotide depletion but not to limit PARPi-induced ssDNA gaps. Thus, these findings suggest that nucleotide depletion and PARPi trigger gaps via distinct mechanisms and that the NTD of BRCA2 prevents nucleotide depletion-induced ssDNA gaps.
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12
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Rothi MH, Greer EL. From correlation to causation: The new frontier of transgenerational epigenetic inheritance. Bioessays 2023; 45:e2200118. [PMID: 36351255 PMCID: PMC9772138 DOI: 10.1002/bies.202200118] [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: 06/16/2022] [Revised: 10/03/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022]
Abstract
While heredity is predominantly controlled by what deoxyribonucleic acid (DNA) sequences are passed from parents to their offspring, a small but growing number of traits have been shown to be regulated in part by the non-genetic inheritance of information. Transgenerational epigenetic inheritance is defined as heritable information passed from parents to their offspring without changing the DNA sequence. Work of the past seven decades has transitioned what was previously viewed as rare phenomenology, into well-established paradigms by which numerous traits can be modulated. For the most part, studies in model organisms have correlated transgenerational epigenetic inheritance phenotypes with changes in epigenetic modifications. The next steps for this field will entail transitioning from correlative studies to causal ones. Here, we delineate the major molecules that have been implicated in transgenerational epigenetic inheritance in both mammalian and non-mammalian models, speculate on additional molecules that could be involved, and highlight some of the tools which might help transition this field from correlation to causation.
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Affiliation(s)
- M. Hafiz Rothi
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
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13
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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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14
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Zhu C, Iwase M, Li Z, Wang F, Quinet A, Vindigni A, Shao J. Profilin-1 regulates DNA replication forks in a context-dependent fashion by interacting with SNF2H and BOD1L. Nat Commun 2022; 13:6531. [PMID: 36319634 PMCID: PMC9626489 DOI: 10.1038/s41467-022-34310-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/21/2022] [Indexed: 12/04/2022] Open
Abstract
DNA replication forks are tightly controlled by a large protein network consisting of well-known core regulators and many accessory factors which remain functionally undefined. In this study, we report previously unknown nuclear functions of the actin-binding factor profilin-1 (PFN1) in DNA replication, which occur in a context-dependent fashion and require its binding to poly-L-proline (PLP)-containing proteins instead of actin. In unperturbed cells, PFN1 increases DNA replication initiation and accelerates fork progression by binding and stimulating the PLP-containing nucleosome remodeler SNF2H. Under replication stress, PFN1/SNF2H increases fork stalling and functionally collaborates with fork reversal enzymes to enable the over-resection of unprotected forks. In addition, PFN1 binds and functionally attenuates the PLP-containing fork protector BODL1 to increase the resection of a subset of stressed forks. Accordingly, raising nuclear PFN1 level decreases genome stability and cell survival during replication stress. Thus, PFN1 is a multi-functional regulator of DNA replication with exploitable anticancer potential.
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Affiliation(s)
- Cuige Zhu
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mari Iwase
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ziqian Li
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Faliang Wang
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Annabel Quinet
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- UMR Genetic Stability Stem Cells and Radiation, University of Paris and University of Paris-Saclay, INSERM, iRCM/IBFJ CEA, Fontenay-aux-Roses, France
| | - Alessandro Vindigni
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jieya Shao
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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15
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Nguyen NH, Vu NT, Cheong JJ. Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants. Int J Mol Sci 2022; 23:12918. [PMID: 36361708 PMCID: PMC9654142 DOI: 10.3390/ijms232112918] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2023] Open
Abstract
Plants respond to drought stress by producing abscisic acid, a chemical messenger that regulates gene expression and thereby expedites various physiological and cellular processes including the stomatal operation to mitigate stress and promote tolerance. To trigger or suppress gene transcription under drought stress conditions, the surrounding chromatin architecture must be converted between a repressive and active state by epigenetic remodeling, which is achieved by the dynamic interplay among DNA methylation, histone modifications, loop formation, and non-coding RNA generation. Plants can memorize chromatin status under drought conditions to enable them to deal with recurrent stress. Furthermore, drought tolerance acquired during plant growth can be transmitted to the next generation. The epigenetically modified chromatin architectures of memory genes under stressful conditions can be transmitted to newly developed cells by mitotic cell division, and to germline cells of offspring by overcoming the restraints on meiosis. In mammalian cells, the acquired memory state is completely erased and reset during meiosis. The mechanism by which plant cells overcome this resetting during meiosis to transmit memory is unclear. In this article, we review recent findings on the mechanism underlying transcriptional stress memory and the transgenerational inheritance of drought tolerance in plants.
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Affiliation(s)
- Nguyen Hoai Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam
| | - Nam Tuan Vu
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
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16
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Identification of unique DNA methylation sites in Kabuki syndrome using whole genome bisulfite sequencing and targeted hybridization capture followed by enzymatic methylation sequencing. J Hum Genet 2022; 67:711-720. [PMID: 36167771 DOI: 10.1038/s10038-022-01083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/01/2022] [Accepted: 09/11/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND Kabuki syndrome (KS) is a congenital malformation syndrome caused by mutations in the KMT2D and KDM6A genes that encode histone modification enzymes. Although KS is considered a single gene disorder, its symptoms vary widely. Recently, disease-specific DNA methylation patterns, or episignatures, have been recognized and used as a diagnostic tool for KS. Because of various crosstalk mechanisms between histone modifications and DNA methylation, DNA methylation analysis may have high potential for investigations into the pathogenesis of KS. RESULTS In this study, we investigated altered CpG-methylation sites that were specific to KS to find important genes associated with the various phenotypes or pathogenesis of KS. Whole genome bisulfite sequencing (WGBS) was performed to select target CpG islands, and enzymatic conversion technology was applied after hybridization capture to confirm KS-specific episignatures of 130 selected differently methylated target regions (DMTRs) in DNA samples from the 65 participants, 31 patients with KS and 34 unaffected individuals, in this study. We identified 26 candidate genes in 22 DMTRs that may be associated with KS. Our results indicate that disease-specific methylation sites can be identified from a small number of WGBS samples, and hybridization capture followed by enzymatic methylation sequencing can simultaneously test the sites. CONCLUSIONS Although DNA methylation can be tissue-specific, our results suggest that methylation profiling of DNA extracted from peripheral blood may be a powerful approach to study the pathogenesis of diseases.
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17
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Saxton DS, Rine J. Distinct silencer states generate epigenetic states of heterochromatin. Mol Cell 2022; 82:3566-3579.e5. [PMID: 36041432 DOI: 10.1016/j.molcel.2022.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/23/2022] [Accepted: 07/30/2022] [Indexed: 11/26/2022]
Abstract
Heterochromatic loci can exhibit different transcriptional states in genetically identical cells. A popular model posits that the inheritance of modified histones is sufficient for inheritance of the silenced state. However, silencing inheritance requires silencers and therefore cannot be driven by the inheritance of modified histones alone. To address these observations, we determined the chromatin architectures produced by strong and weak silencers in Saccharomyces. Strong silencers recruited Sir proteins and silenced the locus in all cells. Strikingly, weakening these silencers reduced Sir protein recruitment and stably silenced the locus in some cells; however, this silenced state could probabilistically convert to an expressed state that lacked Sir protein recruitment. Additionally, changes in the constellation of silencer-bound proteins or the concentration of a structural Sir protein modulated the probability that a locus exhibited the silenced or expressed state. These findings argued that distinct silencer states generate epigenetic states and regulate their dynamics.
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Affiliation(s)
- Daniel S Saxton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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18
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Krajewski WA. Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to “Functionalize” Nucleosomes. Front Genet 2022; 13:873398. [PMID: 35571051 PMCID: PMC9096104 DOI: 10.3389/fgene.2022.873398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 12/25/2022] Open
Abstract
Tight packaging of DNA in chromatin severely constrains DNA accessibility and dynamics. In contrast, nucleosomes in active chromatin state are highly flexible, can exchange their histones, and are virtually “transparent” to RNA polymerases, which transcribe through gene bodies at rates comparable to that of naked DNA. Defining mechanisms that revert nucleosome repression, in addition to their value for basic science, is of key importance for the diagnosis and treatment of genetic diseases. Chromatin activity is largely regulated by histone posttranslational modifications, ranging from small chemical groups up to the yet understudied “bulky” ubiquitylation and sumoylation. However, it is to be revealed how histone marks are “translated” to permissive or repressive changes in nucleosomes: it is a general opinion that histone modifications act primarily as “signals” for recruiting the regulatory proteins or as a “neutralizer” of electrostatic shielding of histone tails. Here, we would like to discuss recent evidence suggesting that histone ubiquitylation, in a DNA stress–dependent manner, can directly regulate the dynamics of the nucleosome and their primary structure and can promote nucleosome decomposition to hexasome particles or additionally stabilize nucleosomes against unwrapping. In addition, nucleosome repression/ derepression studies are usually performed with single mononucleosomes as a model. We would like to review and discuss recent findings showing that internucleosomal interactions could strongly modulate the dynamics and rearrangements of nucleosomes. Our hypothesis is that bulky histone modifications, nucleosome inherent dynamics, internucleosome interactions, and DNA torsions could act in cooperation to orchestrate the formation of different dynamic states of arrayed nucleosomes and thus promote chromatin functionality and diversify epigenetic programming methods.
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19
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Porazzi P, Petruk S, Pagliaroli L, De Dominici M, Deming D, Puccetti MV, Kushinsky S, Kumar G, Minieri V, Barbieri E, Deliard S, Grande A, Trizzino M, Gardini A, Canaani E, Palmisiano N, Porcu P, Ertel A, Fortina PM, Eischen CM, Mazo A, Calabretta B. Targeting chemotherapy to de-condensed H3K27me3-marked chromatin of AML cells enhances leukemia suppression. Cancer Res 2021; 82:458-471. [PMID: 34903608 DOI: 10.1158/0008-5472.can-21-1297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 09/15/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022]
Abstract
Despite treatment with intensive chemotherapy, acute myeloid leukemia (AML) remains an aggressive malignancy with a dismal outcome in most patients. We found that AML cells exhibit an unusually rapid accumulation of the repressive histone mark H3K27me3 on nascent DNA. In cell lines, primary cells and xenograft mouse models, inhibition of the H3K27 histone methyltransferase EZH2 to de-condense the H3K27me3-marked chromatin of AML cells enhanced chromatin accessibility and chemotherapy-induced DNA damage, apoptosis, and leukemia suppression. These effects were further promoted when chromatin de-condensation of AML cells was induced upon S-phase entry after release from a transient G1 arrest mediated by CDK4/6 inhibition. In the p53-null KG-1 and THP-1 AML cell lines, EZH2 inhibitor and doxorubicin co-treatment induced transcriptional reprogramming that was, in part, dependent on de-repression of H3K27me3-marked gene promoters and led to increased expression of cell death-promoting and growth-inhibitory genes. In conclusion, decondensing H3K27me3-marked chromatin by EZH2 inhibition represents a promising approach to improve the efficacy of DNA-damaging cytotoxic agents in AML patients. This strategy might allow for a lowering of chemotherapy doses with a consequent reduction of treatment-related side effects in elderly AML patients or those with significant comorbidities.
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Affiliation(s)
- Patrizia Porazzi
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Luca Pagliaroli
- Department of Biochemistry and Molecular Biology and Sidney Kimmel Cancer Center,, Thomas Jefferson University
| | | | - David Deming
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Matthew V Puccetti
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Saul Kushinsky
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Gaurav Kumar
- Department of Cancer Biology, Thomas Jefferson University
| | - Valentina Minieri
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
| | - Elisa Barbieri
- Gene Expression and Regulation Program, The Wistar Institute
| | - Sandra Deliard
- Gene Expression and Regulation Program, The Wistar Institute
| | - Alexis Grande
- Department of Life Sciences, University of Modena and Reggio Emilia
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | | | - Eli Canaani
- The Department of Molecular Cell Biology, Weizmann Institute of Science
| | | | | | - Adam Ertel
- Department of Cancer Biology, Thomas Jefferson University
| | | | | | - Alexander Mazo
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center,, Thomas Jefferson University
| | - Bruno Calabretta
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University
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20
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Lin CYG, Näger AC, Lunardi T, Vančevska A, Lossaint G, Lingner J. The human telomeric proteome during telomere replication. Nucleic Acids Res 2021; 49:12119-12135. [PMID: 34747482 PMCID: PMC8643687 DOI: 10.1093/nar/gkab1015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Telomere shortening can cause detrimental diseases and contribute to aging. It occurs due to the end replication problem in cells lacking telomerase. Furthermore, recent studies revealed that telomere shortening can be attributed to difficulties of the semi-conservative DNA replication machinery to replicate the bulk of telomeric DNA repeats. To investigate telomere replication in a comprehensive manner, we develop QTIP-iPOND - Quantitative Telomeric chromatin Isolation Protocol followed by isolation of Proteins On Nascent DNA - which enables purification of proteins that associate with telomeres specifically during replication. In addition to the core replisome, we identify a large number of proteins that specifically associate with telomere replication forks. Depletion of several of these proteins induces telomere fragility validating their importance for telomere replication. We also find that at telomere replication forks the single strand telomere binding protein POT1 is depleted, whereas histone H1 is enriched. Our work reveals the dynamic changes of the telomeric proteome during replication, providing a valuable resource of telomere replication proteins. To our knowledge, this is the first study that examines the replisome at a specific region of the genome.
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Affiliation(s)
- Chih-Yi Gabriela Lin
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anna Christina Näger
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Thomas Lunardi
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Aleksandra Vančevska
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Gérald Lossaint
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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21
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Temporally distinct post-replicative repair mechanisms fill PRIMPOL-dependent ssDNA gaps in human cells. Mol Cell 2021; 81:4026-4040.e8. [PMID: 34624216 DOI: 10.1016/j.molcel.2021.09.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/20/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022]
Abstract
PRIMPOL repriming allows DNA replication to skip DNA lesions, leading to ssDNA gaps. These gaps must be filled to preserve genome stability. Using a DNA fiber approach to directly monitor gap filling, we studied the post-replicative mechanisms that fill the ssDNA gaps generated in cisplatin-treated cells upon increased PRIMPOL expression or when replication fork reversal is defective because of SMARCAL1 inactivation or PARP inhibition. We found that a mechanism dependent on the E3 ubiquitin ligase RAD18, PCNA monoubiquitination, and the REV1 and POLζ translesion synthesis polymerases promotes gap filling in G2. The E2-conjugating enzyme UBC13, the RAD51 recombinase, and REV1-POLζ are instead responsible for gap filling in S, suggesting that temporally distinct pathways of gap filling operate throughout the cell cycle. Furthermore, we found that BRCA1 and BRCA2 promote gap filling by limiting MRE11 activity and that simultaneously targeting fork reversal and gap filling enhances chemosensitivity in BRCA-deficient cells.
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22
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The Paramount Role of Drosophila melanogaster in the Study of Epigenetics: From Simple Phenotypes to Molecular Dissection and Higher-Order Genome Organization. INSECTS 2021; 12:insects12100884. [PMID: 34680653 PMCID: PMC8537509 DOI: 10.3390/insects12100884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 01/06/2023]
Abstract
Simple Summary Since its adoption as a model organism more than a hundred years ago, the fruit fly Drosophila melanogaster has led to major discoveries in biology, notably in epigenetics. Epigenetics studies the changes in gene function inherited through mitosis or meiosis that are not due to modifications in the DNA sequence. The first discoveries in epigenetics emerged from analyses of the perturbations of simple phenotypes such as the bristle position or cuticle pigmentation. Identification of the mutated genes led to the discovery of major chromatin regulators, which were found to be conserved in other insects, and unexpectedly, in all metazoans. Many of them deposit post-translational modifications on histones, the proteins around which the DNA is wrapped. Others are chromatin remodeling complexes that move, eject, or exchange nucleosomes. We review here the role of D. melanogaster research in three important epigenetic fields: The formation of heterochromatin, the repression of mobile DNA elements by small RNAs, and the regulation of gene expression by the antagonistic Polycomb and Trithorax complexes. We then review how genetic tools available in D. melanogaster have allowed us to examine the role of histone marks and led to more global discoveries on chromatin organization. Lastly, we discuss the impact of varying environmental conditions on epigenetic regulation. Abstract Drosophila melanogaster has played a paramount role in epigenetics, the study of changes in gene function inherited through mitosis or meiosis that are not due to changes in the DNA sequence. By analyzing simple phenotypes, such as the bristle position or cuticle pigmentation, as read-outs of regulatory processes, the identification of mutated genes led to the discovery of major chromatin regulators. These are often conserved in distantly related organisms such as vertebrates or even plants. Many of them deposit, recognize, or erase post-translational modifications on histones (histone marks). Others are members of chromatin remodeling complexes that move, eject, or exchange nucleosomes. We review the role of D. melanogaster research in three epigenetic fields: Heterochromatin formation and maintenance, the repression of transposable elements by piRNAs, and the regulation of gene expression by the antagonistic Polycomb and Trithorax complexes. We then describe how genetic tools available in D. melanogaster allowed to examine the role of histone marks and show that some histone marks are dispensable for gene regulation, whereas others play essential roles. Next, we describe how D. melanogaster has been particularly important in defining chromatin types, higher-order chromatin structures, and their dynamic changes during development. Lastly, we discuss the role of epigenetics in a changing environment.
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23
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Burton NO, Greer EL. Multigenerational epigenetic inheritance: Transmitting information across generations. Semin Cell Dev Biol 2021; 127:121-132. [PMID: 34426067 DOI: 10.1016/j.semcdb.2021.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023]
Abstract
Inherited epigenetic information has been observed to regulate a variety of complex organismal phenotypes across diverse taxa of life. This continually expanding body of literature suggests that epigenetic inheritance plays a significant, and potentially fundamental, role in inheritance. Despite the important role these types of effects play in biology, the molecular mediators of this non-genetic transmission of information are just now beginning to be deciphered. Here we provide an intellectual framework for interpreting these findings and how they can interact with each other. We also define the different types of mechanisms that have been found to mediate epigenetic inheritance and to regulate whether epigenetic information persists for one or many generations. The field of epigenetic inheritance is entering an exciting phase, in which we are beginning to understand the mechanisms by which non-genetic information is transmitted to, and deciphered by, subsequent generations to maintain essential environmental information without permanently altering the genetic code. A more complete understanding of how and when epigenetic inheritance occurs will advance our understanding of numerous different aspects of biology ranging from how organisms cope with changing environments to human pathologies influenced by a parent's environment.
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Affiliation(s)
- Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Eric L Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.
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24
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Ihle M, Biber S, Schroeder IS, Blattner C, Deniz M, Damia G, Gottifredi V, Wiesmüller L. Impact of the interplay between stemness features, p53 and pol iota on replication pathway choices. Nucleic Acids Res 2021; 49:7457-7475. [PMID: 34165573 PMCID: PMC8287946 DOI: 10.1093/nar/gkab526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Using human embryonic, adult and cancer stem cells/stem cell-like cells (SCs), we demonstrate that DNA replication speed differs in SCs and their differentiated counterparts. While SCs decelerate DNA replication, differentiated cells synthesize DNA faster and accumulate DNA damage. Notably, both replication phenotypes depend on p53 and polymerase iota (POLι). By exploring protein interactions and newly synthesized DNA, we show that SCs promote complex formation of p53 and POLι at replication sites. Intriguingly, in SCs the translocase ZRANB3 is recruited to POLι and required for slow-down of DNA replication. The known role of ZRANB3 in fork reversal suggests that the p53–POLι complex mediates slow but safe bypass of replication barriers in SCs. In differentiated cells, POLι localizes more transiently to sites of DNA synthesis and no longer interacts with p53 facilitating fast POLι-dependent DNA replication. In this alternative scenario, POLι associates with the p53 target p21, which antagonizes PCNA poly-ubiquitination and, thereby potentially disfavors the recruitment of translocases. Altogether, we provide evidence for diametrically opposed DNA replication phenotypes in SCs and their differentiated counterparts putting DNA replication-based strategies in the spotlight for the creation of therapeutic opportunities targeting SCs.
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Affiliation(s)
- Michaela Ihle
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Stephanie Biber
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Insa S Schroeder
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt 64291, Germany
| | - Christine Blattner
- Institute for Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Karlsruhe 76021, Germany
| | - Miriam Deniz
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Giovanna Damia
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS Milan, Milan 20156, Italy
| | - Vanesa Gottifredi
- Cell cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, Buenos Aires C1405BWE, Argentina
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
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25
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The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival. Chromosoma 2021; 130:215-234. [PMID: 34331109 PMCID: PMC8426247 DOI: 10.1007/s00412-021-00762-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
Abstract
The Drosophila Trithorax group (TrxG) protein ASH1 remains associated with mitotic chromatin through mechanisms that are poorly understood. ASH1 dimethylates histone H3 at lysine 36 via its SET domain. Here, we identify domains of the TrxG protein ASH1 that are required for mitotic chromatin attachment in living Drosophila. Quantitative live imaging demonstrates that ASH1 requires AT hooks and the BAH domain but not the SET domain for full chromatin binding in metaphase, and that none of these domains are essential for interphase binding. Genetic experiments show that disruptions of the AT hooks and the BAH domain together, but not deletion of the SET domain alone, are lethal. Transcriptional profiling demonstrates that intact ASH1 AT hooks and the BAH domain are required to maintain expression levels of a specific set of genes, including several involved in cell identity and survival. This study identifies in vivo roles for specific ASH1 domains in mitotic binding, gene regulation, and survival that are distinct from its functions as a histone methyltransferase.
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26
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Zhang P, Zhu C, Geng Y, Wang Y, Yang Y, Liu Q, Guo W, Chachar S, Riaz A, Yan S, Yang L, Yi K, Wu C, Gu X. Rice and Arabidopsis homologs of yeast CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4 commonly interact with Polycomb complexes but exert divergent regulatory functions. THE PLANT CELL 2021; 33:1417-1429. [PMID: 33647940 PMCID: PMC8254485 DOI: 10.1093/plcell/koab047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/29/2021] [Indexed: 05/02/2023]
Abstract
Both genetic and epigenetic information must be transferred from mother to daughter cells during cell division. The mechanisms through which information about chromatin states and epigenetic marks like histone 3 lysine 27 trimethylation (H3K27me3) are transferred have been characterized in animals; these processes are less well understood in plants. Here, based on characterization of a dwarf rice (Oryza sativa) mutant (dwarf-related wd40 protein 1, drw1) deficient for yeast CTF4 (CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4), we discovered that CTF4 orthologs in plants use common cellular machinery yet accomplish divergent functional outcomes. Specifically, drw1 exhibited no flowering-related phenotypes (as in the putatively orthologous Arabidopsis thaliana eol1 mutant), but displayed cell cycle arrest and DNA damage responses. Mechanistically, we demonstrate that DRW1 sustains normal cell cycle progression by modulating the expression of cell cycle inhibitors KIP-RELATED PROTEIN 1 (KRP1) and KRP5, and show that these effects are mediated by DRW1 binding their promoters and increasing H3K27me3 levels. Thus, although CTF4 orthologs ENHANCER OF LHP1 1 (EOL1) in Arabidopsis and DRW1 in rice are both expressed uniquely in dividing cells, commonly interact with several Polycomb complex subunits, and promote H3K27me3 deposition, we now know that their regulatory functions diverged substantially during plant evolution. Moreover, our work experimentally illustrates specific targets of CTF4/EOL1/DRW1, their protein-proteininteraction partners, and their chromatin/epigenetic effects in plants.
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Affiliation(s)
- Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunmei Zhu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuke Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ying Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sadaruddin Chachar
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Adeel Riaz
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Author for correspondence: (K.Y.), (C.W.), (X.G.)
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Author for correspondence: (K.Y.), (C.W.), (X.G.)
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Author for correspondence: (K.Y.), (C.W.), (X.G.)
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27
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Kummeling J, Stremmelaar DE, Raun N, Reijnders MRF, Willemsen MH, Ruiterkamp-Versteeg M, Schepens M, Man CCO, Gilissen C, Cho MT, McWalter K, Sinnema M, Wheless JW, Simon MEH, Genetti CA, Casey AM, Terhal PA, van der Smagt JJ, van Gassen KLI, Joset P, Bahr A, Steindl K, Rauch A, Keller E, Raas-Rothschild A, Koolen DA, Agrawal PB, Hoffman TL, Powell-Hamilton NN, Thiffault I, Engleman K, Zhou D, Bodamer O, Hoefele J, Riedhammer KM, Schwaibold EMC, Tasic V, Schubert D, Top D, Pfundt R, Higgs MR, Kramer JM, Kleefstra T. Characterization of SETD1A haploinsufficiency in humans and Drosophila defines a novel neurodevelopmental syndrome. Mol Psychiatry 2021; 26:2013-2024. [PMID: 32346159 DOI: 10.1038/s41380-020-0725-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/18/2022]
Abstract
Defects in histone methyltransferases (HMTs) are major contributing factors in neurodevelopmental disorders (NDDs). Heterozygous variants of SETD1A involved in histone H3 lysine 4 (H3K4) methylation were previously identified in individuals with schizophrenia. Here, we define the clinical features of the Mendelian syndrome associated with haploinsufficiency of SETD1A by investigating 15 predominantly pediatric individuals who all have de novo SETD1A variants. These individuals present with a core set of symptoms comprising global developmental delay and/or intellectual disability, subtle facial dysmorphisms, behavioral and psychiatric problems. We examined cellular phenotypes in three patient-derived lymphoblastoid cell lines with three variants: p.Gly535Alafs*12, c.4582-2_4582delAG, and p.Tyr1499Asp. These patient cell lines displayed DNA damage repair defects that were comparable to previously observed RNAi-mediated depletion of SETD1A. This suggested that these variants, including the p.Tyr1499Asp in the catalytic SET domain, behave as loss-of-function (LoF) alleles. Previous studies demonstrated a role for SETD1A in cell cycle control and differentiation. However, individuals with SETD1A variants do not show major structural brain defects or severe microcephaly, suggesting that defective proliferation and differentiation of neural progenitors is unlikely the single underlying cause of the disorder. We show here that the Drosophila melanogaster SETD1A orthologue is required in postmitotic neurons of the fly brain for normal memory, suggesting a role in post development neuronal function. Together, this study defines a neurodevelopmental disorder caused by dominant de novo LoF variants in SETD1A and further supports a role for H3K4 methyltransferases in the regulation of neuronal processes underlying normal cognitive functioning.
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Affiliation(s)
- Joost Kummeling
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Diante E Stremmelaar
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Nicholas Raun
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada
| | - Margot R F Reijnders
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6229 ER, Maastricht, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Martina Ruiterkamp-Versteeg
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Marga Schepens
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Calvin C O Man
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | | | - Margje Sinnema
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6229 ER, Maastricht, The Netherlands
| | - James W Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Memphis, TN, USA.,Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Casie A Genetti
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Alicia M Casey
- Division of Pulmonary and Respiratory Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jasper J van der Smagt
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Elmar Keller
- Division of Neuropediatrics, Cantonal Hospital Graubuenden, Chur, Switzerland
| | - Annick Raas-Rothschild
- Institute of Rare Disease, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Trevor L Hoffman
- Regional Department of Genetics, Southern California Kaiser Permanente Medical Group, 1188N. Euclid Street, Anaheim, CA, 92801, USA
| | - Nina N Powell-Hamilton
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.,Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.,Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Kendra Engleman
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Dihong Zhou
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Velibor Tasic
- Medical School Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Deniz Top
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jamie M Kramer
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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28
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Zarrizi R, Higgs MR, Voßgröne K, Rossing M, Bertelsen B, Bose M, Kousholt AN, Rösner H, Network TC, Ejlertsen B, Stewart GS, Nielsen FC, Sørensen CS. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability. J Clin Invest 2021; 130:4069-4080. [PMID: 32379725 DOI: 10.1172/jci127521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Haploinsufficiency of factors governing genome stability underlies hereditary breast and ovarian cancer. One significant pathway that is disabled as a result is homologous recombination repair (HRR). With the aim of identifying new candidate genes, we examined early-onset breast cancer patients negative for BRCA1 and BRCA2 pathogenic variants. Here, we focused on CtIP (RBBP8 gene), which mediates HRR through the end resection of DNA double-strand breaks (DSBs). Notably, these patients exhibited a number of rare germline RBBP8 variants. Functional analysis revealed that these variants did not affect DNA DSB end resection efficiency. However, expression of a subset of variants led to deleterious nucleolytic degradation of stalled DNA replication forks in a manner similar to that of cells lacking BRCA1 or BRCA2. In contrast to BRCA1 and BRCA2, CtIP deficiency promoted the helicase-driven destabilization of RAD51 nucleofilaments at damaged DNA replication forks. Taken together, our work identifies CtIP as a critical regulator of DNA replication fork integrity, which, when compromised, may predispose to the development of early-onset breast cancer.
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Affiliation(s)
- Reihaneh Zarrizi
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Karolin Voßgröne
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Birgitte Bertelsen
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Muthiah Bose
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Heike Rösner
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Finn Cilius Nielsen
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claus S Sørensen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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29
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Auboiron M, Vasseur P, Tonazzini S, Fall A, Castro FR, Sučec I, El Koulali K, Urbach S, Radman-Livaja M. TrIPP-a method for tracking the inheritance patterns of proteins in living cells-reveals retention of Tup1p, Fpr4p, and Rpd3L in the mother cell. iScience 2021; 24:102075. [PMID: 33644711 PMCID: PMC7889982 DOI: 10.1016/j.isci.2021.102075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/27/2020] [Accepted: 01/15/2021] [Indexed: 01/16/2023] Open
Abstract
Inheritance of chromatin-bound proteins theoretically plays a role in the epigenetic transmission of cellular phenotypes. Protein segregation during cell division is however poorly understood. We now describe TrIPP (Tracking the Inheritance Patterns of Proteins): a live cell imaging method for tracking maternal proteins during asymmetric cell divisions of budding yeast. Our analysis of the partitioning pattern of a test set of 18 chromatin-associated proteins reveals that abundant and moderately abundant maternal proteins segregate stochastically and symmetrically between the two cells with the exception of Rxt3p, Fpr4p, and Tup1p, which are preferentially retained in the mother. Low abundance proteins also tend to be retained in the mother cell with the exception of Sir2p and the linker histone H1. Our analysis of chromatin protein behavior in single cells reveals potentially general trends such as coupled protein synthesis and decay and a correlation between protein half-lives and cell-cycle duration.
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Affiliation(s)
- Morgane Auboiron
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Pauline Vasseur
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Saphia Tonazzini
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Arame Fall
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Francesc Rubert Castro
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Iva Sučec
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Khadija El Koulali
- Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France.,Functional Proteomics Platform, IGF _ CNRS INSERM, Université de Montpellier, 141 rue de la Cardonille, 34094 Montpellier cedex 5, France
| | - Serge Urbach
- Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France.,Functional Proteomics Platform, IGF _ CNRS INSERM, Université de Montpellier, 141 rue de la Cardonille, 34094 Montpellier cedex 5, France
| | - Marta Radman-Livaja
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.,Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
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30
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Shiu JL, Wu CK, Chang SB, Sun YJ, Chen YJ, Lai CC, Chiu WT, Chang WT, Myung K, Su WP, Liaw H. The HLTF-PARP1 interaction in the progression and stability of damaged replication forks caused by methyl methanesulfonate. Oncogenesis 2020; 9:104. [PMID: 33281189 PMCID: PMC7719709 DOI: 10.1038/s41389-020-00289-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/04/2020] [Accepted: 11/17/2020] [Indexed: 11/27/2022] Open
Abstract
Human HLTF participates in the lesion-bypass mechanism through the fork reversal structure, known as template switching of post-replication repair. However, the mechanism by which HLTF promotes the replication progression and fork stability of damaged forks remains unclear. Here, we identify a novel protein–protein interaction between HLTF and PARP1. The depletion of HLTF and PARP1 increases chromosome breaks, further reduces the length of replication tracks, and concomitantly increases the number of stalled forks after methyl methanesulfonate treatment according to a DNA fiber analysis. The progression of replication also depends on BARD1 in the presence of MMS treatment. By combining 5-ethynyl-2′-deoxyuridine with a proximity ligation assay, we revealed that the HLTF, PARP1, and BRCA1/BARD1/RAD51 proteins were initially recruited to damaged forks. However, prolonged stalling of damaged forks results in fork collapse. HLTF and PCNA dissociate from the collapsed forks, with increased accumulation of PARP1 and BRCA1/BARD1/RAD51 at the collapsed forks. Our results reveal that HLTF together with PARP1 and BARD1 participates in the stabilization of damaged forks, and the PARP1–BARD1 interaction is further involved in the repair of collapse forks.
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Affiliation(s)
- Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Cheng-Kuei Wu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan City, 704, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Yan-Jhih Sun
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Yen-Ju Chen
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, College of Life Science, National Chung Hsing University, No.145 Xingda Rd. South Dist., Taichung City, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Wen-Tsan Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Kyungjae Myung
- IBS Center for Genomic Integrity, UNIST-gil 50, Ulsan, 689-798, Republic of Korea
| | - Wen-Pin Su
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan City, 704, Taiwan. .,Departments of Oncology and Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, 704, Taiwan.
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan.
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31
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Sauty SM, Shaban K, Yankulov K. Gene repression in S. cerevisiae-looking beyond Sir-dependent gene silencing. Curr Genet 2020; 67:3-17. [PMID: 33037902 DOI: 10.1007/s00294-020-01114-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 01/09/2023]
Abstract
Gene silencing by the SIR (Silent Information Region) family of proteins in S. cerevisiae has been extensively studied and has served as a founding paradigm for our general understanding of gene repression and its links to histone deacetylation and chromatin structure. In recent years, our understanding of other mechanisms of gene repression in S.cerevisiae was significantly advanced. In this review, we focus on such Sir-independent mechanisms of gene repression executed by various Histone Deacetylases (HDACs) and Histone Methyl Transferases (HMTs). We focus on the genes regulated by these enzymes and their known mechanisms of action. We describe the cooperation and redundancy between HDACs and HMTs, and their involvement in gene repression by non-coding RNAs or by their non-histone substrates. We also propose models of epigenetic transmission of the chromatin structures produced by these enzymes and discuss these in the context of gene repression phenomena in other organisms. These include the recycling of the epigenetic marks imposed by HMTs or the recycling of the complexes harboring HDACs.
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Affiliation(s)
- Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
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32
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Kim S, Kang N, Park SH, Wells J, Hwang T, Ryu E, Kim BG, Hwang S, Kim SJ, Kang S, Lee S, Stirling P, Myung K, Lee KY. ATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork. Nucleic Acids Res 2020; 48:7218-7238. [PMID: 32542338 PMCID: PMC7367208 DOI: 10.1093/nar/gkaa501] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 12/27/2022] Open
Abstract
R-loops are formed when replicative forks collide with the transcriptional machinery and can cause genomic instability. However, it is unclear how R-loops are regulated at transcription-replication conflict (TRC) sites and how replisome proteins are regulated to prevent R-loop formation or mediate R-loop tolerance. Here, we report that ATAD5, a PCNA unloader, plays dual functions to reduce R-loops both under normal and replication stress conditions. ATAD5 interacts with RNA helicases such as DDX1, DDX5, DDX21 and DHX9 and increases the abundance of these helicases at replication forks to facilitate R-loop resolution. Depletion of ATAD5 or ATAD5-interacting RNA helicases consistently increases R-loops during the S phase and reduces the replication rate, both of which are enhanced by replication stress. In addition to R-loop resolution, ATAD5 prevents the generation of new R-loops behind the replication forks by unloading PCNA which, otherwise, accumulates and persists on DNA, causing a collision with the transcription machinery. Depletion of ATAD5 reduces transcription rates due to PCNA accumulation. Consistent with the role of ATAD5 and RNA helicases in maintaining genomic integrity by regulating R-loops, the corresponding genes were mutated or downregulated in several human tumors.
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Affiliation(s)
- Sangin Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Nalae Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - James Wells
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada
| | - Taejoo Hwang
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Seong-Jung Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
| | - Semin Lee
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Peter Stirling
- Terry Fox laboratory, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea
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33
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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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34
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Sato H, Singer RH, Greally JM. Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry. Bio Protoc 2020; 10:e3738. [PMID: 33043098 DOI: 10.21769/bioprotoc.3738] [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: 11/02/2022] Open
Abstract
Dynamic histone changes occur as a central part of chromatin regulation. Deposition of histone variants and post-translational modifications of histones are strongly associated with properties of chromatin status. Characterizing the kinetics of histone variants allows important insights into transcription regulation, chromatin maintenance and other chromatin properties. Here we provide a protocol of quantitative and sensitive approaches to test the timing of incorporation and dissociation of histones using a two-color SNAP-labeling system, labelling pre-existing and newly-incorporated histones distinctly. Together with cell cycle synchronization methods and cell cycle markers, this approach enables a pulse-chase analysis to determine the turnover of histone variants during the cell cycle, detected using imaging or flow cytometry methods at single cell resolution. As well as testing global histone turnover, cell cycle-dependent cellular localization of histone variants can be also addressed using imaging approaches.
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Affiliation(s)
- Hanae Sato
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA.,Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn. VA 20147, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave, Bronx, NY 10461, USA
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35
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Joseph SA, Taglialatela A, Leuzzi G, Huang JW, Cuella-Martin R, Ciccia A. Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease. DNA Repair (Amst) 2020; 95:102943. [PMID: 32971328 DOI: 10.1016/j.dnarep.2020.102943] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Over the course of DNA replication, DNA lesions, transcriptional intermediates and protein-DNA complexes can impair the progression of replication forks, thus resulting in replication stress. Failure to maintain replication fork integrity in response to replication stress leads to genomic instability and predisposes to the development of cancer and other genetic disorders. Multiple DNA damage and repair pathways have evolved to allow completion of DNA replication following replication stress, thus preserving genomic integrity. One of the processes commonly induced in response to replication stress is fork reversal, which consists in the remodeling of stalled replication forks into four-way DNA junctions. In normal conditions, fork reversal slows down replication fork progression to ensure accurate repair of DNA lesions and facilitates replication fork restart once the DNA lesions have been removed. However, in certain pathological situations, such as the deficiency of DNA repair factors that protect regressed forks from nuclease-mediated degradation, fork reversal can cause genomic instability. In this review, we describe the complex molecular mechanisms regulating fork reversal, with a focus on the role of the SNF2-family fork remodelers SMARCAL1, ZRANB3 and HLTF, and highlight the implications of fork reversal for tumorigenesis and cancer therapy.
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Affiliation(s)
- Sarah A Joseph
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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36
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Ridenour JB, Möller M, Freitag M. Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi. Genes (Basel) 2020; 11:E638. [PMID: 32527036 PMCID: PMC7348808 DOI: 10.3390/genes11060638] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.
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Affiliation(s)
| | | | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis OR 97331, USA; (J.B.R.); (M.M.)
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37
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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: 12] [Impact Index Per Article: 3.0] [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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38
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Morita S, Ota R, Hayashi M, Kobayashi S. Repression of G1/S Transition by Transient Inhibition of miR-10404 Expression in Drosophila Primordial Germ Cells. iScience 2020; 23:100950. [PMID: 32179474 PMCID: PMC7075979 DOI: 10.1016/j.isci.2020.100950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/20/2020] [Accepted: 02/24/2020] [Indexed: 01/30/2023] Open
Abstract
Cell-cycle quiescence is a common feature of early germline development in many animal species. In Drosophila germline progenitors (pole cells), both G2/M and G1/S transitions are blocked. G2/M transition is repressed by maternal Nanos through suppression of Cyclin B production. However, the molecular mechanism underlying blockage of G1/S transition remains elusive. We found that repression of miR-10404 expression is required to block G1/S transition in pole cells. Expression of miR-10404, a microRNA encoded within the internal transcribed spacer 1 of rDNA, is repressed in early pole cells by maternal polar granule component. This repression delays the degradation of maternal dacapo mRNA, which encodes an inhibitor of G1/S transition. Moreover, derepression of G1/S transition in pole cells causes defects in their maintenance and their migration into the gonads. Our observations reveal the mechanism inhibiting G1/S transition in pole cells and its requirement for proper germline development.
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Affiliation(s)
- Shumpei Morita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Ryoma Ota
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Makoto Hayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Satoru Kobayashi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.
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39
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Fröhlich J, Grundhoff A. Epigenetic control in Kaposi sarcoma-associated herpesvirus infection and associated disease. Semin Immunopathol 2020; 42:143-157. [PMID: 32219477 PMCID: PMC7174275 DOI: 10.1007/s00281-020-00787-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) is the etiologic agent of several malignancies of endothelial and B-cell origin. The fact that latently infected tumor cells in these malignancies do not express classical viral oncogenes suggests that pathogenesis of KSHV-associated disease results from multistep processes that, in addition to constitutive viral gene expression, may require accumulation of cellular alterations. Heritable changes of the epigenome have emerged as an important co-factor that contributes to the pathogenesis of many non-viral cancers. Since KSHV encodes a number of factors that directly or indirectly manipulate host cell chromatin, it is an intriguing possibility that epigenetic reprogramming also contributes to the pathogenesis of KSHV-associated tumors. The fact that heritable histone modifications have also been shown to regulate viral gene expression programs in KSHV-infected tumor cells underlines the importance of epigenetic control during latency and tumorigenesis. We here review what is presently known about the role of epigenetic regulation of viral and host chromatin in KSHV infection and discuss how viral manipulation of these processes may contribute to the development of KSHV-associated disease.
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Affiliation(s)
- Jacqueline Fröhlich
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
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40
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Aiello FA, Palma A, Malacaria E, Zheng L, Campbell JL, Shen B, Franchitto A, Pichierri P. RAD51 and mitotic function of mus81 are essential for recovery from low-dose of camptothecin in the absence of the WRN exonuclease. Nucleic Acids Res 2020; 47:6796-6810. [PMID: 31114910 PMCID: PMC6648349 DOI: 10.1093/nar/gkz431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 11/13/2022] Open
Abstract
Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN exonuclease has been linked to protection of stalled forks from degradation. Alternative processing of perturbed forks has been associated to chemoresistance of BRCA-deficient cancer cells. Thus, we used WRN exonuclease-deficiency as a model to investigate the fate of perturbed forks undergoing degradation, but in a BRCA wild-type condition. We find that, upon treatment with clinically-relevant nanomolar doses of the Topoisomerase I inhibitor camptothecin, loss of WRN exonuclease stimulates fork inactivation and accumulation of parental gaps, which engages RAD51. Such mechanism affects reinforcement of CHK1 phosphorylation and causes persistence of RAD51 during recovery from treatment. Notably, in WRN exonuclease-deficient cells, persistence of RAD51 correlates with elevated mitotic phosphorylation of MUS81 at Ser87, which is essential to prevent excessive mitotic abnormalities. Altogether, these findings indicate that aberrant fork degradation, in the presence of a wild-type RAD51 axis, stimulates RAD51-mediated post-replicative repair and engagement of the MUS81 complex to limit genome instability and cell death.
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Affiliation(s)
- Francesca Antonella Aiello
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Anita Palma
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Roma, Italy
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41
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Xiao G, Lundine D, Annor GK, Canar J, Ellison V, Polotskaia A, Donabedian PL, Reiner T, Khramtsova GF, Olopade OI, Mazo A, Bargonetti J. Gain-of-Function Mutant p53 R273H Interacts with Replicating DNA and PARP1 in Breast Cancer. Cancer Res 2019; 80:394-405. [PMID: 31776133 DOI: 10.1158/0008-5472.can-19-1036] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 09/13/2019] [Accepted: 11/22/2019] [Indexed: 12/25/2022]
Abstract
Over 80% of triple-negative breast cancers (TNBC) express mutant p53 (mtp53) and some contain oncogenic gain-of-function (GOF) p53. We previously reported that GOF mtp53 R273H upregulates the chromatin association of mini chromosome maintenance (MCM) proteins MCM2-7 and PARP and named this the mtp53-PARP-MCM axis. In this study, we dissected the function and association between mtp53 and PARP using a number of different cell lines, patient-derived xenografts (PDX), tissue microarrays (TMA), and The Cancer Genome Atlas (TCGA) database. Endogenous mtp53 R273H and exogenously expressed R273H and R248W bound to nascent 5-ethynyl-2´-deoxyuridine-labeled replicating DNA. Increased mtp53 R273H enhanced the association of mtp53 and PARP on replicating DNA. Blocking poly-ADP-ribose gylcohydrolase also enhanced this association. Moreover, mtp53 R273H expression enhanced overall MCM2 levels, promoted cell proliferation, and improved the synergistic cytotoxicity of treatment with the alkylating agent temozolomide in combination with the PARP inhibitor (PARPi) talazoparib. Staining of p53 and PARP1 in breast cancer TMAs and comparison with the TCGA database indicated a higher double-positive signal in basal-like breast cancer than in luminal A or luminal B subtypes. Higher PARP1 protein levels and PAR proteins were detected in mtp53 R273H than in wild-type p53-expressing PDX samples. These results indicate that mtp53 R273H and PARP1 interact with replicating DNA and should be considered as dual biomarkers for identifying breast cancers that may respond to combination PARPi treatments. SIGNIFICANCE: p53 gain-of-function mutant 273H and PARP1 interact with replication forks and could serve as potential biomarkers for breast cancer sensitivity to PARP inhibitors. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/3/394/F1.large.jpg.
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Affiliation(s)
- Gu Xiao
- The Department of Biological Sciences Hunter College, Belfer Building, City University of New York, New York, New York
| | - Devon Lundine
- The Department of Biological Sciences Hunter College, Belfer Building, City University of New York, New York, New York.,The Graduate Center Biology and Biochemistry PhD Programs of City University of New York, New York, New York
| | - George K Annor
- The Department of Biological Sciences Hunter College, Belfer Building, City University of New York, New York, New York.,The Graduate Center Biology and Biochemistry PhD Programs of City University of New York, New York, New York
| | - Jorge Canar
- The Department of Biological Sciences Hunter College, Belfer Building, City University of New York, New York, New York
| | - Viola Ellison
- The Department of Biological Sciences Hunter College, Belfer Building, City University of New York, New York, New York
| | - Alla Polotskaia
- The Department of Biological Sciences Hunter College, Belfer Building, City University of New York, New York, New York
| | - Patrick L Donabedian
- Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Thomas Reiner
- Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, New York.,Department of Radiology, Weill Cornell Medical College, New York City, New York.,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Galina F Khramtsova
- Center for Clinical Cancer Genetics and Global Health and Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health and Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology and Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jill Bargonetti
- The Department of Biological Sciences Hunter College, Belfer Building, City University of New York, New York, New York. .,The Graduate Center Biology and Biochemistry PhD Programs of City University of New York, New York, New York.,Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York
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42
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Brothers M, Rine J. Mutations in the PCNA DNA Polymerase Clamp of Saccharomyces cerevisiae Reveal Complexities of the Cell Cycle and Ploidy on Heterochromatin Assembly. Genetics 2019; 213:449-463. [PMID: 31451562 PMCID: PMC6781887 DOI: 10.1534/genetics.119.302452] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/23/2019] [Indexed: 01/19/2023] Open
Abstract
In Saccharomyces cerevisiae, transcriptional silencing at HML and HMR maintains mating-type identity. The repressive chromatin structure at these loci is replicated every cell cycle and must be re-established quickly to prevent transcription of the genes at these loci. Mutations in a component of the replisome, the proliferating cell nuclear antigen (PCNA), encoded by POL30, cause a loss of transcriptional silencing at HMR We used an assay that captures transient losses of silencing at HML and HMR to perform extended genetic analyses of the pol30-6, pol30-8, and pol30-79 alleles. All three alleles destabilized silencing only transiently and only in cycling cells. Whereas pol30-8 caused loss of silencing by disrupting the function of Chromatin Assembly Factor 1, pol30-6 and pol30-79 acted through a separate genetic pathway, but one still dependent on histone chaperones. Surprisingly, the silencing-loss phenotypes of pol30-6 and pol30-79 depended on ploidy, but not on POL30 dosage or mating-type identity. Separately from silencing loss, the pol30-6 and pol30-79 alleles also displayed high levels of mitotic recombination in diploids. These results established that histone trafficking involving PCNA at replication forks is crucial to the maintenance of chromatin state and genome stability during DNA replication. They also raised the possibility that increased ploidy may protect chromatin states when the replisome is perturbed.
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Affiliation(s)
- Molly Brothers
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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43
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Roy S, Schlacher K. SIRF: A Single-cell Assay for in situ Protein Interaction with Nascent DNA Replication Forks. Bio Protoc 2019; 9:e3377. [PMID: 33654873 DOI: 10.21769/bioprotoc.3377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 11/02/2022] Open
Abstract
The duplication of DNA is a fundamental process that is required for the transfer of the genetic information from parent to daughter cells. Aberrant DNA replication processes are associated with diverse disease phenotypes, including developmental defects, ageing disorders, blood disorders such as Fanconi Anemia, increased inflammation and cancer. Therefore, the development of tools to study proteins associated with error-free DNA replication processes is of paramount importance. So far, methods to study proteins associated with nascent replication forks relied on conventional immunofluorescence and immunoprecipitation assays of 5'-ethylene-2'-deoxyuridine (EdU) labeled DNA (iPOND). While greatly informative and important, these methods lack specificities for nascent fork interactions (e.g., IF) or assay an average change of millions of cells without single-cell resolution (e.g., iPOND). The assay system described here combines proximity ligation assay (PLA) with EdU coupled click-iT chemistry, which we termed "in situ protein interaction with nascent DNA replication forks (SIRF)". This method enables sensitive and quantitative analysis of protein interactions with nascent DNA replication forks with single-cell resolution, and can further be paired with conventional immunofluorescence marker analysis for added multi-parameter analysis.
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Affiliation(s)
- Sunetra Roy
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katharina Schlacher
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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44
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Crump NT, Milne TA. Why are so many MLL lysine methyltransferases required for normal mammalian development? Cell Mol Life Sci 2019; 76:2885-2898. [PMID: 31098676 PMCID: PMC6647185 DOI: 10.1007/s00018-019-03143-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022]
Abstract
The mixed lineage leukemia (MLL) family of proteins became known initially for the leukemia link of its founding member. Over the decades, the MLL family has been recognized as an important class of histone H3 lysine 4 (H3K4) methyltransferases that control key aspects of normal cell physiology and development. Here, we provide a brief history of the discovery and study of this family of proteins. We address two main questions: why are there so many H3K4 methyltransferases in mammals; and is H3K4 methylation their key function?
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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45
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Abstract
As the process that silences gene expression ensues during development, the stage is set for the activity of Polycomb-repressive complex 2 (PRC2) to maintain these repressed gene profiles. PRC2 catalyzes a specific histone posttranslational modification (hPTM) that fosters chromatin compaction. PRC2 also facilitates the inheritance of this hPTM through its self-contained "write and read" activities, key to preserving cellular identity during cell division. As these changes in gene expression occur without changes in DNA sequence and are inherited, the process is epigenetic in scope. Mutants of mammalian PRC2 or of its histone substrate contribute to the cancer process and other diseases, and research into these aberrant pathways is yielding viable candidates for therapeutic targeting. The effectiveness of PRC2 hinges on its being recruited to the proper chromatin sites; however, resolving the determinants to this process in the mammalian case was not straightforward and thus piqued the interest of many in the field. Here, we chronicle the latest advances toward exposing mammalian PRC2 and its high maintenance.
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Affiliation(s)
- Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ozgur Oksuz
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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46
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Polosoro A, Enggarini W, Ohmido N. Global epigenetic changes of histone modification under environmental stresses in rice root. Chromosome Res 2019; 27:287-298. [PMID: 31280458 DOI: 10.1007/s10577-019-09611-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 01/11/2023]
Abstract
Abiotic stresses are non-living factors with negative morphological and physiological effects on living organisms. Substantial evidence exists that gene expression changes during plant cell growth are regulated by chromatin reconfiguration and histone modification. Several types of histone modifications are dramatically transformed in stress-responsive gene regions under drought stress conditions. Environmental stresses also cause the root apical meristem (RAM) region to decelerate root growth. In this study, we investigated how quantitative changes in epigenetic markers in this region influence rice morphology and physiology. Both iron and salinity treatments changed the epigenetic landscape from euchromatic to heterochromatic according to heterochromatin (H3K9me2) and euchromatin (H3K4me) markers, especially in the proximal meristem region. Moreover, supplementation with external abscisic acid (ABA) was able to mimic the effect of environmental stresses on global epigenetic changes. In contrast, the addition of external auxin (IAA) to rice under saline conditions affected heterochromatin formation without influencing euchromatin transformation. Chromatin dynamics is therefore believed to be directly connected to plant growth regulator signaling. We discuss insights into the role of plant growth regulators: ABA and IAA, peroxide signaling, and their effects on the global epigenetic change of histone modification under abiotic stresses.
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Affiliation(s)
- Aqwin Polosoro
- Indonesian Center for Agricultural Biotechnology and Genetic Resource Research and Development (ICABIOGRD), Bogor, Indonesia.,Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Wening Enggarini
- Indonesian Center for Agricultural Biotechnology and Genetic Resource Research and Development (ICABIOGRD), Bogor, Indonesia
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan.
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Dakik P, Medkour Y, Mohammad K, Titorenko VI. Mechanisms Through Which Some Mitochondria-Generated Metabolites Act as Second Messengers That Are Essential Contributors to the Aging Process in Eukaryotes Across Phyla. Front Physiol 2019; 10:461. [PMID: 31057428 PMCID: PMC6482166 DOI: 10.3389/fphys.2019.00461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/02/2019] [Indexed: 12/21/2022] Open
Abstract
Recent studies have revealed that some low-molecular weight molecules produced in mitochondria are essential contributing factors to aging and aging-associated pathologies in evolutionarily distant eukaryotes. These molecules are intermediates or products of certain metabolic reactions that are activated in mitochondria in response to specific changes in the nutrient, stress, proliferation, or age status of the cell. After being released from mitochondria, these metabolites directly or indirectly change activities of a distinct set of protein sensors that reside in various cellular locations outside of mitochondria. Because these protein sensors control the efficiencies of some pro- or anti-aging cellular processes, such changes in their activities allow to create a pro- or anti-aging cellular pattern. Thus, mitochondria can function as signaling platforms that respond to certain changes in cell stress and physiology by remodeling their metabolism and releasing a specific set of metabolites known as "mitobolites." These mitobolites then define the pace of cellular and organismal aging because they regulate some longevity-defining processes taking place outside of mitochondria. In this review, we discuss recent progress in understanding mechanisms underlying the ability of mitochondria to function as such signaling platforms in aging and aging-associated diseases.
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A Noncanonical Function of Polycomb Repressive Complexes Promotes Human Cytomegalovirus Lytic DNA Replication and Serves as a Novel Cellular Target for Antiviral Intervention. J Virol 2019; 93:JVI.02143-18. [PMID: 30814291 DOI: 10.1128/jvi.02143-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/07/2019] [Indexed: 12/14/2022] Open
Abstract
Chromatin-based modifications of herpesviral genomes play a crucial role in dictating the outcome of infection. Consistent with this, host cell multiprotein complexes, such as polycomb repressive complexes (PRCs), were proposed to act as epigenetic regulators of herpesviral latency. In particular, PRC2 has recently been shown to contribute to the silencing of human cytomegalovirus (HCMV) genomes. Here, we identify a novel proviral role of PRC1 and PRC2, the two main polycomb repressive complexes, during productive HCMV infection. Western blot analyses revealed strong HCMV-mediated upregulation of RING finger protein 1B (RING1B) and B lymphoma Moloney murine leukemia virus insertion region 1 homolog (BMI1) as well as of enhancer of zeste homolog 2 (EZH2), suppressor of zeste 12 (SUZ12), and embryonic ectoderm development (EED), which constitute the core components of PRC1 and PRC2, respectively. Furthermore, we observed a relocalization of PRC components to viral replication compartments, whereas histone modifications conferred by the respective PRCs were specifically excluded from these sites. Depletion of individual PRC1/PRC2 proteins by RNA interference resulted in a significant reduction of newly synthesized viral genomes and, in consequence, a decreased release of viral particles. Furthermore, accelerated native isolation of protein on nascent DNA (aniPOND) revealed a physical association of EZH2 and BMI1 with nascent HCMV DNA, suggesting a direct contribution of PRC proteins to viral DNA replication. Strikingly, substances solely inhibiting the enzymatic activity of PRC1/2 did not exert antiviral effects, while drugs affecting the abundance of PRC core components strongly compromised HCMV genome synthesis and particle release. Taken together, our data reveal an enzymatically independent, noncanonical function of both PRC1 and PRC2 during HCMV DNA replication, which may serve as a novel cellular target for antiviral therapy.IMPORTANCE Polycomb group (PcG) proteins are primarily known as transcriptional repressors that modify chromatin and contribute to the establishment and maintenance of cell fates. Furthermore, emerging evidence indicates that overexpression of PcG proteins in various types of cancers contributes to the dysregulation of cellular proliferation. Consequently, several inhibitors targeting PcG proteins are presently undergoing preclinical and clinical evaluation. Here, we show that infection with human cytomegalovirus also induces a strong upregulation of several PcG proteins. Our data suggest that viral DNA replication depends on a noncanonical function of polycomb repressor complexes which is independent of the so-far-described enzymatic activities of individual PcG factors. Importantly, we observe that a subclass of inhibitory drugs that affect the abundance of PcG proteins strongly interferes with viral replication. This principle may serve as a novel promising target for antiviral treatment.
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Rad52 prevents excessive replication fork reversal and protects from nascent strand degradation. Nat Commun 2019; 10:1412. [PMID: 30926821 PMCID: PMC6441034 DOI: 10.1038/s41467-019-09196-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 02/26/2019] [Indexed: 01/02/2023] Open
Abstract
Stabilisation of stalled replication forks prevents excessive fork reversal and their pathological degradation, which can undermine genome integrity. Here we investigate a physiological role of RAD52 at stalled replication forks by using human cell models depleted of RAD52, a specific small-molecule inhibitor of the RAD52-ssDNA interaction, in vitro and single-molecule analyses. We demonstrate that RAD52 prevents excessive degradation of reversed replication forks by MRE11. Mechanistically, RAD52 binds to the stalled replication fork, promotes its occlusion and counteracts loading of SMARCAL1 in vitro and in vivo. Loss of the RAD52 function results in a slightly-defective replication restart, persistence of under-replicated regions and chromosome instability. Moreover, the RAD52-inhibited cells rely on RAD51 for completion of replication and viability upon replication arrest. Collectively, our data suggest an unexpected gatekeeper mechanism by which RAD52 limits excessive remodelling of stalled replication forks, thus indirectly assisting RAD51 and BRCA2 in protecting forks from unscheduled degradation and preventing genome instability. Stabilisation of stalled replication forks prevents excessive fork reversal and genome instability. Here authors reveal a RAD52-dependent replication fork protection mechanism.
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Fenstermaker TK, Sun G, Mazo A, Petruk S. A Proximity Ligation-Based Method to Detect RNA-DNA Association. Methods Mol Biol 2019; 2008:121-129. [PMID: 31124093 PMCID: PMC7528808 DOI: 10.1007/978-1-4939-9537-0_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We recently developed a method for assessing RNA-DNA interactions using proximity ligation assays (PLA). This technique, termed the "RNA-DNA interaction assay" (RDIA), involves differentially labeling DNA and RNA with EdU and BrU, respectively. Once labeled, PLA is performed to assess if the labeled molecules are in close proximity. Here we provide a detailed description of the modified RDIA protocol utilizing currently commercially available BrdU antibodies. As an example, we show its ability to detect nascent transcripts on recently synthesized DNA in both cultured H1299 cells and mouse embryonic stem cells.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology and Kimmel
Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Guizhi Sun
- Department of Biochemistry and Molecular Biology and Kimmel
Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology and Kimmel
Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology and Kimmel
Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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