1
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Chen B, MacAlpine HK, Hartemink AJ, MacAlpine DM. Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase. Genome Res 2023; 33:2108-2118. [PMID: 38081658 PMCID: PMC10760526 DOI: 10.1101/gr.278273.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023]
Abstract
Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2 tetramers as part of the replication-dependent chromatin assembly process. Loss of CAF-1 leads to a delay in chromatin maturation, albeit with minimal impact on steady-state chromatin structure. However, the mechanisms by which CAF-1 mediates the deposition of (H3-H4)2 tetramers and the phenotypic consequences of CAF-1-associated assembly defects are not well understood. We used nascent chromatin occupancy profiling to track the spatiotemporal kinetics of chromatin maturation in both wild-type (WT) and CAF-1 mutant yeast cells. Our results show that loss of CAF-1 leads to a heterogeneous rate of nucleosome assembly, with some nucleosomes maturing at near WT kinetics and others showing significantly slower maturation kinetics. The slow-to-mature nucleosomes are enriched in intergenic and poorly transcribed regions, suggesting that transcription-dependent assembly mechanisms can reset the slow-to-mature nucleosomes following replication. Nucleosomes with slow maturation kinetics are also associated with poly(dA:dT) sequences, which implies that CAF-1 deposits histones in a manner that counteracts resistance from the inflexible DNA sequence, promoting the formation of histone octamers as well as ordered nucleosome arrays. In addition, we show that the delay in chromatin maturation is accompanied by a transient and S-phase-specific loss of gene silencing and transcriptional regulation, revealing that the DNA replication program can directly shape the chromatin landscape and modulate gene expression through the process of chromatin maturation.
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Affiliation(s)
- Boning Chen
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Heather K MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA;
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2
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Soni A, Klebanov-Akopyan O, Erben E, Plaschkes I, Benyamini H, Mitesser V, Harel A, Yamin K, Onn I, Shlomai J. UMSBP2 is chromatin remodeler that functions in regulation of gene expression and suppression of antigenic variation in trypanosomes. Nucleic Acids Res 2023; 51:5678-5698. [PMID: 37207337 PMCID: PMC10287944 DOI: 10.1093/nar/gkad402] [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: 12/16/2021] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.
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Affiliation(s)
- Awakash Soni
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Olga Klebanov-Akopyan
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Esteban Erben
- Heidelberg University Center for Molecular Biology at Heidelberg University, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Inbar Plaschkes
- The Info-Core Bioinformatics Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Hadar Benyamini
- The Info-Core Bioinformatics Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Vera Mitesser
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Katereena Yamin
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Itay Onn
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Joseph Shlomai
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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3
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Chen B, MacAlpine HK, Hartemink AJ, MacAlpine DM. Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.541209. [PMID: 37292814 PMCID: PMC10245875 DOI: 10.1101/2023.05.25.541209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proper maintenance of epigenetic information after replication is dependent on the rapid assembly and maturation of chromatin. Chromatin Assembly Complex 1 (CAF-1) is a conserved histone chaperone that deposits (H3-H4)2 tetramers as part of the replication-dependent chromatin assembly process. Loss of CAF-1 leads to a delay in chromatin maturation, albeit with minimal impact on steady-state chromatin structure. However, the mechanisms by which CAF-1 mediates the deposition of (H3-H4)2 tetramers and the phenotypic consequences of CAF-1-associated assembly defects are not well understood. We used nascent chromatin occupancy profiling to track the spatiotemporal kinetics of chromatin maturation in both wild-type (WT) and CAF-1 mutant yeast cells. Our results show that loss of CAF-1 leads to a heterogeneous rate of nucleosome assembly, with some nucleosomes maturing at near WT kinetics and others exhibiting significantly slower maturation kinetics. The slow-to-mature nucleosomes are enriched in intergenic and poorly transcribed regions, suggesting that transcription-dependent assembly mechanisms can reset the slow-to-mature nucleosomes following replication. Nucleosomes with slow maturation kinetics are also associated with poly(dA:dT) sequences, which implies that CAF-1 deposits histones in a manner that counteracts resistance from the inflexible DNA sequence, promoting the formation of histone octamers as well as ordered nucleosome arrays. In addition, we demonstrate that the delay in chromatin maturation is accompanied by a transient and S-phase specific loss of gene silencing and transcriptional regulation, revealing that the DNA replication program can directly shape the chromatin landscape and modulate gene expression through the process of chromatin maturation.
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Affiliation(s)
- Boning Chen
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Heather K. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | | | - David M. MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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4
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Gospodinov A, Dzhokova S, Petrova M, Ugrinova I. Chromatin regulators in DNA replication and genome stability maintenance during S-phase. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:243-280. [PMID: 37061334 DOI: 10.1016/bs.apcsb.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The duplication of genetic information is central to life. The replication of genetic information is strictly controlled to ensure that each piece of genomic DNA is copied only once during a cell cycle. Factors that slow or stop replication forks cause replication stress. Replication stress is a major source of genome instability in cancer cells. Multiple control mechanisms facilitate the unimpeded fork progression, prevent fork collapse and coordinate fork repair. Chromatin alterations, caused by histone post-translational modifications and chromatin remodeling, have critical roles in normal replication and in avoiding replication stress and its consequences. This text reviews the chromatin regulators that ensure DNA replication and the proper response to replication stress. We also briefly touch on exploiting replication stress in therapeutic strategies. As chromatin regulators are frequently mutated in cancer, manipulating their activity could provide many possibilities for personalized treatment.
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Affiliation(s)
- Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Stefka Dzhokova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Petrova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iva Ugrinova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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5
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Multiple roles of Pol epsilon in eukaryotic chromosome replication. Biochem Soc Trans 2022; 50:309-320. [PMID: 35129614 PMCID: PMC9022971 DOI: 10.1042/bst20210082] [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: 10/15/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 11/17/2022]
Abstract
Pol epsilon is a tetrameric assembly that plays distinct roles during eukaryotic chromosome replication. It catalyses leading strand DNA synthesis; yet this function is dispensable for viability. Its non-catalytic domains instead play an essential role in the assembly of the active replicative helicase and origin activation, while non-essential histone-fold subunits serve a critical function in parental histone redeposition onto newly synthesised DNA. Furthermore, Pol epsilon plays a structural role in linking the RFC–Ctf18 clamp loader to the replisome, supporting processive DNA synthesis, DNA damage response signalling as well as sister chromatid cohesion. In this minireview, we discuss recent biochemical and structural work that begins to explain various aspects of eukaryotic chromosome replication, with a focus on the multiple roles of Pol epsilon in this process.
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6
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Safaric B, Chacin E, Scherr MJ, Rajappa L, Gebhardt C, Kurat CF, Cordes T, Duderstadt KE. The fork protection complex recruits FACT to reorganize nucleosomes during replication. Nucleic Acids Res 2022; 50:1317-1334. [PMID: 35061899 PMCID: PMC8860610 DOI: 10.1093/nar/gkac005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/21/2021] [Accepted: 01/05/2022] [Indexed: 01/14/2023] Open
Abstract
Chromosome replication depends on efficient removal of nucleosomes by accessory factors to ensure rapid access to genomic information. Here, we show this process requires recruitment of the nucleosome reorganization activity of the histone chaperone FACT. Using single-molecule FRET, we demonstrate that reorganization of nucleosomal DNA by FACT requires coordinated engagement by the middle and C-terminal domains of Spt16 and Pob3 but does not require the N-terminus of Spt16. Using structure-guided pulldowns, we demonstrate instead that the N-terminal region is critical for recruitment by the fork protection complex subunit Tof1. Using in vitro chromatin replication assays, we confirm the importance of these interactions for robust replication. Our findings support a mechanism in which nucleosomes are removed through the coordinated engagement of multiple FACT domains positioned at the replication fork by the fork protection complex.
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Affiliation(s)
- Barbara Safaric
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Erika Chacin
- Biomedical Center (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg, Germany
| | - Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Christoph F Kurat
- Biomedical Center (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.,Physics Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
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7
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Willhoft O, Costa A. A structural framework for DNA replication and transcription through chromatin. Curr Opin Struct Biol 2021; 71:51-58. [PMID: 34218162 DOI: 10.1016/j.sbi.2021.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
In eukaryotic cells, DNA replication and transcription machineries uncoil nucleosomes along the double helix, to achieve the exposure of the single-stranded DNA template for nucleic acid synthesis. The replisome and RNA polymerases then redeposit histones onto DNA behind the advancing molecular motor, in a process that is crucial for epigenetic inheritance and homeostasis, respectively. Here, we compare and contrast the mechanisms by which these molecular machines advance through nucleosome arrays and discuss how chromatin remodellers can facilitate DNA replication and transcription.
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Affiliation(s)
- Oliver Willhoft
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
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8
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Caught in the act: structural dynamics of replication origin activation and fork progression. Biochem Soc Trans 2021; 48:1057-1066. [PMID: 32369549 PMCID: PMC7329347 DOI: 10.1042/bst20190998] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/03/2023]
Abstract
This review discusses recent advances in single-particle cryo-EM and single-molecule approaches used to visualise eukaryotic DNA replication reactions reconstituted in vitro. We comment on the new challenges facing structural biologists, as they turn to describing the dynamic cascade of events that lead to replication origin activation and fork progression.
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9
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Wooten M, Li Y, Snedeker J, Nizami ZF, Gall JG, Chen X. Superresolution imaging of chromatin fibers to visualize epigenetic information on replicative DNA. Nat Protoc 2020; 15:1188-1208. [PMID: 32051613 PMCID: PMC7255620 DOI: 10.1038/s41596-019-0283-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
Abstract
During DNA replication, the genetic information of a cell is copied. Subsequently, identical genetic information is segregated reliably to the two daughter cells through cell division. Meanwhile, DNA replication is intrinsically linked to the process of chromatin duplication, which is required for regulating gene expression and establishing cell identities. Understanding how chromatin is established, maintained or changed during DNA replication represents a fundamental question in biology. Recently, we developed a method to directly visualize chromatin components at individual replication forks undergoing DNA replication. This method builds upon the existing chromatin fiber technique and combines it with cell type-specific chromatin labeling and superresolution microscopy. In this method, a short pulse of nucleoside analog labels replicative regions in the cells of interest. Chromatin fibers are subsequently isolated and attached to a glass slide, after which a laminar flow of lysis buffer extends the lysed chromatin fibers parallel with the direction of the flow. Fibers are then immunostained for different chromatin-associated proteins and mounted for visualization using superresolution microscopy. Replication foci, or 'bubbles,' are identified by the presence of the incorporated nucleoside analog. For researchers experienced in molecular biology and superresolution microscopy, this protocol typically takes 2-3 d from sample preparation to data acquisition, with an additional day for data processing and quantification.
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Affiliation(s)
- Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Yingying Li
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA
| | - Zehra F Nizami
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD, USA.
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10
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Wooten M, Ranjan R, Chen X. Asymmetric Histone Inheritance in Asymmetrically Dividing Stem Cells. Trends Genet 2020; 36:30-43. [PMID: 31753528 PMCID: PMC6925335 DOI: 10.1016/j.tig.2019.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Abstract
Epigenetic mechanisms play essential roles in determining distinct cell fates during the development of multicellular organisms. Histone proteins represent crucial epigenetic components that help specify cell identities. Previous work has demonstrated that during the asymmetric cell division of Drosophila male germline stem cells (GSCs), histones H3 and H4 are asymmetrically inherited, such that pre-existing (old) histones are segregated towards the self-renewing GSC whereas newly synthesized (new) histones are enriched towards the differentiating daughter cell. In order to further understand the molecular mechanisms underlying this striking phenomenon, two key questions must be answered: when and how old and new histones are differentially incorporated by sister chromatids, and how epigenetically distinct sister chromatids are specifically recognized and segregated. Here, we discuss recent advances in our understanding of the molecular mechanisms and cellular bases underlying these fundamental and important biological processes responsible for generating two distinct cells through one cell division.
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Affiliation(s)
- Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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11
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Keller A, Chavez JD, Bruce JE. Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks. Bioinformatics 2019; 35:895-897. [PMID: 30137231 DOI: 10.1093/bioinformatics/bty720] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/12/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION Peptides crosslinked with cleavable chemical crosslinkers are identified with mass spectrometry by independent database search of spectra associated with the two linked peptides. A major challenge is to combine together the evidence of the two peptides into an overall assessment of the two-peptide crosslink. RESULTS Here, we describe software that models crosslink specific information to automatically validate XL-MS cleavable peptide crosslinks. Using a dataset of crosslinked protein mixtures, we demonstrate that it computes accurate and highly discriminating probabilities, enabling as many as 75% more identifications than was previously possible using only search scores and a predictable false discovery rate. AVAILABILITY AND IMPLEMENTATION XLinkProphet software is freely available on the web at http://brucelab.gs.washington.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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12
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Sauer PV, Gu Y, Liu WH, Mattiroli F, Panne D, Luger K, Churchill MEA. Mechanistic insights into histone deposition and nucleosome assembly by the chromatin assembly factor-1. Nucleic Acids Res 2018; 46:9907-9917. [PMID: 30239791 PMCID: PMC6212844 DOI: 10.1093/nar/gky823] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/15/2018] [Indexed: 02/03/2023] Open
Abstract
Eukaryotic chromatin is a highly dynamic structure with essential roles in virtually all DNA-dependent cellular processes. Nucleosomes are a barrier to DNA access, and during DNA replication, they are disassembled ahead of the replication machinery (the replisome) and reassembled following its passage. The Histone chaperone Chromatin Assembly Factor-1 (CAF-1) interacts with the replisome and deposits H3-H4 directly onto newly synthesized DNA. Therefore, CAF-1 is important for the establishment and propagation of chromatin structure. The molecular mechanism by which CAF-1 mediates H3-H4 deposition has remained unclear. However, recent studies have revealed new insights into the architecture and stoichiometry of the trimeric CAF-1 complex and how it interacts with and deposits H3-H4 onto substrate DNA. The CAF-1 trimer binds to a single H3-H4 dimer, which induces a conformational rearrangement in CAF-1 promoting its interaction with substrate DNA. Two CAF-1•H3-H4 complexes co-associate on nucleosome-free DNA depositing (H3-H4)2 tetramers in the first step of nucleosome assembly. Here, we review the progress made in our understanding of CAF-1 structure, mechanism of action, and how CAF-1 contributes to chromatin dynamics during DNA replication.
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Affiliation(s)
- Paul V Sauer
- European Molecular Biology Laboratory, 38042 Grenoble, France
| | - Yajie Gu
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Wallace H Liu
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Daniel Panne
- European Molecular Biology Laboratory, 38042 Grenoble, France,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, UK
| | - Karolin Luger
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Mair EA Churchill
- Department of Pharmacology and Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA,To whom correspondence should be addressed. Tel: +1 303 724 3670;
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13
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Aze A, Maiorano D. Recent advances in understanding DNA replication: cell type-specific adaptation of the DNA replication program. F1000Res 2018; 7. [PMID: 30228862 PMCID: PMC6117848 DOI: 10.12688/f1000research.15408.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2018] [Indexed: 12/11/2022] Open
Abstract
DNA replication is an essential process occurring prior to cell division. Cell division coupled to proliferation ensures the growth and renewal of a large variety of specialized cell types generated during embryonic development. Changes in the DNA replication program occur during development. Embryonic undifferentiated cells show a high replication rate and fast proliferation, whereas more differentiated cells are characterized by reduced DNA synthesis and a low proliferation rate. Hence, the DNA replication program must adapt to the specific features of cells committed to different fates. Recent findings on DNA synthesis regulation in different cell types open new perspectives for developing efficient and more adapted therapies to treat various diseases such as genetic diseases and cancer. This review will put the emphasis on recent progress made in this field.
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Affiliation(s)
- Antoine Aze
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, Montpellier, 34396 Cedex 5, France
| | - Domenico Maiorano
- Institute of Human Genetics, UMR9002, CNRS-University of Montpellier, Montpellier, 34396 Cedex 5, France
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14
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Evrin C, Maman JD, Diamante A, Pellegrini L, Labib K. Histone H2A-H2B binding by Pol α in the eukaryotic replisome contributes to the maintenance of repressive chromatin. EMBO J 2018; 37:embj.201899021. [PMID: 30104407 PMCID: PMC6166128 DOI: 10.15252/embj.201899021] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/18/2018] [Accepted: 07/24/2018] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic replisome disassembles parental chromatin at DNA replication forks, but then plays a poorly understood role in the re‐deposition of the displaced histone complexes onto nascent DNA. Here, we show that yeast DNA polymerase α contains a histone‐binding motif that is conserved in human Pol α and is specific for histones H2A and H2B. Mutation of this motif in budding yeast cells does not affect DNA synthesis, but instead abrogates gene silencing at telomeres and mating‐type loci. Similar phenotypes are produced not only by mutations that displace Pol α from the replisome, but also by mutation of the previously identified histone‐binding motif in the CMG helicase subunit Mcm2, the human orthologue of which was shown to bind to histones H3 and H4. We show that chromatin‐derived histone complexes can be bound simultaneously by Mcm2, Pol α and the histone chaperone FACT that is also a replisome component. These findings indicate that replisome assembly unites multiple histone‐binding activities, which jointly process parental histones to help preserve silent chromatin during the process of chromosome duplication.
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Affiliation(s)
- Cecile Evrin
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joseph D Maman
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Aurora Diamante
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, UK
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15
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Nucleosomes of polyploid trophoblast giant cells mostly consist of histone variants and form a loose chromatin structure. Sci Rep 2018; 8:5811. [PMID: 29643413 PMCID: PMC5895725 DOI: 10.1038/s41598-018-23832-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/20/2018] [Indexed: 12/31/2022] Open
Abstract
Trophoblast giant cells (TGCs) are one of the cell types that form the placenta and play multiple essential roles in maintaining pregnancy in rodents. TGCs have large, polyploid nuclei resulting from endoreduplication. While previous studies have shown distinct gene expression profiles of TGCs, their chromatin structure remains largely unknown. An appropriate combination of canonical and non-canonical histones, also known as histone variants, allows each cell to exert its cell type-specific functions. Here, we aimed to reveal the dynamics of histone usage and chromatin structure during the differentiation of trophoblast stem cells (TSCs) into TGCs. Although the expression of most genes encoding canonical histones was downregulated, the expression of a few genes encoding histone variants such as H2AX, H2AZ, and H3.3 was maintained at a relatively high level in TGCs. Both the micrococcal nuclease digestion assay and nucleosome stability assay using a microfluidic device indicated that chromatin became increasingly loose as TSCs differentiated. Combinatorial experiments involving H3.3-knockdown and -overexpression demonstrated that variant H3.3 resulted in the formation of loose nucleosomes in TGCs. In conclusion, our study revealed that TGCs possessed loose nucleosomes owing to alterations in their histone composition during differentiation.
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Garbacz MA, Lujan SA, Burkholder AB, Cox PB, Wu Q, Zhou ZX, Haber JE, Kunkel TA. Evidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae. Nat Commun 2018; 9:858. [PMID: 29487291 PMCID: PMC5829166 DOI: 10.1038/s41467-018-03270-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 02/01/2018] [Indexed: 01/01/2023] Open
Abstract
To investigate nuclear DNA replication enzymology in vivo, we have studied Saccharomyces cerevisiae strains containing a pol2-16 mutation that inactivates the catalytic activities of DNA polymerase ε (Pol ε). Although pol2-16 mutants survive, they present very tiny spore colonies, increased doubling time, larger than normal cells, aberrant nuclei, and rapid acquisition of suppressor mutations. These phenotypes reveal a severe growth defect that is distinct from that of strains that lack only Pol ε proofreading (pol2-4), consistent with the idea that Pol ε is the major leading-strand polymerase used for unstressed DNA replication. Ribonucleotides are incorporated into the pol2-16 genome in patterns consistent with leading-strand replication by Pol δ when Pol ε is absent. More importantly, ribonucleotide distributions at replication origins suggest that in strains encoding all three replicases, Pol δ contributes to initiation of leading-strand replication. We describe two possible models. DNA polymerases δ and ε (Pols δ and ε) are thought to be responsible for lagging and leading strand synthesis, respectively. Here the authors present evidence that Pol δ contributes to the initiation of leading strand replication in budding yeast by synthesizing DNA of both strands at replication origins.
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Affiliation(s)
- Marta A Garbacz
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Adam B Burkholder
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Phillip B Cox
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Qiuqin Wu
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 02454, USA
| | - Zhi-Xiong Zhou
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA
| | - James E Haber
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, 02454, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA.
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17
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Okada T, Okabe G, Tak YS, Mimura S, Takisawa H, Kubota Y. Suppression of targeting of Dbf4-dependent kinase to pre-replicative complex in G0 nuclei. Genes Cells 2018; 23:94-104. [PMID: 29314475 DOI: 10.1111/gtc.12556] [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: 10/11/2017] [Accepted: 12/01/2017] [Indexed: 12/01/2022]
Abstract
Intact G0 nuclei isolated from quiescent cells are not capable of DNA replication in interphase Xenopus egg extracts, which allow efficient replication of permeabilized G0 nuclei. Previous studies have shown multiple control mechanisms for maintaining the quiescent state, but DNA replication inhibition of intact G0 nuclei in the extracts remains poorly understood. Here, we showed that pre-RC is assembled on chromatin, but its activation is inhibited after incubating G0 nuclei isolated from quiescent NIH3T3 cells in the extracts. Concomitant with the inhibition of replication, Mcm4 phosphorylation mediated by Dbf4-dependent kinase (DDK) as well as chromatin binding of DDK is suppressed in G0 nuclei without affecting the nuclear transport of DDK. We further found that the nuclear extracts of G0 but not proliferating cells inhibit the binding of recombinant DDK to pre-RC assembled plasmids. In addition, we observed rapid activation of checkpoint kinases after incubating G0 nuclei in the egg extracts. However, specific inhibitors of ATR/ATM are unable to promote DNA replication in G0 nuclei in the egg extracts. We suggest that a novel inhibitory mechanism is functional to prevent the targeting of DDK to pre-RC in G0 nuclei, thereby suppressing DNA replication in Xenopus egg extracts.
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Affiliation(s)
- Takuya Okada
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.,Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, Japan
| | - Gaku Okabe
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.,Engineering Integration Department, Air Water Inc., Osaka, Japan
| | - Yon-Soo Tak
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Satoru Mimura
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Haruhiko Takisawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Yumiko Kubota
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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18
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Riera A, Barbon M, Noguchi Y, Reuter LM, Schneider S, Speck C. From structure to mechanism-understanding initiation of DNA replication. Genes Dev 2017; 31:1073-1088. [PMID: 28717046 PMCID: PMC5538431 DOI: 10.1101/gad.298232.117] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this Review, Riera et al. review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability.
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Affiliation(s)
- Alberto Riera
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Marta Barbon
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Medical Research Council (MRC) London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
| | - Yasunori Noguchi
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - L Maximilian Reuter
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Sarah Schneider
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
| | - Christian Speck
- DNA Replication Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Medical Research Council (MRC) London Institute of Medical Sciences (LMS), London W12 0NN, United Kingdom
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