1
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Wu J, Jiang Y, Zhang Q, Mao X, Wu T, Hao M, Zhang S, Meng Y, Wan X, Qiu L, Han J. KDM6A-SND1 interaction maintains genomic stability by protecting the nascent DNA and contributes to cancer chemoresistance. Nucleic Acids Res 2024:gkae487. [PMID: 38850159 DOI: 10.1093/nar/gkae487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/10/2024] Open
Abstract
Genomic instability is one of the hallmarks of cancer. While loss of histone demethylase KDM6A increases the risk of tumorigenesis, its specific role in maintaining genomic stability remains poorly understood. Here, we propose a mechanism in which KDM6A maintains genomic stability independently on its demethylase activity. This occurs through its interaction with SND1, resulting in the establishment of a protective chromatin state that prevents replication fork collapse by recruiting of RPA and Ku70 to nascent DNA strand. Notably, KDM6A-SND1 interaction is up-regulated by KDM6A SUMOylation, while KDM6AK90A mutation almost abolish the interaction. Loss of KDM6A or SND1 leads to increased enrichment of H3K9ac and H4K8ac but attenuates the enrichment of Ku70 and H3K4me3 at nascent DNA strand. This subsequently results in enhanced cellular sensitivity to genotoxins and genomic instability. Consistent with these findings, knockdown of KDM6A and SND1 in esophageal squamous cell carcinoma (ESCC) cells increases genotoxin sensitivity. Intriguingly, KDM6A H101D & P110S, N1156T and D1216N mutations identified in ESCC patients promote genotoxin resistance via increased SND1 association. Our finding provides novel insights into the pivotal role of KDM6A-SND1 in genomic stability and chemoresistance, implying that targeting KDM6A and/or its interaction with SND1 may be a promising strategy to overcome the chemoresistance.
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Affiliation(s)
- Jian Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yixin Jiang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qin Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaobing Mao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tong Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mengqiu Hao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Su Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Meng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaowen Wan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lei Qiu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Junhong Han
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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2
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Lichauco C, Foss EJ, Gatbonton-Schwager T, Athow NF, Lofts BR, Acob R, Taylor E, Lao U, Miles S, Bedalov A. Sir2 and Fun30 regulate ribosomal DNA replication timing via Mcm helicase positioning and nucleosome occupancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586113. [PMID: 38585982 PMCID: PMC10996493 DOI: 10.1101/2024.03.21.586113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well-known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA arrays (rDNA). We have previously reported that in the absence of SIR2, a derepressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the non-displaced MCMs. Furthermore, we found that both, activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity of FUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication origin in vivo relies on the nucleosome context shaped by a single chromatin remodeler.
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Affiliation(s)
- Carmina Lichauco
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Eric J. Foss
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Tonibelle Gatbonton-Schwager
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Nelson F. Athow
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Brandon R. Lofts
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Robin Acob
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Erin Taylor
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Uyen Lao
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Shawna Miles
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Antonio Bedalov
- Translational Sciences and Therapeutics Division, Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Biochemistry and Department of Medicine, University of Washington, Seattle, WA
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3
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Chanou A, Weiβ M, Holler K, Sajid A, Straub T, Krietsch J, Sanchi A, Ummethum H, Lee CSK, Kruse E, Trauner M, Werner M, Lalonde M, Lopes M, Scialdone A, Hamperl S. Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency. Nucleic Acids Res 2023; 51:12303-12324. [PMID: 37956271 PMCID: PMC10711542 DOI: 10.1093/nar/gkad1022] [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: 11/25/2022] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Stochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of four specific genomic loci. MATAC-Seq relies on preferential modification of accessible DNA by methyltransferases combined with Nanopore-Sequencing for direct readout of methylated DNA-bases. Applying MATAC-Seq to selected early-efficient and late-inefficient yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an accessible nucleosome-free region in combination with well-positioned +1 and +2 nucleosomes as a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during eukaryotic DNA replication. Consequently, our single-molecule chromatin accessibility assay will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.
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Affiliation(s)
- Anna Chanou
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Matthias Weiβ
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Karoline Holler
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Atiqa Sajid
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Tobias Straub
- Core Facility Bioinformatics, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henning Ummethum
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Clare S K Lee
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Elisabeth Kruse
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Manuel Trauner
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Marcel Werner
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Maxime Lalonde
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stephan Hamperl
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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4
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Jonas F, Vidavski M, Benuck E, Barkai N, Yaakov G. Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA-protein binding. Nucleic Acids Res 2023; 51:8496-8513. [PMID: 37493599 PMCID: PMC10484674 DOI: 10.1093/nar/gkad615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023] Open
Abstract
DNA packaging within chromatin depends on histone chaperones and remodelers that form and position nucleosomes. Cells express multiple such chromatin regulators with overlapping in-vitro activities. Defining specific in-vivo activities requires monitoring histone dynamics during regulator depletion, which has been technically challenging. We have recently generated histone-exchange sensors in Saccharomyces cerevisiae, which we now use to define the contributions of 15 regulators to histone dynamics genome-wide. While replication-independent exchange in unperturbed cells maps to promoters, regulator depletions primarily affected gene bodies. Depletion of Spt6, Spt16 or Chd1 sharply increased nucleosome replacement sequentially at the beginning, middle or end of highly expressed gene bodies. They further triggered re-localization of chaperones to affected gene body regions, which compensated for nucleosome loss during transcription complex passage, but concurred with extensive TF binding in gene bodies. We provide a unified quantitative screen highlighting regulator roles in retaining nucleosome binding during transcription and preserving genomic packaging.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Matan Vidavski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eli Benuck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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5
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Islam RA, Rallis C. Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging. EPIGENOMES 2023; 7:17. [PMID: 37606454 PMCID: PMC10443367 DOI: 10.3390/epigenomes7030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
Although reported in the literature, ribosome heterogeneity is a phenomenon whose extent and implications in cell and organismal biology is not fully appreciated. This has been the case due to the lack of the appropriate techniques and approaches. Heterogeneity can arise from alternative use and differential content of protein and RNA constituents, as well as from post-transcriptional and post-translational modifications. In the few examples we have, it is apparent that ribosomal heterogeneity offers an additional level and potential for gene expression regulation and might be a way towards tuning metabolism, stress, and growth programs to external and internal stimuli and needs. Here, we introduce ribosome biogenesis and discuss ribosomal heterogeneity in various reported occasions. We conclude that a systematic approach in multiple organisms will be needed to delineate this biological phenomenon and its contributions to growth, aging, and disease. Finally, we discuss ribosome mutations and their roles in disease.
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Affiliation(s)
- Rowshan Ara Islam
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Charalampos Rallis
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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6
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Qi H, Li Y, Cai M, He J, Liu J, Song X, Ma Z, Xu H, Qiao M. High‐copy genome integration and stable production of
p
‐coumaric acid via a
POT1
‐mediated strategy in
Saccharomyces cerevisiae. J Appl Microbiol 2022; 133:707-719. [DOI: 10.1111/jam.15593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Hang Qi
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
| | - Yuanzi Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
- School of Light Industry Beijing Technology and Business University (BTBU), Beijing 100048 China
| | - Miao Cai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
| | - Jiaze He
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
| | - Jiayu Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
| | - Xiaofei Song
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
- College Biotechnology and Bioengineering Zhejiang University of Technology (ZJUT), Hangzhou 310014 China
| | - Zhongqiang Ma
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences Nankai University Tianjin 300071 China
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7
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Schächner C, Merkl PE, Pilsl M, Schwank K, Hergert K, Kruse S, Milkereit P, Tschochner H, Griesenbeck J. Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes. Methods Mol Biol 2022; 2533:25-38. [PMID: 35796980 PMCID: PMC9761505 DOI: 10.1007/978-1-0716-2501-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In growing eukaryotic cells, nuclear ribosomal (r)RNA synthesis by RNA polymerase (RNAP) I accounts for the vast majority of cellular transcription. This high output is achieved by the presence of multiple copies of rRNA genes in eukaryotic genomes transcribed at a high rate. In contrast to most of the other transcribed genomic loci, actively transcribed rRNA genes are largely devoid of nucleosomes adapting a characteristic "open" chromatin state, whereas a significant fraction of rRNA genes resides in a transcriptionally inactive nucleosomal "closed" chromatin state. Here, we review our current knowledge about the nature of open rRNA gene chromatin and discuss how this state may be established.
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Affiliation(s)
- Christopher Schächner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp E Merkl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
- TUM ForTe, Technische Universität München, Munich, Germany
| | - Michael Pilsl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Katrin Schwank
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Kristin Hergert
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Sebastian Kruse
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp Milkereit
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Herbert Tschochner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Joachim Griesenbeck
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
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8
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Singh AK, Schauer T, Pfaller L, Straub T, Mueller-Planitz F. The biogenesis and function of nucleosome arrays. Nat Commun 2021; 12:7011. [PMID: 34853297 PMCID: PMC8636622 DOI: 10.1038/s41467-021-27285-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 11/09/2021] [Indexed: 11/24/2022] Open
Abstract
Numerous chromatin remodeling enzymes position nucleosomes in eukaryotic cells. Aside from these factors, transcription, DNA sequence, and statistical positioning of nucleosomes also shape the nucleosome landscape. The precise contributions of these processes remain unclear due to their functional redundancy in vivo. By incisive genome engineering, we radically decreased their redundancy in Saccharomyces cerevisiae. The transcriptional machinery strongly disrupts evenly spaced nucleosomes. Proper nucleosome density and DNA sequence are critical for their biogenesis. The INO80 remodeling complex helps space nucleosomes in vivo and positions the first nucleosome over genes in an H2A.Z-independent fashion. INO80 requires its Arp8 subunit but unexpectedly not the Nhp10 module for spacing. Cells with irregularly spaced nucleosomes suffer from genotoxic stress including DNA damage, recombination and transpositions. We derive a model of the biogenesis of the nucleosome landscape and suggest that it evolved not only to regulate but also to protect the genome.
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Affiliation(s)
- Ashish Kumar Singh
- grid.5252.00000 0004 1936 973XMolecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany
| | - Tamás Schauer
- grid.5252.00000 0004 1936 973XBioinformatics Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany
| | - Lena Pfaller
- grid.5252.00000 0004 1936 973XMolecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany ,grid.419481.10000 0001 1515 9979Present Address: Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Tobias Straub
- grid.5252.00000 0004 1936 973XBioinformatics Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany
| | - Felix Mueller-Planitz
- Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, München, Germany. .,Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
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9
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Kim JM, Visanpattanasin P, Jou V, Liu S, Tang X, Zheng Q, Li KY, Snedeker J, Lavis LD, Lionnet T, Wu C. Single-molecule imaging of chromatin remodelers reveals role of ATPase in promoting fast kinetics of target search and dissociation from chromatin. eLife 2021; 10:e69387. [PMID: 34313223 PMCID: PMC8352589 DOI: 10.7554/elife.69387] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending 'tug-of-war' that controls a temporally shifting window of accessibility for the transcription initiation machinery.
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Affiliation(s)
- Jee Min Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | | | - Vivian Jou
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Sheng Liu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Xiaona Tang
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Qinsi Zheng
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Kai Yu Li
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jonathan Snedeker
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Timothee Lionnet
- Institute of Systems Genetics, Langone Medical Center, New York UniversityNew YorkUnited States
| | - Carl Wu
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins School of MedicineBaltimoreUnited States
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10
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Guo MS, Kawamura R, Littlehale ML, Marko JF, Laub MT. High-resolution, genome-wide mapping of positive supercoiling in chromosomes. eLife 2021; 10:e67236. [PMID: 34279217 PMCID: PMC8360656 DOI: 10.7554/elife.67236] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to Escherichia coli and Saccharomyces cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently oriented genes, consistent with the 'twin-domain' model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin-binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.
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Affiliation(s)
- Monica S Guo
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Ryo Kawamura
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Megan L Littlehale
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - John F Marko
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Department of Physics and Astronomy, Northwestern UniversityEvanstonUnited States
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
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11
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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12
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Malcı K, Walls LE, Rios-Solis L. Multiplex Genome Engineering Methods for Yeast Cell Factory Development. Front Bioeng Biotechnol 2020; 8:589468. [PMID: 33195154 PMCID: PMC7658401 DOI: 10.3389/fbioe.2020.589468] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
As biotechnological applications of synthetic biology tools including multiplex genome engineering are expanding rapidly, the construction of strategically designed yeast cell factories becomes increasingly possible. This is largely due to recent advancements in genome editing methods like CRISPR/Cas tech and high-throughput omics tools. The model organism, baker's yeast (Saccharomyces cerevisiae) is an important synthetic biology chassis for high-value metabolite production. Multiplex genome engineering approaches can expedite the construction and fine tuning of effective heterologous pathways in yeast cell factories. Numerous multiplex genome editing techniques have emerged to capitalize on this recently. This review focuses on recent advancements in such tools, such as delta integration and rDNA cluster integration coupled with CRISPR-Cas tools to greatly enhance multi-integration efficiency. Examples of pre-placed gate systems which are an innovative alternative approach for multi-copy gene integration were also reviewed. In addition to multiple integration studies, multiplexing of alternative genome editing methods are also discussed. Finally, multiplex genome editing studies involving non-conventional yeasts and the importance of automation for efficient cell factory design and construction are considered. Coupling the CRISPR/Cas system with traditional yeast multiplex genome integration or donor DNA delivery methods expedites strain development through increased efficiency and accuracy. Novel approaches such as pre-placing synthetic sequences in the genome along with improved bioinformatics tools and automation technologies have the potential to further streamline the strain development process. In addition, the techniques discussed to engineer S. cerevisiae, can be adapted for use in other industrially important yeast species for cell factory development.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| | - Laura E Walls
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
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13
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Yu Y, Rasool A, Liu H, Lv B, Chang P, Song H, Wang Y, Li C. Engineering Saccharomyces cerevisiae for high yield production of α-amyrin via synergistic remodeling of α-amyrin synthase and expanding the storage pool. Metab Eng 2020; 62:72-83. [DOI: 10.1016/j.ymben.2020.08.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/15/2020] [Accepted: 08/15/2020] [Indexed: 12/19/2022]
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14
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Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D. Trends Genet 2020; 36:967-980. [PMID: 32713597 DOI: 10.1016/j.tig.2020.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
In eukaryotes, DNA replication progresses through a finely orchestrated temporal and spatial program. The 3D genome structure and nuclear architecture have recently emerged as fundamental determinants of the replication program. Factors with established roles in replication have been recognized as genome organization regulators. Exploiting paradigms from yeasts and mammals, we discuss how DNA replication is regulated in time and space through DNA-associated trans-acting factors, diffusible limiting replication initiation factors, higher-order chromatin folding, dynamic origin localization, and specific nuclear microenvironments. We present an integrated model for the regulation of DNA replication in 3D and highlight the importance of accurate spatio-temporal regulation of DNA replication in physiology and disease.
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15
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Chen L, Huang W, Wang L, Zhang Z, Zhang F, Zheng S, Kong D. The effects of epigenetic modification on the occurrence and progression of liver diseases and the involved mechanism. Expert Rev Gastroenterol Hepatol 2020; 14:259-270. [PMID: 32124651 DOI: 10.1080/17474124.2020.1736042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Epigenetic modification is a type of gene expression and regulation that does not involve changes in DNA sequences. An increasing number of studies have proven that epigenetic modifications play an important role in the occurrence and progression of liver diseases through the gene regulation and protein expressions of hepatocellular lipid metabolism, inflammatory reaction, cell proliferation, and activation, etc.Areas covered: In this study, we elaborated and analyzed the underlying functional mechanism of epigenetic modification in alcoholic liver disease (ALD), nonalcoholic fatty liver disease (NAFLD), liver fibrosis (LF), viral hepatitis, hepatocellular carcinoma (HCC), and research progress of recent years.Expert opinion: The further understanding of epigenetic mechanisms that can regulate gene expression and cell phenotype leads to new insights in epigenetic control of chronic liver disease. Currently, hepatologists are exploring the role of DNA methylation, histone/chromatin modification, and non-coding RNA in specific liver pathology. These findings have led to advances in direct epigenetic biomarker testing of patient tissue or body fluid specimens, as well as quantitative analysis. Based on these findings, drug validation of some targets involved in the epigenetic mechanism of liver disease is gradually being carried out clinically.
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Affiliation(s)
- Liping Chen
- Chinese Medicine Modernization and Big Data Research Center, Nanjing Hospital of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Weifang Huang
- Department of Pharmacology, School of Integral Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling Wang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zili Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Feng Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shizhong Zheng
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Desong Kong
- Chinese Medicine Modernization and Big Data Research Center, Nanjing Hospital of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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16
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Forey R, Poveda A, Sharma S, Barthe A, Padioleau I, Renard C, Lambert R, Skrzypczak M, Ginalski K, Lengronne A, Chabes A, Pardo B, Pasero P. Mec1 Is Activated at the Onset of Normal S Phase by Low-dNTP Pools Impeding DNA Replication. Mol Cell 2020; 78:396-410.e4. [PMID: 32169162 DOI: 10.1016/j.molcel.2020.02.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/09/2020] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
The Mec1 and Rad53 kinases play a central role during acute replication stress in budding yeast. They are also essential for viability in normal growth conditions, but the signal that activates the Mec1-Rad53 pathway in the absence of exogenous insults is currently unknown. Here, we show that this pathway is active at the onset of normal S phase because deoxyribonucleotide triphosphate (dNTP) levels present in G1 phase may not be sufficient to support processive DNA synthesis and impede DNA replication. This activation can be suppressed experimentally by increasing dNTP levels in G1 phase. Moreover, we show that unchallenged cells entering S phase in the absence of Rad53 undergo irreversible fork collapse and mitotic catastrophe. Together, these data indicate that cells use suboptimal dNTP pools to detect the onset of DNA replication and activate the Mec1-Rad53 pathway, which in turn maintains functional forks and triggers dNTP synthesis, allowing the completion of DNA replication.
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Affiliation(s)
- Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Ana Poveda
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France; Instituto de Investigación en Salud Pública y Zoonosis, Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Ismael Padioleau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Claire Renard
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Robin Lambert
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Benjamin Pardo
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
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17
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Soudet J, Stutz F. Regulation of Gene Expression and Replication Initiation by Non‐Coding Transcription: A Model Based on Reshaping Nucleosome‐Depleted Regions. Bioessays 2019; 41:e1900043. [DOI: 10.1002/bies.201900043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/19/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Julien Soudet
- Department of Cell BiologyUniversity of Geneva 1211 Geneva Switzerland
| | - Françoise Stutz
- Department of Cell BiologyUniversity of Geneva 1211 Geneva Switzerland
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