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Engl W, Kunstar-Thomas A, Chen S, Ng WS, Sielaff H, Zhao ZW. Single-molecule imaging of SWI/SNF chromatin remodelers reveals bromodomain-mediated and cancer-mutants-specific landscape of multi-modal DNA-binding dynamics. Nat Commun 2024; 15:7646. [PMID: 39223123 PMCID: PMC11369179 DOI: 10.1038/s41467-024-52040-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Despite their prevalent cancer implications, the in vivo dynamics of SWI/SNF chromatin remodelers and how misregulation of such dynamics underpins cancer remain poorly understood. Using live-cell single-molecule tracking, we quantify the intranuclear diffusion and chromatin-binding of three key subunits common to all major human SWI/SNF remodeler complexes (BAF57, BAF155 and BRG1), and resolve two temporally distinct stable binding modes for the fully assembled complex. Super-resolved density mapping reveals heterogeneous, nanoscale remodeler binding "hotspots" across the nucleoplasm where multiple binding events (especially longer-lived ones) preferentially cluster. Importantly, we uncover distinct roles of the bromodomain in modulating chromatin binding/targeting in a DNA-accessibility-dependent manner, pointing to a model where successive longer-lived binding within "hotspots" leads to sustained productive remodeling. Finally, systematic comparison of six common BRG1 mutants implicated in various cancers unveils alterations in chromatin-binding dynamics unique to each mutant, shedding insight into a multi-modal landscape regulating the spatio-temporal organizational dynamics of SWI/SNF remodelers.
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Affiliation(s)
- Wilfried Engl
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Aliz Kunstar-Thomas
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Siyi Chen
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore.
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, 119077, Singapore.
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2
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Malone HA, Roberts CWM. Chromatin remodellers as therapeutic targets. Nat Rev Drug Discov 2024; 23:661-681. [PMID: 39014081 DOI: 10.1038/s41573-024-00978-5] [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] [Accepted: 05/28/2024] [Indexed: 07/18/2024]
Abstract
Large-scale cancer genome sequencing studies have revealed that chromatin regulators are frequently mutated in cancer. In particular, more than 20% of cancers harbour mutations in genes that encode subunits of SWI/SNF (BAF) chromatin remodelling complexes. Additional links of SWI/SNF complexes to disease have emerged with the findings that some oncogenes drive transformation by co-opting SWI/SNF function and that germline mutations in select SWI/SNF subunits are the basis of several neurodevelopmental disorders. Other chromatin remodellers, including members of the ISWI, CHD and INO80/SWR complexes, have also been linked to cancer and developmental disorders. Consequently, therapeutic manipulation of SWI/SNF and other remodelling complexes has become of great interest, and drugs that target SWI/SNF subunits have entered clinical trials. Genome-wide perturbation screens in cancer cell lines with SWI/SNF mutations have identified additional synthetic lethal targets and led to further compounds in clinical trials, including one that has progressed to FDA approval. Here, we review the progress in understanding the structure and function of SWI/SNF and other chromatin remodelling complexes, mechanisms by which SWI/SNF mutations cause cancer and neurological diseases, vulnerabilities that arise because of these mutations and efforts to target SWI/SNF complexes and synthetic lethal targets for therapeutic benefit.
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Affiliation(s)
- Hayden A Malone
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA.
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3
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Affiliation(s)
- Kangjing Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Junjie Yuan
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China,Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, Beijing, China
| | - Youyang Sia
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Zhucheng Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China,Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, Beijing, China,CONTACT Zhucheng Chen MOE Key Laboratory of Protein Science, Tsinghua University, Beijing100084, P.R. China
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4
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Saha D, Hailu S, Hada A, Lee J, Luo J, Ranish JA, Lin YC, Feola K, Persinger J, Jain A, Liu B, Lu Y, Sen P, Bartholomew B. The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming. Nat Commun 2023; 14:4682. [PMID: 37542049 PMCID: PMC10403523 DOI: 10.1038/s41467-023-40386-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit's AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Solomon Hailu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- Illumina, 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Arjan Hada
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jeff A Ranish
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Yuan-Chi Lin
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- BioAgilytix, Durham, NC, 27713, USA
| | - Kyle Feola
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- Department of Internal Medicine (Nephrology) and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jim Persinger
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Abhinav Jain
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA.
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA.
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5
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Singh A, Modak SB, Chaturvedi MM, Purohit JS. SWI/SNF Chromatin Remodelers: Structural, Functional and Mechanistic Implications. Cell Biochem Biophys 2023:10.1007/s12013-023-01140-5. [PMID: 37119511 DOI: 10.1007/s12013-023-01140-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
The nuclear events of a eukaryotic cell, such as replication, transcription, recombination and repair etc. require the transition of the compactly arranged chromatin into an uncompacted state and vice-versa. This is mediated by post-translational modification of the histones, exchange of histone variants and ATP-dependent chromatin remodeling. The SWI/SNF chromatin remodeling complexes are one of the most well characterized families of chromatin remodelers. In addition to their role in modulating chromatin, they have also been assigned roles in cancer and health-related anomalies such as developmental, neurocognitive, and intellectual disabilities. Owing to their vital cellular and medical connotations, developing an understanding of the structural and functional aspects of the complex becomes imperative. However, due to the intricate nature of higher-order chromatin as well as compositional heterogeneity of the SWI/SNF complex, intra-species isoforms and inter-species homologs, this often becomes challenging. To this end, the present review attempts to present an amalgamated perspective on the discovery, structure, function, and regulation of the SWI/SNF complex.
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Affiliation(s)
- Abhilasha Singh
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | | | - Madan M Chaturvedi
- Department of Zoology, University of Delhi, Delhi, 110007, India
- SGT University, Gurugram (Delhi-NCR), Haryana, 122505, India
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6
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Sadek M, Sheth A, Zimmerman G, Hays E, Vélez-Cruz R. The role of SWI/SNF chromatin remodelers in the repair of DNA double strand breaks and cancer therapy. Front Cell Dev Biol 2022; 10:1071786. [PMID: 36605718 PMCID: PMC9810387 DOI: 10.3389/fcell.2022.1071786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Switch/Sucrose non-fermenting (SWI/SNF) chromatin remodelers hydrolyze ATP to push and slide nucleosomes along the DNA thus modulating access to various genomic loci. These complexes are the most frequently mutated epigenetic regulators in human cancers. SWI/SNF complexes are well known for their function in transcription regulation, but more recent work has uncovered a role for these complexes in the repair of DNA double strand breaks (DSBs). As radiotherapy and most chemotherapeutic agents kill cancer cells by inducing double strand breaks, by identifying a role for these complexes in double strand break repair we are also identifying a DNA repair vulnerability that can be exploited therapeutically in the treatment of SWI/SNF-mutated cancers. In this review we summarize work describing the function of various SWI/SNF subunits in the repair of double strand breaks with a focus on homologous recombination repair and discuss the implication for the treatment of cancers with SWI/SNF mutations.
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Affiliation(s)
- Maria Sadek
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Anand Sheth
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL, United States
| | - Grant Zimmerman
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL, United States
| | - Emily Hays
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
| | - Renier Vélez-Cruz
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL, United States
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies, Midwestern University, Downers Grove, IL, United States
- Chicago College of Optometry, Midwestern University, Downers Grove, IL, United States
- Chicago College of Pharmacy, Midwestern University, Downers Grove, IL, United States
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7
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Wang L, Yu J, Yu Z, Wang Q, Li W, Ren Y, Chen Z, He S, Xu Y. Structure of nucleosome-bound human PBAF complex. Nat Commun 2022; 13:7644. [PMID: 36496390 PMCID: PMC9741621 DOI: 10.1038/s41467-022-34859-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.
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Affiliation(s)
- Li Wang
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.11841.3d0000 0004 0619 8943The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Jiali Yu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Zishuo Yu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Qianmin Wang
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Wanjun Li
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Yulei Ren
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Zhenguo Chen
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443The Fifth People’s Hospital of Shanghai, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Shuang He
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Yanhui Xu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.11841.3d0000 0004 0619 8943The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433 China
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8
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Bhat JA, Balliano AJ, Hayes JJ. Histone protein surface accessibility dictates direction of RSC-dependent nucleosome mobilization. Nucleic Acids Res 2022; 50:10376-10384. [PMID: 36161493 PMCID: PMC9561379 DOI: 10.1093/nar/gkac790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/23/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Chromatin remodeling enzymes use energy derived from ATP hydrolysis to mobilize nucleosomes and alter their structure to facilitate DNA access. The Remodels the Structure of Chromatin (RSC) complex has been extensively studied, yet aspects of how this complex functionally interacts with nucleosomes remain unclear. We introduce a steric mapping approach to determine how RSC activity depends on interaction with specific surfaces within the nucleosome. We find that blocking SHL + 4.5/–4.5 via streptavidin binding to the H2A N-terminal tail domains results in inhibition of RSC nucleosome mobilization. However, restriction enzyme assays indicate that remodeling-dependent exposure of an internal DNA site near the nucleosome dyad is not affected. In contrast, occlusion of both protein faces of the nucleosome by streptavidin attachment near the acidic patch completely blocks both remodeling-dependent nucleosome mobilization and internal DNA site exposure. However, we observed partial inhibition when only one protein surface is occluded, consistent with abrogation of one of two productive RSC binding orientations. Our results indicate that nucleosome mobilization requires RSC access to the trailing but not the leading protein surface, and reveals a mechanism by which RSC and related complexes may drive unidirectional movement of nucleosomes to regulate cis-acting DNA sequences in vivo.
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Affiliation(s)
- Javeed Ahmad Bhat
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Angela J Balliano
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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9
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Cooper GW, Hong AL. SMARCB1-Deficient Cancers: Novel Molecular Insights and Therapeutic Vulnerabilities. Cancers (Basel) 2022; 14:cancers14153645. [PMID: 35892904 PMCID: PMC9332782 DOI: 10.3390/cancers14153645] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Loss of SMARCB1 has been identified as the sole mutation in a number of rare pediatric and adult cancers, most of which have a poor prognosis despite intensive therapies including surgery, radiation, and chemotherapy. Thus, a more robust understanding of the mechanisms driving this set of cancers is vital to improving patient treatment and outcomes. This review outlines recent advances made in our understanding of the function of SMARCB1 and how these advances have been used to discover putative therapeutic vulnerabilities. Abstract SMARCB1 is a critical component of the BAF complex that is responsible for global chromatin remodeling. Loss of SMARCB1 has been implicated in the initiation of cancers such as malignant rhabdoid tumor (MRT), atypical teratoid rhabdoid tumor (ATRT), and, more recently, renal medullary carcinoma (RMC). These SMARCB1-deficient tumors have remarkably stable genomes, offering unique insights into the epigenetic mechanisms in cancer biology. Given the lack of druggable targets and the high mortality associated with SMARCB1-deficient tumors, a significant research effort has been directed toward understanding the mechanisms of tumor transformation and proliferation. Accumulating evidence suggests that tumorigenicity arises from aberrant enhancer and promoter regulation followed by dysfunctional transcriptional control. In this review, we outline key mechanisms by which loss of SMARCB1 may lead to tumor formation and cover how these mechanisms have been used for the design of targeted therapy.
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Affiliation(s)
- Garrett W. Cooper
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Andrew L. Hong
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
- Correspondence:
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10
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Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Nature 2022; 605:166-171. [PMID: 35477757 DOI: 10.1038/s41586-022-04658-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
DNA wraps around the histone octamer to form nucleosomes1, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy of ATP binding and hydrolysis to reposition and recompose the nucleosome, and have vital roles in various chromatin-based transactions2,3. Here we report the cryo-electron microscopy structure of the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome. The motor subunit SMARCA4 engages the nucleosome in the active conformation, which reveals clustering of multiple disease-associated mutations at the interfaces that are essential for chromatin-remodelling activity. SMARCA4 recognizes the H2A-H2B acidic pocket of the nucleosome through three arginine anchors of the Snf2 ATP coupling (SnAc) domain. PBAF shows notable functional modularity, and most of the auxiliary subunits are interwoven into three lobe-like submodules for nucleosome recognition. The PBAF-specific auxiliary subunit ARID2 acts as the structural core for assembly of the DNA-binding lobe, whereas PBRM1, PHF10 and BRD7 are collectively incorporated into the lobe for histone tail binding. Together, our findings provide mechanistic insights into nucleosome recognition by PBAF and a structural basis for understanding SMARCA4-related human diseases.
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11
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Acidic patch histone mutations and their effects on nucleosome remodeling. Biochem Soc Trans 2022; 50:907-919. [PMID: 35356970 DOI: 10.1042/bst20210773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 12/15/2022]
Abstract
Structural and biochemical studies have identified a histone surface on each side of the nucleosome disk termed 'the nucleosome acidic patch' that acts as a regulatory hub for the function of numerous nuclear proteins, including ATP-dependent chromatin complexes (remodelers). Four major remodeler subfamilies, SWI/SNF, ISWI, CHD, and INO80, have distinct modes of interaction with one or both nucleosome acidic patches, contributing to their specific remodeling outcomes. Genome-wide sequencing analyses of various human cancers have uncovered high-frequency mutations in histone coding genes, including some that map to the acidic patch. How cancer-related acidic patch histone mutations affect nucleosome remodeling is mainly unknown. Recent advances in in vitro chromatin reconstitution have enabled access to physiologically relevant nucleosomes, including asymmetric nucleosomes that possess both wild-type and acidic patch mutant histone copies. Biochemical investigation of these substrates revealed unexpected remodeling outcomes with far-reaching implications for alteration of chromatin structure. This review summarizes recent findings of how different remodeler families interpret wild-type and mutant acidic patches for their remodeling functions and discusses models for remodeler-mediated changes in chromatin landscapes as a consequence of acidic patch mutations.
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12
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Rowland ME, Jajarmi JM, Osborne TSM, Ciernia AV. Insights Into the Emerging Role of Baf53b in Autism Spectrum Disorder. Front Mol Neurosci 2022; 15:805158. [PMID: 35185468 PMCID: PMC8852769 DOI: 10.3389/fnmol.2022.805158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Accurate and precise regulation of gene expression is necessary to ensure proper brain development and plasticity across the lifespan. As an ATP-dependent chromatin-remodeling complex, the BAF (Brg1 Associated Factor) complex can alter histone-DNA interactions, facilitating dynamic changes in gene expression by controlling DNA accessibility to the transcriptional machinery. Mutations in 12 of the potential 29 subunit genes that compose the BAF nucleosome remodeling complex have been identified in several developmental disorders including Autism spectrum disorders (ASD) and intellectual disability. A novel, neuronal version of BAF (nBAF) has emerged as promising candidate in the development of ASD as its expression is tied to neuron differentiation and it’s hypothesized to coordinate expression of synaptic genes across brain development. Recently, mutations in BAF53B, one of the neuron specific subunits of the nBAF complex, have been identified in patients with ASD and Developmental and epileptic encephalopathy-76 (DEE76), indicating BAF53B is essential for proper brain development. Recent work in cultured neurons derived from patients with BAF53B mutations suggests links between loss of nBAF function and neuronal dendritic spine formation. Deletion of one or both copies of mouse Baf53b disrupts dendritic spine development, alters actin dynamics and results in fewer synapses in vitro. In the mouse, heterozygous loss of Baf53b severely impacts synaptic plasticity and long-term memory that is reversible with reintroduction of Baf53b or manipulations of the synaptic plasticity machinery. Furthermore, surviving Baf53b-null mice display ASD-related behaviors, including social impairments and repetitive behaviors. This review summarizes the emerging evidence linking deleterious variants of BAF53B identified in human neurodevelopmental disorders to abnormal transcriptional regulation that produces aberrant synapse development and behavior.
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Kim B, Luo Y, Zhan X, Zhang Z, Shi X, Yi J, Xuan Z, Wu J. Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation. Cell Rep 2021; 36:109357. [PMID: 34260936 PMCID: PMC8315893 DOI: 10.1016/j.celrep.2021.109357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/16/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Neuronal activity-induced enhancers drive gene activation. We demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. We identify a serine phosphorylation site in BRG1 that is induced by neuronal stimulations and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, including the NuRD repressor complex and cohesin, possibly modulating BRG1-mediated transcription outcomes. Using mice with knockin mutations, we show that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases enhancer activity and inducibility. These mutant mice display anxiety-like phenotypes and altered responses to stress. Therefore, we reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.
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Affiliation(s)
- BongWoo Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Luo
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zilai Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuanming Shi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiaqing Yi
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Jiang Wu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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14
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Structural basis of ALC1/CHD1L autoinhibition and the mechanism of activation by the nucleosome. Nat Commun 2021; 12:4057. [PMID: 34210977 PMCID: PMC8249414 DOI: 10.1038/s41467-021-24320-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/09/2021] [Indexed: 12/20/2022] Open
Abstract
Chromatin remodeler ALC1 (amplification in liver cancer 1) is crucial for repairing damaged DNA. It is autoinhibited and activated by nucleosomal epitopes. However, the mechanisms by which ALC1 is regulated remain unclear. Here we report the crystal structure of human ALC1 and the cryoEM structure bound to the nucleosome. The structure shows the macro domain of ALC1 binds to lobe 2 of the ATPase motor, sequestering two elements for nucleosome recognition, explaining the autoinhibition mechanism of the enzyme. The H4 tail competes with the macro domain for lobe 2-binding, explaining the requirement for this nucleosomal epitope for ALC1 activation. A dual-arginine-anchor motif of ALC1 recognizes the acidic pocket of the nucleosome, which is critical for chromatin remodeling in vitro. Together, our findings illustrate the structures of ALC1 and shed light on its regulation mechanisms, paving the way for the discovery of drugs targeting ALC1 for the treatment of cancer. The oncogenic chromatin remodeler ALC1 (amplification in liver cancer 1), also known as CHD1L is an ATP-dependent chromatin remodeler that relaxes chromatin and plays an important role in the poly(ADP-ribose) polymerase 1 -mediated DNA repair pathway. Here, the authors present the ALC1 crystal structure and a cryo-EM structure of ALC1 bound to a nucleosome, which reveal that ALC1 is autoinhibited and how it becomes activated.
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15
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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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16
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Yao B, Gui T, Zeng X, Deng Y, Wang Z, Wang Y, Yang D, Li Q, Xu P, Hu R, Li X, Chen B, Wang J, Zen K, Li H, Davis MJ, Herold MJ, Pan HF, Jiang ZW, Huang DCS, Liu M, Ju J, Zhao Q. PRMT1-mediated H4R3me2a recruits SMARCA4 to promote colorectal cancer progression by enhancing EGFR signaling. Genome Med 2021; 13:58. [PMID: 33853662 PMCID: PMC8048298 DOI: 10.1186/s13073-021-00871-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/17/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Aberrant changes in epigenetic mechanisms such as histone modifications play an important role in cancer progression. PRMT1 which triggers asymmetric dimethylation of histone H4 on arginine 3 (H4R3me2a) is upregulated in human colorectal cancer (CRC) and is essential for cell proliferation. However, how this dysregulated modification might contribute to malignant transitions of CRC remains poorly understood. METHODS In this study, we integrated biochemical assays including protein interaction studies and chromatin immunoprecipitation (ChIP), cellular analysis including cell viability, proliferation, colony formation, and migration assays, clinical sample analysis, microarray experiments, and ChIP-Seq data to investigate the potential genomic recognition pattern of H4R3me2s in CRC cells and its effect on CRC progression. RESULTS We show that PRMT1 and SMARCA4, an ATPase subunit of the SWI/SNF chromatin remodeling complex, act cooperatively to promote colorectal cancer (CRC) progression. We find that SMARCA4 is a novel effector molecule of PRMT1-mediated H4R3me2a. Mechanistically, we show that H4R3me2a directly recruited SMARCA4 to promote the proliferative, colony-formative, and migratory abilities of CRC cells by enhancing EGFR signaling. We found that EGFR and TNS4 were major direct downstream transcriptional targets of PRMT1 and SMARCA4 in colon cells, and acted in a PRMT1 methyltransferase activity-dependent manner to promote CRC cell proliferation. In vivo, knockdown or inhibition of PRMT1 profoundly attenuated the growth of CRC cells in the C57BL/6 J-ApcMin/+ CRC mice model. Importantly, elevated expression of PRMT1 or SMARCA4 in CRC patients were positively correlated with expression of EGFR and TNS4, and CRC patients had shorter overall survival. These findings reveal a critical interplay between epigenetic and transcriptional control during CRC progression, suggesting that SMARCA4 is a novel key epigenetic modulator of CRC. Our findings thus highlight PRMT1/SMARCA4 inhibition as a potential therapeutic intervention strategy for CRC. CONCLUSION PRMT1-mediated H4R3me2a recruits SMARCA4, which promotes colorectal cancer progression by enhancing EGFR signaling.
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Affiliation(s)
- Bing Yao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.,Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Tao Gui
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xiangwei Zeng
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Yexuan Deng
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Zhi Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Dongjun Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Qixiang Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Peipei Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ruifeng Hu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Xinyu Li
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Bing Chen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Jin Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ke Zen
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Hua-Feng Pan
- Department of General Surgery, the Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi-Wei Jiang
- Department of General Surgery, the Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
| | - Junyi Ju
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Hematology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, China-Australia Institute of Translational Medicine, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China.
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17
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Marcum RD, Reyes AA, He Y. Structural Insights into the Evolutionarily Conserved BAF Chromatin Remodeling Complex. BIOLOGY 2020; 9:biology9070146. [PMID: 32629987 PMCID: PMC7408276 DOI: 10.3390/biology9070146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022]
Abstract
The switch/sucrose nonfermentable (SWI/SNF) family of proteins acts to regulate chromatin accessibility and plays an essential role in multiple cellular processes. A high frequency of mutations has been found in SWI/SNF family subunits by exome sequencing in human cancer, and multiple studies support its role in tumor suppression. Recent structural studies of yeast SWI/SNF and its human homolog, BAF (BRG1/BRM associated factor), have provided a model for their complex assembly and their interaction with nucleosomal substrates, revealing the molecular function of individual subunits as well as the potential impact of cancer-associated mutations on the remodeling function. Here we review the structural conservation between yeast SWI/SNF and BAF and examine the role of highly mutated subunits within the BAF complex.
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Affiliation(s)
- Ryan D. Marcum
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; (R.D.M.); (A.A.R.)
| | - Alexis A. Reyes
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; (R.D.M.); (A.A.R.)
- Interdisciplinary Biological Sciences Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; (R.D.M.); (A.A.R.)
- Interdisciplinary Biological Sciences Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, 676 N. St. Clair, Chicago, IL 60611, USA
- Correspondence:
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18
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Willhoft O, Wigley DB. INO80 and SWR1 complexes: the non-identical twins of chromatin remodelling. Curr Opin Struct Biol 2020; 61:50-58. [PMID: 31838293 PMCID: PMC7171469 DOI: 10.1016/j.sbi.2019.09.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/07/2019] [Indexed: 02/06/2023]
Abstract
The INO80 family of chromatin remodellers are multisubunit complexes that perform a variety of tasks on nucleosomes. Family members are built around a heterohexamer of RuvB-like protein, an ATP-dependent DNA translocase,nuclear actin and actin-related proteins, and a few complex-specific subunits. They modify chromatin in a number of ways including nucleosome sliding and exchange of variant histones. Recent structural information on INO80 and SWR1 complexes has revealed similarities in the basic architecture of the complexes. However, structural and biochemical data on the complexes bound to nucleosomes reveal these similarities to be somewhat superficial and their biochemical activities and mechanisms are very different. Consequently, the INO80 family displays a surprising diversity of function that is based upon a similar structural framework.
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Affiliation(s)
- Oliver Willhoft
- Section of Structural and Synthetic Biology, Dept. Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Dale B Wigley
- Section of Structural and Synthetic Biology, Dept. Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
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19
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Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome. Nature 2020; 579:448-451. [PMID: 32188943 PMCID: PMC7093204 DOI: 10.1038/s41586-020-2088-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/08/2020] [Indexed: 12/25/2022]
Abstract
Chromatin remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted, transcriptionally active promoter regions (NDRs)1,2. The essential Saccharomyces cerevisiae SWI/SNF complex RSC3 contains 16 subunits, including the ATP-dependent DNA translocase Sth14,5. RSC removes nucleosomes from promoter regions6,7 and positions the specialized +1 and –1 nucleosomes that flank NDRs8,9. Here, we present the cryo-EM structure of RSC in complex with a nucleosome substrate. The structure reveals that RSC forms five protein modules and suggests key features of the remodelling mechanism. The body module serves as a scaffold for the four flexible modules that we call DNA-interacting, ATPase, arm and ARP modules. The DNA-interacting module binds extra-nucleosomal DNA and is involved in the recognition of promoter DNA elements8,10,11 that influence RSC functionality12. The ATPase and arm modules sandwich the nucleosome disc with their ‘SnAC’ and ‘finger’ elements, respectively. The translocase motor of the ATPase module engages with the edge of the nucleosome at superhelical location +2. The mobile ARP module may modulate translocase-nucleosome interactions to regulate RSC activity5. The RSC-nucleosome structure provides a basis for understanding NDR formation and the structure and function of human SWI/SNF complexes that are frequently mutated in cancer13.
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20
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He S, Wu Z, Tian Y, Yu Z, Yu J, Wang X, Li J, Liu B, Xu Y. Structure of nucleosome-bound human BAF complex. Science 2020; 367:875-881. [PMID: 32001526 DOI: 10.1126/science.aaz9761] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/10/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022]
Abstract
Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.
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Affiliation(s)
- Shuang He
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zihan Wu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yuan Tian
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jiali Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jie Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Bijun Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China. .,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.,Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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21
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Kang H, Wu D, Fan T, Zhu Y. Activities of Chromatin Remodeling Factors and Histone Chaperones and Their Effects in Root Apical Meristem Development. Int J Mol Sci 2020; 21:ijms21030771. [PMID: 31991579 PMCID: PMC7038114 DOI: 10.3390/ijms21030771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic genes are packaged into dynamic but stable chromatin structures to deal with transcriptional reprogramming and inheritance during development. Chromatin remodeling factors and histone chaperones are epigenetic factors that target nucleosomes and/or histones to establish and maintain proper chromatin structures during critical physiological processes such as DNA replication and transcriptional modulation. Root apical meristems are vital for plant root development. Regarding the well-characterized transcription factors involved in stem cell proliferation and differentiation, there is increasing evidence of the functional implications of epigenetic regulation in root apical meristem development. In this review, we focus on the activities of chromatin remodeling factors and histone chaperones in the root apical meristems of the model plant species Arabidopsis and rice.
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22
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Yan L, Chen Z. A Unifying Mechanism of DNA Translocation Underlying Chromatin Remodeling. Trends Biochem Sci 2019; 45:217-227. [PMID: 31623923 DOI: 10.1016/j.tibs.2019.09.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022]
Abstract
Chromatin remodelers alter the position and composition of nucleosomes, and play key roles in the regulation of chromatin structure and various chromatin-based transactions. Recent cryo-electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) studies have shed mechanistic light on the fundamental question of how the remodeling enzymes couple with ATP hydrolysis to slide nucleosomes. Structures of the chromatin remodeler Snf2 bound to the nucleosome reveal the conformational cycle of the enzyme and the induced DNA distortion. Investigations on ISWI, Chd1, and INO80 support a unifying fundamental mechanism of DNA translocation. Finally, studies of the SWR1 complex suggest that the enzyme distorts the DNA abnormally to achieve histone exchange without net DNA translocation.
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Affiliation(s)
- Lijuan Yan
- Ministry of Education (MOE) Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, PRC; School of Life Science, Tsinghua University, Beijing 100084, PRC
| | - Zhucheng Chen
- Ministry of Education (MOE) Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, PRC; School of Life Science, Tsinghua University, Beijing 100084, PRC; Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing 100084, PRC.
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Jayaprakash S, Drakulic S, Zhao Z, Sander B, Golas MM. The ATPase BRG1/SMARCA4 is a protein interaction platform that recruits BAF subunits and the transcriptional repressor REST/NRSF in neural progenitor cells. Mol Cell Biochem 2019; 461:171-182. [DOI: 10.1007/s11010-019-03600-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
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Regulation of ATP-dependent chromatin remodelers: accelerators/brakes, anchors and sensors. Biochem Soc Trans 2018; 46:1423-1430. [PMID: 30467122 DOI: 10.1042/bst20180043] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022]
Abstract
All ATP-dependent chromatin remodelers have a DNA translocase domain that moves along double-stranded DNA when hydrolyzing ATP, which is the key action leading to DNA moving through nucleosomes. Recent structural and biochemical data from a variety of different chromatin remodelers have revealed that there are three basic ways in which these remodelers self-regulate their chromatin remodeling activity. In several instances, different domains within the catalytic subunit or accessory subunits through direct protein-protein interactions can modulate the ATPase and DNA translocation properties of the DNA translocase domain. These domains or subunits can stabilize conformations that either promote or interfere with the ability of the translocase domain to bind or retain DNA during translocation or alter the ability of the enzyme to hydrolyze ATP. Second, other domains or subunits are often necessary to anchor the remodeler to nucleosomes to couple DNA translocation and ATP hydrolysis to DNA movement around the histone octamer. These anchors provide a fixed point by which remodelers can generate sufficient torque to disrupt histone-DNA interactions and mobilize nucleosomes. The third type of self-regulation is in those chromatin remodelers that space nucleosomes or stop moving nucleosomes when a particular length of linker DNA has been reached. We refer to this third class as DNA sensors that can allosterically regulate nucleosome mobilization. In this review, we will show examples of these from primarily the INO80/SWR1, SWI/SNF and ISWI/CHD families of remodelers.
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Partial Inactivation of the Chromatin Remodelers SMARCA2 and SMARCA4 in Virus-Infected Cells by Caspase-Mediated Cleavage. J Virol 2018; 92:JVI.00343-18. [PMID: 29848589 DOI: 10.1128/jvi.00343-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/22/2018] [Indexed: 01/18/2023] Open
Abstract
The BAF-chromatin remodeling complex, with its mutually exclusive ATPases SMARCA2 and SMARCA4, is essential for the transcriptional activation of numerous genes, including a subset of interferon-stimulated genes (ISGs). Here, we show that C-terminally truncated forms of both SMARCA2 and SMARCA4 accumulate in cells infected with different RNA or DNA viruses. The levels of truncated SMARCA2 or SMARCA4 strongly correlate with the degree of cell damage and death observed after virus infection. The use of a pan-caspase inhibitor and genetically modified cell lines unable to undergo apoptosis revealed that the truncated forms result from the activity of caspases downstream of the activated intrinsic apoptotic pathway. C-terminally cleaved SMARCA2 and SMARCA4 lack potential nuclear localization signals as well as the bromo- and SnAC domain, with the latter two domains believed to be essential for chromatin association and remodeling. Consistent with this belief, C-terminally truncated SMARCA2 was partially relocated to the cytoplasm. However, the remaining nuclear protein was sufficient to induce ISG expression and inhibit the replication of vesicular stomatitis virus and influenza A virus. This suggests that virus-induced apoptosis does not occur at the expense of an intact interferon-mediated antiviral response pathway.IMPORTANCE Efficient induction of interferon-stimulated genes (ISGs) prior to infection is known to effectively convert a cell into an antiviral state, blocking viral replication. Additionally, cells can undergo caspase-mediated apoptosis to control viral infection. Here, we identify SMARCA2 and SMARCA4 to be essential for the efficient induction of ISGs but also to be targeted by cellular caspases downstream of the intrinsic apoptotic pathway. We find that C-terminally cleaved SMARCA2 and SMARCA4 accumulate at late stages of infection, when cell damage already had occurred. Cleavage of the C terminus removes domains important for nuclear localization and chromatin binding of SMARCA2 and SMARCA4. Consequently, the cleaved forms are unable to efficiently accumulate in the cell nucleus. Intriguingly, the remaining nuclear C-terminally truncated SMARCA2 still induced ISG expression, although to lower levels. These data suggest that in virus-infected cells caspase-mediated cell death does not completely inactivate the SMARCA2- and SMARCA4-dependent interferon signaling pathway.
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Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase. Commun Biol 2018; 1:1. [PMID: 29809203 PMCID: PMC5969521 DOI: 10.1038/s42003-017-0002-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The catalytic subunits of SWI/SNF-family and INO80-family chromatin remodelers bind actin and actin-related proteins (Arps) through an N-terminal helicase/SANT-associated (HSA) domain. Between the HSA and ATPase domains lies a conserved post-HSA (pHSA) domain. The HSA domain of Sth1, the catalytic subunit of the yeast SWI/SNF-family remodeler RSC, recruits the Rtt102-Arp7/9 heterotrimer. Rtt102-Arp7/9 regulates RSC function, but the mechanism is unclear. We show that the pHSA domain interacts directly with another conserved region of the catalytic subunit, protrusion-1. Rtt102-Arp7/9 binding to the HSA domain weakens this interaction and promotes the formation of stable, monodisperse complexes with DNA and nucleosomes. A crystal structure of Rtt102-Arp7/9 shows that ATP binds to Arp7 but not Arp9. However, Arp7 does not hydrolyze ATP. Together, the results suggest that Rtt102 and ATP stabilize a conformation of Arp7/9 that potentiates binding to the HSA domain, which releases intramolecular interactions within Sth1 and controls DNA and nucleosome binding. Bengi Turegun et al. report an interaction of the highly-conserved pHSA and P1 domains of Sth1, the catalytic subunit of the SWI/SNF-family chromatin remodeler RSC. This interaction is released when ATP-bound Rtt102-Arp7/9 binds to the HSA domain, modulating DNA and nucleosome binding by Sth.
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Marquez-Vilendrer SB, Thompson K, Lu L, Reisman D. Mechanism of BRG1 silencing in primary cancers. Oncotarget 2018; 7:56153-56169. [PMID: 27486753 PMCID: PMC5302903 DOI: 10.18632/oncotarget.10593] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/19/2016] [Indexed: 11/25/2022] Open
Abstract
BRG1 (SMARCA4) is a documented tumor suppressor and a key subunit of the SWI/SNF chromatin remodeling complex that is silenced in many cancer types. Studies have shown that BRG1 is mutated in cancer-derived cell lines, which led to the assertion that BRG1 is also mutated in primary human tumors. However, the sequencing of BRG1-deficient tumors has revealed a paucity of mutations; hence, the cause of BRG1 silencing in tumors remains an enigma. We conducted immunohistochemistry (IHC) on a number of tumor microarrays to characterize the frequency of BRG1 loss in different tumor types. We also analyzed BRG1-deficient tumors by sequencing the genomic DNA and the mRNA. We then tested if BRG1 expression could be induced in BRG1-negative cell lines (i.e., that lack mutations in BRG1) after the application of several different epigenetic agents, including drugs that inhibit the AKT pathway. We found that a subset of BRG1-negative cell lines also demonstrated aberrant splicing of BRG1, and in at least 30% of BRG1-deficient tumors, BRG1 expression appeared to be suppressed due to aberrant BRG1 splicing. As the majority of BRG1-deficient tumors lack mutations or splicing defects that could drive BRG1 loss of expression, this suggests that other mechanisms underlie BRG1 silencing. To this end, we analyzed 3 BRG1-deficient nonmutated cancer cell lines and found that BRG1 was inducible in these cell lines upon inhibition of the AKT pathway. We show that the loss of BRG1 is associated with the loss of E-cadherin and up-regulation of Vimentin in primary tumors, which explains why BRG1 loss is associated with a poor prognosis in multiple tumor types.
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Affiliation(s)
| | - Kenneth Thompson
- Division of Hematology/Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Li Lu
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - David Reisman
- Division of Hematology/Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
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Sen P, Luo J, Hada A, Hailu SG, Dechassa ML, Persinger J, Brahma S, Paul S, Ranish J, Bartholomew B. Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex. Cell Rep 2017; 18:2135-2147. [PMID: 28249160 DOI: 10.1016/j.celrep.2017.02.017] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 11/16/2016] [Accepted: 02/02/2017] [Indexed: 02/07/2023] Open
Abstract
The SWI/SNF chromatin remodeling complex is highly conserved from yeast to human, and aberrant SWI/SNF complexes contribute to human disease. The Snf5/SMARCB1/INI1 subunit of SWI/SNF is a tumor suppressor frequently lost in pediatric rhabdoid cancers. We examined the effects of Snf5 loss on the composition, nucleosome binding, recruitment, and remodeling activities of yeast SWI/SNF. The Snf5 subunit is shown by crosslinking-mass spectrometry (CX-MS) and subunit deletion analysis to interact with the ATPase domain of Snf2 and to form a submodule consisting of Snf5, Swp82, and Taf14. Snf5 promotes binding of the Snf2 ATPase domain to nucleosomal DNA and enhances the catalytic and nucleosome remodeling activities of SWI/SNF. Snf5 is also required for SWI/SNF recruitment by acidic transcription factors. RNA-seq analysis suggests that both the recruitment and remodeling functions of Snf5 are required in vivo for SWI/SNF regulation of gene expression. Thus, loss of SNF5 alters the structure and function of SWI/SNF.
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Affiliation(s)
- Payel Sen
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, IL 62901, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Arjan Hada
- UT MD Anderson Cancer Center, Smithville, TX 78597, USA; UT MD Anderson Center for Cancer Epigenetics, Smithville, TX 78597, USA
| | - Solomon G Hailu
- UT MD Anderson Cancer Center, Smithville, TX 78597, USA; UT MD Anderson Center for Cancer Epigenetics, Smithville, TX 78597, USA
| | - Mekonnen Lemma Dechassa
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, IL 62901, USA
| | - Jim Persinger
- UT MD Anderson Cancer Center, Smithville, TX 78597, USA; UT MD Anderson Center for Cancer Epigenetics, Smithville, TX 78597, USA
| | | | - Somnath Paul
- UT MD Anderson Cancer Center, Smithville, TX 78597, USA
| | - Jeff Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Blaine Bartholomew
- UT MD Anderson Cancer Center, Smithville, TX 78597, USA; UT MD Anderson Center for Cancer Epigenetics, Smithville, TX 78597, USA.
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29
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Hota SK, Bruneau BG. ATP-dependent chromatin remodeling during mammalian development. Development 2017; 143:2882-97. [PMID: 27531948 DOI: 10.1242/dev.128892] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Precise gene expression ensures proper stem and progenitor cell differentiation, lineage commitment and organogenesis during mammalian development. ATP-dependent chromatin-remodeling complexes utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression. These complexes contain diverse subunits that together provide a multitude of functions, from early embryogenesis through cell differentiation and development into various adult tissues. Here, we review the functions of chromatin remodelers and their different subunits during mammalian development. We discuss the mechanisms by which chromatin remodelers function and highlight their specificities during mammalian cell differentiation and organogenesis.
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Affiliation(s)
- Swetansu K Hota
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Department of Pediatrics, University of California, San Francisco, CA 94143, USA Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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30
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Manning BJ, Yusufzai T. The ATP-dependent chromatin remodeling enzymes CHD6, CHD7, and CHD8 exhibit distinct nucleosome binding and remodeling activities. J Biol Chem 2017; 292:11927-11936. [PMID: 28533432 PMCID: PMC5512084 DOI: 10.1074/jbc.m117.779470] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/19/2017] [Indexed: 01/04/2023] Open
Abstract
Proper chromatin regulation is central to genome function and maintenance. The group III chromodomain–helicase–DNA-binding (CHD) family of ATP-dependent chromatin remodeling enzymes, comprising CHD6, CHD7, CHD8, and CHD9, has well-documented roles in transcription regulation, impacting both organism development and disease etiology. These four enzymes are similar in their constituent domains, but they fill surprisingly non-redundant roles in the cell, with deficiencies in individual enzymes leading to dissimilar disease states such as CHARGE syndrome or autism spectrum disorders. The mechanisms explaining their divergent, non-overlapping functions are unclear. In this study, we performed an in-depth biochemical analysis of purified CHD6, CHD7, and CHD8 and discovered distinct differences in chromatin remodeling specificities and activities among them. We report that CHD6 and CHD7 both bind with high affinity to short linker DNA, whereas CHD8 requires longer DNA for binding. As a result, CHD8 slides nucleosomes into positions with more flanking linker DNA than CHD7. Moreover, we found that, although CHD7 and CHD8 slide nucleosomes, CHD6 disrupts nucleosomes in a distinct non-sliding manner. The different activities of these enzymes likely lead to differences in chromatin structure and, thereby, transcriptional control, at the enhancer and promoter loci where these enzymes bind. Overall, our work provides a mechanistic basis for both the non-redundant roles and the diverse mutant disease states of these enzymes in vivo.
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Affiliation(s)
- Benjamin J Manning
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215.
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31
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Wu Q, Lian JB, Stein JL, Stein GS, Nickerson JA, Imbalzano AN. The BRG1 ATPase of human SWI/SNF chromatin remodeling enzymes as a driver of cancer. Epigenomics 2017; 9:919-931. [PMID: 28521512 PMCID: PMC5705788 DOI: 10.2217/epi-2017-0034] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mammalian SWI/SNF enzymes are ATP-dependent remodelers of chromatin structure. These multisubunit enzymes are heterogeneous in composition; there are two catalytic ATPase subunits, BRM and BRG1, that are mutually exclusive, and additional subunits are incorporated in a combinatorial manner. Recent findings indicate that approximately 20% of human cancers contain mutations in SWI/SNF enzyme subunits, leading to the conclusion that the enzyme subunits are critical tumor suppressors. However, overexpression of specific subunits without apparent mutation is emerging as an alternative mechanism by which cellular transformation may occur. Here we highlight recent evidence linking elevated expression of the BRG1 ATPase to tissue-specific cancers and work suggesting that inhibiting BRG1 may be an effective therapeutic strategy.
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Affiliation(s)
- Qiong Wu
- Department of Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jane B Lian
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Gary S Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Jeffrey A Nickerson
- Department of Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Anthony N Imbalzano
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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Clapier CR, Iwasa J, Cairns BR, Peterson CL. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol 2017; 18:407-422. [PMID: 28512350 DOI: 10.1038/nrm.2017.26] [Citation(s) in RCA: 719] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize diverse ATP-dependent nucleosome-remodelling complexes to carry out histone sliding, ejection or the incorporation of histone variants, suggesting that different mechanisms of action are used by the various chromatin-remodelling complex subfamilies. However, all chromatin-remodelling complex subfamilies contain an ATPase-translocase 'motor' that translocates DNA from a common location within the nucleosome. In this Review, we discuss (and illustrate with animations) an alternative, unifying mechanism of chromatin remodelling, which is based on the regulation of DNA translocation. We propose the 'hourglass' model of remodeller function, in which each remodeller subfamily utilizes diverse specialized proteins and protein domains to assist in nucleosome targeting or to differentially detect nucleosome epitopes. These modules converge to regulate a common DNA translocation mechanism, to inform the conserved ATPase 'motor' on whether and how to apply DNA translocation, which together achieve the various outcomes of chromatin remodelling: nucleosome assembly, chromatin access and nucleosome editing.
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Affiliation(s)
- Cedric R Clapier
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Structure and regulation of the chromatin remodeller ISWI. Nature 2016; 540:466-469. [PMID: 27919072 DOI: 10.1038/nature20590] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/27/2016] [Indexed: 01/19/2023]
Abstract
ISWI is a member of the SWI2/SNF2 family of chromatin remodellers, which also includes Snf2, Chd1, and Ino80. ISWI is the catalytic subunit of several chromatin remodelling complexes, which mobilize nucleosomes along genomic DNA, promoting replication progression, transcription repression, heterochromatin formation, and many other nuclear processes. The ATPase motor of ISWI is an autonomous remodelling machine, whereas its carboxy (C)-terminal HAND-SAND-SLIDE (HSS) domain functions in binding extranucleosomal linker DNA. The activity of the catalytic core of ISWI is inhibited by the regulatory AutoN and NegC domains, which are in turn antagonized by the H4 tail and extranucleosomal DNA, respectively, to ensure the appropriate chromatin landscape in cells. How AutoN and NegC inhibit ISWI and regulate its nucleosome-centring activity remains elusive. Here we report the crystal structures of ISWI from the thermophilic yeast Myceliophthora thermophila and its complex with a histone H4 peptide. Our data show the amino (N)-terminal AutoN domain contains two inhibitory elements, which collectively bind the second RecA-like domain (core2), holding the enzyme in an inactive conformation. The H4 peptide binds to the core2 domain coincident with one of the AutoN-binding sites, explaining the ISWI activation by H4. The H4-binding surface is conserved in Snf2 and functions beyond AutoN regulation. The C-terminal NegC domain is involved in binding to the core2 domain and functions as an allosteric element for ISWI to respond to the extranucleosomal DNA length.
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34
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Structure of chromatin remodeler Swi2/Snf2 in the resting state. Nat Struct Mol Biol 2016; 23:722-9. [PMID: 27399259 DOI: 10.1038/nsmb.3259] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/15/2016] [Indexed: 12/29/2022]
Abstract
SWI2/SNF2 family proteins regulate a myriad of nucleic acid transactions by sliding, removing and reconstructing nucleosomes in eukaryotic cells. They contain two RecA-like core domains, which couple ATP hydrolysis and DNA translocation to chromatin remodeling. Here we report the crystal structure of Snf2 from the yeast Myceliophthora thermophila. The data show the two RecA-like core domains of Snf2 stacking together and twisting their ATP-binding motifs away from each other, thus explaining the inactivity of the protein in the ground state. We identified several DNA-binding elements, which are fully exposed to solvent, thus suggesting that the protein is poised for its incoming substrate. The catalytic core of Snf2 showed a high chromatin-remodeling activity, which was suppressed by the N-terminal HSA domain. Our findings reveal that the catalytic core of Snf2 is a competent remodeling machine, which rests in an inactive conformation and requires a large conformational change upon activation.
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35
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Abstract
Chromatin remodeling motors play essential roles in all DNA-based processes. These motors catalyze diverse outcomes ranging from sliding the smallest units of chromatin, known as nucleosomes, to completely disassembling chromatin. The broad range of actions carried out by these motors on the complex template presented by chromatin raises many stimulating mechanistic questions. Other well-studied nucleic acid motors provide examples of the depth of mechanistic understanding that is achievable from detailed biophysical studies. We use these studies as a guiding framework to discuss the current state of knowledge of chromatin remodeling mechanisms and highlight exciting open questions that would continue to benefit from biophysical analyses.
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Affiliation(s)
- Coral Y Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158; , , ,
| | - Stephanie L Johnson
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158; , , ,
| | - Nathan I Gamarra
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158; , , ,
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158; , , ,
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36
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Peirats-Llobet M, Han SK, Gonzalez-Guzman M, Jeong CW, Rodriguez L, Belda-Palazon B, Wagner D, Rodriguez PL. A Direct Link between Abscisic Acid Sensing and the Chromatin-Remodeling ATPase BRAHMA via Core ABA Signaling Pathway Components. MOLECULAR PLANT 2016; 9:136-147. [PMID: 26499068 DOI: 10.1016/j.molp.2015.10.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 05/04/2023]
Abstract
Optimal response to drought is critical for plant survival and will affect biodiversity and crop performance during climate change. Mitotically heritable epigenetic or dynamic chromatin state changes have been implicated in the plant response to the drought stress hormone abscisic acid (ABA). The Arabidopsis SWI/SNF chromatin-remodeling ATPase BRAHMA (BRM) modulates response to ABA by preventing premature activation of stress response pathways during germination. We show that core ABA signaling pathway components physically interact with BRM and post-translationally modify BRM by phosphorylation/dephosphorylation. Genetic evidence suggests that BRM acts downstream of SnRK2.2/2.3 kinases, and biochemical studies identified phosphorylation sites in the C-terminal region of BRM at SnRK2 target sites that are evolutionarily conserved. Finally, the phosphomimetic BRM(S1760D S1762D) mutant displays ABA hypersensitivity. Prior studies showed that BRM resides at target loci in the ABA pathway in the presence and absence of the stimulus, but is only active in the absence of ABA. Our data suggest that SnRK2-dependent phosphorylation of BRM leads to its inhibition, and PP2CA-mediated dephosphorylation of BRM restores the ability of BRM to repress ABA response. These findings point to the presence of a rapid phosphorylation-based switch to control BRM activity; this property could be potentially harnessed to improve drought tolerance in plants.
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Affiliation(s)
- Marta Peirats-Llobet
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Miguel Gonzalez-Guzman
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Cheol Woong Jeong
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lesia Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Borja Belda-Palazon
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 Valencia, Spain.
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37
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Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J, Bartholomew B, Shen X. Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes Dev 2015; 29:591-602. [PMID: 25792597 PMCID: PMC4378192 DOI: 10.1101/gad.257626.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Kapoor et al. found that the SWI/SNF chromatin remodeling complex is capable of regulating the activity of S. cerevisiae checkpoint kinase Mec1. SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dbp11. The subunit requirement of SWI/SNF-mediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. These findings suggest that ATP-dependent chromatin remodeling complexes can regulate non-chromatin substrates such as a checkpoint kinase. ATP-dependent chromatin remodeling complexes alter chromatin structure through interactions with chromatin substrates such as DNA, histones, and nucleosomes. However, whether chromatin remodeling complexes have the ability to regulate nonchromatin substrates remains unclear. Saccharomyces cerevisiae checkpoint kinase Mec1 (ATR in mammals) is an essential master regulator of genomic integrity. Here we found that the SWI/SNF chromatin remodeling complex is capable of regulating Mec1 kinase activity. In vivo, Mec1 activity is reduced by the deletion of Snf2, the core ATPase subunit of the SWI/SNF complex. SWI/SNF interacts with Mec1, and cross-linking studies revealed that the Snf2 ATPase is the main interaction partner for Mec1. In vitro, SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dpb11. The subunit requirement of SWI/SNF-mediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. Functionally, SWI/SNF-mediated Mec1 regulation specifically occurs in S phase of the cell cycle. Together, these findings identify a novel regulator of Mec1 kinase activity and suggest that ATP-dependent chromatin remodeling complexes can regulate nonchromatin substrates such as a checkpoint kinase.
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Affiliation(s)
- Prabodh Kapoor
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Yunhe Bao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Jing Xiao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, Washington 98109, USA
| | - Jianfeng Shen
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jim Persinger
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jeff Ranish
- Institute for Systems Biology, Seattle, Washington 98109, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Xuetong Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA;
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Cajigas I, Leib DE, Cochrane J, Luo H, Swyter KR, Chen S, Clark BS, Thompson J, Yates JR, Kingston RE, Kohtz JD. Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling. Development 2015; 142:2641-52. [PMID: 26138476 DOI: 10.1242/dev.126318] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/09/2015] [Indexed: 01/12/2023]
Abstract
Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control the site-specific expression of thousands of target genes. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases the association of transcriptional activators (DLX homeodomain proteins) with key DNA enhancers but represses gene expression. In this report, mass spectrometry shows that the Evf2-DLX1 ribonucleoprotein (RNP) contains the SWI/SNF-related chromatin remodelers Brahma-related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in the developing mouse forebrain. Evf2 RNA colocalizes with BRG1 in nuclear clouds and increases BRG1 association with key DNA regulatory enhancers in the developing forebrain. While BRG1 directly interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies show that both RNA-BRG1 binding and RNA inhibition of BRG1 ATPase/remodeling activity are promiscuous, suggesting that context is a crucial factor in RNA-dependent chromatin remodeling inhibition. Together, these experiments support a model in which RNAs convert an active enhancer to a repressed enhancer by directly inhibiting chromatin remodeling activity, and address the apparent paradox of RNA-mediated stabilization of transcriptional activators at enhancers with a repressive outcome. The importance of BRG1/RNA and BRG1/homeodomain interactions in neurodevelopmental disorders is underscored by the finding that mutations in Coffin-Siris syndrome, a human intellectual disability disorder, localize to the BRG1 RNA-binding and DLX1-binding domains.
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Affiliation(s)
- Ivelisse Cajigas
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - David E Leib
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Jesse Cochrane
- Department of Molecular Biology, Harvard University, Boston, MA 02114, USA
| | - Hao Luo
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Kelsey R Swyter
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Sean Chen
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Brian S Clark
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | | | - John R Yates
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert E Kingston
- Department of Molecular Biology, Harvard University, Boston, MA 02114, USA
| | - Jhumku D Kohtz
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
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39
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Han SK, Wu MF, Cui S, Wagner D. Roles and activities of chromatin remodeling ATPases in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:62-77. [PMID: 25977075 DOI: 10.1111/tpj.12877] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 05/18/2023]
Abstract
Chromatin remodeling ATPases and their associated complexes can alter the accessibility of the genome in the context of chromatin by using energy derived from the hydrolysis of ATP to change the positioning, occupancy and composition of nucleosomes. In animals and plants, these remodelers have been implicated in diverse processes ranging from stem cell maintenance and differentiation to developmental phase transitions and stress responses. Detailed investigation of their roles in individual processes has suggested a higher level of selectivity of chromatin remodeling ATPase activity than previously anticipated, and diverse mechanisms have been uncovered that can contribute to the selectivity. This review summarizes recent advances in understanding the roles and activities of chromatin remodeling ATPases in plants.
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Affiliation(s)
- Soon-Ki Han
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular Cell Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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40
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Abstract
A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).
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Affiliation(s)
- Blaine Bartholomew
- University of Texas MD Anderson Cancer Center, Department of Molecular Carcinogenesis, Smithville, Texas 78957;
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Mueller-Planitz F, Klinker H, Becker PB. Nucleosome sliding mechanisms: new twists in a looped history. Nat Struct Mol Biol 2013; 20:1026-32. [PMID: 24008565 DOI: 10.1038/nsmb.2648] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/12/2013] [Indexed: 01/11/2023]
Abstract
Nucleosomes, the basic organizational units of chromatin, package and regulate eukaryotic genomes. ATP-dependent nucleosome-remodeling factors endow chromatin with structural flexibility by promoting assembly or disruption of nucleosomes and the exchange of histone variants. Furthermore, most remodeling factors induce nucleosome movements through sliding of histone octamers on DNA. We summarize recent progress toward unraveling the basic nucleosome sliding mechanism and the interplay of the remodelers' DNA translocases with accessory domains. Such domains optimize and regulate the basic sliding reaction and exploit sliding to achieve diverse structural effects, such as nucleosome positioning or eviction, or the regular spacing of nucleosomes in chromatin.
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Affiliation(s)
- Felix Mueller-Planitz
- 1] Adolf-Butenandt-Institute, Ludwig-Maximilians-Universität, Munich, Germany. [2] Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität, Munich, Germany
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42
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Manning BJ, Peterson CL. Releasing the brakes on a chromatin-remodeling enzyme. Nat Struct Mol Biol 2013; 20:5-7. [PMID: 23288358 DOI: 10.1038/nsmb.2482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromatin-remodeling enzymes use the energy from ATP hydrolysis to mobilize, disrupt or change the histone composition of nucleosomes, facilitating nearly every nuclear event. Two recent studies indicate that remodeling enzymes harness the power of an ancient constitutively active DNA translocase and that different remodeling enzymes may use specialized coupling domains that communicate the presence of nucleosomal epitopes to regulate translocase and remodeling activity.
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Affiliation(s)
- Benjamin J Manning
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
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