1
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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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2
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Soshnikova NV, Azieva AM, Klimenko NS, Khamidullina AI, Feoktistov AV, Sheynov AA, Brechalov AV, Tatarskiy VV, Georgieva SG. A novel chromatin-remodeling complex variant, dcPBAF, is involved in maintaining transcription in differentiated neurons. Front Cell Dev Biol 2023; 11:1271598. [PMID: 38033872 PMCID: PMC10682186 DOI: 10.3389/fcell.2023.1271598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
The Polybromo-associated BAF (BRG1- or BRM-associated factors) (PBAF) chromatin-remodeling complex is essential for transcription in mammalian cells. In this study, we describe a novel variant of the PBAF complex from differentiated neuronal cells, called dcPBAF, that differs from the canonical PBAF existing in proliferating neuroblasts. We describe that in differentiated adult neurons, a specific subunit of PBAF, PHF10, is replaced by a PHF10 isoform that lacks N- and C-terminal domains (called PHF10D). In addition, dcPBAF does not contain the canonical BRD7 subunit. dcPBAF binds promoters of the actively transcribed neuron-specific and housekeeping genes in terminally differentiated neurons of adult mice. Furthermore, in differentiated human neuronal cells, PHF10D-containing dcPBAF maintains a high transcriptional level at several neuron-specific genes.
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Affiliation(s)
- Nataliya V. Soshnikova
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Asya M. Azieva
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Nataliya S. Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alvina I. Khamidullina
- Department of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Feoktistov
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey A. Sheynov
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V. Brechalov
- Department of Eukaryotic Transcription Factors, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Victor V. Tatarskiy
- Department of Molecular Oncobiology, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sofia G. Georgieva
- Department of Transcription Factors, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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3
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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: 2] [Impact Index Per Article: 2.0] [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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4
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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: 34] [Impact Index Per Article: 17.0] [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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5
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The BAF chromatin remodeling complexes: structure, function, and synthetic lethalities. Biochem Soc Trans 2021; 49:1489-1503. [PMID: 34431497 DOI: 10.1042/bst20190960] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023]
Abstract
BAF complexes are multi-subunit chromatin remodelers, which have a fundamental role in genomic regulation. Large-scale sequencing efforts have revealed frequent BAF complex mutations in many human diseases, particularly in cancer and neurological disorders. These findings not only underscore the importance of the BAF chromatin remodelers in cellular physiological processes, but urge a more detailed understanding of their structure and molecular action to enable the development of targeted therapeutic approaches for diseases with BAF complex alterations. Here, we review recent progress in understanding the composition, assembly, structure, and function of BAF complexes, and the consequences of their disease-associated mutations. Furthermore, we highlight intra-complex subunit dependencies and synthetic lethal interactions, which have emerged as promising treatment modalities for BAF-related diseases.
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6
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The mechanisms of action of chromatin remodelers and implications in development and disease. Biochem Pharmacol 2020; 180:114200. [DOI: 10.1016/j.bcp.2020.114200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
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7
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Patel AB, Moore CM, Greber BJ, Luo J, Zukin SA, Ranish J, Nogales E. Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement. eLife 2019; 8:e54449. [PMID: 31886770 PMCID: PMC6959994 DOI: 10.7554/elife.54449] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility. The Saccharomyces cerevisiae RSC (Remodeling the Structure of Chromatin) complex, a member of the SWI/SNF chromatin remodeler family, plays critical roles in genome maintenance, transcription, and DNA repair. Here, we report cryo-electron microscopy (cryo-EM) and crosslinking mass spectrometry (CLMS) studies of yeast RSC complex and show that RSC is composed of a rigid tripartite core and two flexible lobes. The core structure is scaffolded by an asymmetric Rsc8 dimer and built with the evolutionarily conserved subunits Sfh1, Rsc6, Rsc9 and Sth1. The flexible ATPase lobe, composed of helicase subunit Sth1, Arp7, Arp9 and Rtt102, is anchored to this core by the N-terminus of Sth1. Our cryo-EM analysis of RSC bound to a nucleosome core particle shows that in addition to the expected nucleosome-Sth1 interactions, RSC engages histones and nucleosomal DNA through one arm of the core structure, composed of the Rsc8 SWIRM domains, Sfh1 and Npl6. Our findings provide structural insights into the conserved assembly process for all members of the SWI/SNF family of remodelers, and illustrate how RSC selects, engages, and remodels nucleosomes.
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Affiliation(s)
- Avinash B Patel
- Biophysics Graduate GroupUniversity of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Camille M Moore
- Molecular and Cell Biology DepartmentUniversity of California, BerkeleyBerkeleyUnited States
| | - Basil J Greber
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- California Institute for Quantitative Biology (QB3)University of California, BerkeleyBerkeleyUnited States
| | - Jie Luo
- The Institute for Systems BiologySeattleUnited States
| | - Stefan A Zukin
- Chemistry DepartmentUniversity of California, BerkeleyBerkeleyUnited States
| | - Jeff Ranish
- The Institute for Systems BiologySeattleUnited States
| | - Eva Nogales
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Molecular and Cell Biology DepartmentUniversity of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biology (QB3)University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
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8
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Nucleosome remodelling: structural insights into ATP-dependent remodelling enzymes. Essays Biochem 2019; 63:45-58. [PMID: 30967479 DOI: 10.1042/ebc20180059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/22/2022]
Abstract
ATP-dependent chromatin remodelling enzymes play a fundamental role in determining how nucleosomes are organised, and render DNA sequences accessible to interacting proteins, thereby enabling precise regulation of eukaryotic genes. Remodelers conserved from yeast to humans are classified into four families based on the domains and motifs present in their ATPase subunits. Insights into overall assembly and the mode of interaction to the nucleosome by these different families of remodelers remained limited due to the complexity of obtaining structural information on these challenging samples. Electron microscopy and single-particle methods have made advancement and uncovered vital structural information on the number of remodelling complexes. In this article, we highlight some of the recent structural work that advanced our understanding on the mechanisms and biological functions of these ATP-dependent remodelling machines.
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9
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Sokpor G, Castro-Hernandez R, Rosenbusch J, Staiger JF, Tuoc T. ATP-Dependent Chromatin Remodeling During Cortical Neurogenesis. Front Neurosci 2018; 12:226. [PMID: 29686607 PMCID: PMC5900035 DOI: 10.3389/fnins.2018.00226] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/22/2018] [Indexed: 12/20/2022] Open
Abstract
The generation of individual neurons (neurogenesis) during cortical development occurs in discrete steps that are subtly regulated and orchestrated to ensure normal histogenesis and function of the cortex. Notably, various gene expression programs are known to critically drive many facets of neurogenesis with a high level of specificity during brain development. Typically, precise regulation of gene expression patterns ensures that key events like proliferation and differentiation of neural progenitors, specification of neuronal subtypes, as well as migration and maturation of neurons in the developing cortex occur properly. ATP-dependent chromatin remodeling complexes regulate gene expression through utilization of energy from ATP hydrolysis to reorganize chromatin structure. These chromatin remodeling complexes are characteristically multimeric, with some capable of adopting functionally distinct conformations via subunit reconstitution to perform specific roles in major aspects of cortical neurogenesis. In this review, we highlight the functions of such chromatin remodelers during cortical development. We also bring together various proposed mechanisms by which ATP-dependent chromatin remodelers function individually or in concert, to specifically modulate vital steps in cortical neurogenesis.
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Affiliation(s)
- Godwin Sokpor
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Ricardo Castro-Hernandez
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Joachim Rosenbusch
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
| | - Tran Tuoc
- Institute for Neuroanatomy, University Medical Center, Georg-August-University Goettingen, Goettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Goettingen, Germany
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10
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Torrado M, Low JKK, Silva APG, Schmidberger JW, Sana M, Sharifi Tabar M, Isilak ME, Winning CS, Kwong C, Bedward MJ, Sperlazza MJ, Williams DC, Shepherd NE, Mackay JP. Refinement of the subunit interaction network within the nucleosome remodelling and deacetylase (NuRD) complex. FEBS J 2017; 284:4216-4232. [PMID: 29063705 DOI: 10.1111/febs.14301] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 07/19/2017] [Accepted: 10/18/2017] [Indexed: 01/29/2023]
Abstract
The nucleosome remodelling and deacetylase (NuRD) complex is essential for the development of complex animals. NuRD has roles in regulating gene expression and repairing damaged DNA. The complex comprises at least six proteins with two or more paralogues of each protein routinely identified when the complex is purified from cell extracts. To understand the structure and function of NuRD, a map of direct subunit interactions is needed. Dozens of published studies have attempted to define direct inter-subunit connectivities. We propose that conclusions reported in many such studies are in fact ambiguous for one of several reasons. First, the expression of many NuRD subunits in bacteria is unlikely to lead to folded, active protein. Second, interaction studies carried out in cells that contain endogenous NuRD complex can lead to false positives through bridging of target proteins by endogenous components. Combining existing information on NuRD structure with a protocol designed to minimize false positives, we report a conservative and robust interaction map for the NuRD complex. We also suggest a 3D model of the complex that brings together the existing data on the complex. The issues and strategies discussed herein are also applicable to the analysis of a wide range of multi-subunit complexes. ENZYMES Micrococcal nuclease (MNase), EC 3.1.31.1; histone deacetylase (HDAC), EC 3.5.1.98.
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Affiliation(s)
- Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney, Australia
| | | | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, Australia
| | | | - Musa E Isilak
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Courtney S Winning
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Cherry Kwong
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Max J Bedward
- School of Life and Environmental Sciences, University of Sydney, Australia
| | - Mary J Sperlazza
- Department of Pathology and Laboratory Medicine, The University of North Carolina - Chapel Hill, NC, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, The University of North Carolina - Chapel Hill, NC, USA
| | - Nicholas E Shepherd
- Institute for Molecular Biosciences, The University of Queensland, St Lucia, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Australia
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11
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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: 673] [Impact Index Per Article: 96.1] [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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12
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Liu X, Li M, Xia X, Li X, Chen Z. Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure. Nature 2017; 544:440-445. [PMID: 28424519 DOI: 10.1038/nature22036] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/28/2017] [Indexed: 12/11/2022]
Abstract
Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling. Snf2 binds to the phosphate backbones of one DNA gyre of the nucleosome mainly through its helicase motifs within the major domain cleft, suggesting a conserved mechanism of substrate engagement across different remodellers. Snf2 contacts the second DNA gyre via a positively charged surface, providing a mechanism to anchor the remodeller at a fixed position of the nucleosome. Snf2 locally deforms nucleosomal DNA at the site of binding, priming the substrate for the remodelling reaction. Together, these findings provide mechanistic insights into chromatin remodelling.
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Affiliation(s)
- Xiaoyu Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Meijing Li
- Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Xian Xia
- Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xueming Li
- Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Zhucheng Chen
- Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing 100084, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
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13
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Dutta A, Sardiu M, Gogol M, Gilmore J, Zhang D, Florens L, Abmayr SM, Washburn MP, Workman JL. Composition and Function of Mutant Swi/Snf Complexes. Cell Rep 2017; 18:2124-2134. [PMID: 28249159 PMCID: PMC5837817 DOI: 10.1016/j.celrep.2017.01.058] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 12/09/2016] [Accepted: 01/23/2017] [Indexed: 12/15/2022] Open
Abstract
The 12-subunit Swi/Snf chromatin remodeling complex is conserved from yeast to humans. It functions to alter nucleosome positions by either sliding nucleosomes on DNA or evicting histones. Interestingly, 20% of all human cancers carry mutations in subunits of the Swi/Snf complex. Many of these mutations cause protein instability and loss, resulting in partial Swi/Snf complexes. Although several studies have shown that histone acetylation and activator-dependent recruitment of Swi/Snf regulate its function, it is less well understood how subunits regulate stability and function of the complex. Using functional proteomic and genomic approaches, we have assembled the network architecture of yeast Swi/Snf. In addition, we find that subunits of the Swi/Snf complex regulate occupancy of the catalytic subunit Snf2, thereby modulating gene transcription. Our findings have direct bearing on how cancer-causing mutations in orthologous subunits of human Swi/Snf may lead to aberrant regulation of gene expression by this complex.
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Affiliation(s)
- Arnob Dutta
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Road, Kingston, RI 02881, USA.
| | - Mihaela Sardiu
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Joshua Gilmore
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Daoyong Zhang
- Institute of Cancer Biological Therapy, Xuzhou Medical University, Jiangsu 221002, China
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Susan M Abmayr
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.
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14
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Volokh OI, Derkacheva NI, Studitsky VM, Sokolova OS. Structural studies of chromatin remodeling factors. Mol Biol 2016. [DOI: 10.1134/s0026893316060212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Hodges C, Kirkland JG, Crabtree GR. The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026930. [PMID: 27413115 DOI: 10.1101/cshperspect.a026930] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During the last decade, a host of epigenetic mechanisms were found to contribute to cancer and other human diseases. Several genomic studies have revealed that ∼20% of malignancies have alterations of the subunits of polymorphic BRG-/BRM-associated factor (BAF) and Polybromo-associated BAF (PBAF) complexes, making them among the most frequently mutated complexes in cancer. Recurrent mutations arise in genes encoding several BAF/PBAF subunits, including ARID1A, ARID2, PBRM1, SMARCA4, and SMARCB1 These subunits share some degree of conservation with subunits from related adenosine triphosphate (ATP)-dependent chromatin remodeling complexes in model organisms, in which a large body of work provides insight into their roles in cancer. Here, we review the roles of BAF- and PBAF-like complexes in these organisms, and relate these findings to recent discoveries in cancer epigenomics. We review several roles of BAF and PBAF complexes in cancer, including transcriptional regulation, DNA repair, and regulation of chromatin architecture and topology. More recent results highlight the need for new techniques to study these complexes.
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Affiliation(s)
- Courtney Hodges
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Jacob G Kirkland
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Gerald R Crabtree
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
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16
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Low JKK, Webb SR, Silva APG, Saathoff H, Ryan DP, Torrado M, Brofelth M, Parker BL, Shepherd NE, Mackay JP. CHD4 Is a Peripheral Component of the Nucleosome Remodeling and Deacetylase Complex. J Biol Chem 2016; 291:15853-66. [PMID: 27235397 DOI: 10.1074/jbc.m115.707018] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 01/08/2023] Open
Abstract
Chromatin remodeling enzymes act to dynamically regulate gene accessibility. In many cases, these enzymes function as large multicomponent complexes that in general comprise a central ATP-dependent Snf2 family helicase that is decorated with a variable number of regulatory subunits. The nucleosome remodeling and deacetylase (NuRD) complex, which is essential for normal development in higher organisms, is one such macromolecular machine. The NuRD complex comprises ∼10 subunits, including the histone deacetylases 1 and 2 (HDAC1 and HDAC2), and is defined by the presence of a CHD family remodeling enzyme, most commonly CHD4 (chromodomain helicase DNA-binding protein 4). The existing paradigm holds that CHD4 acts as the central hub upon which the complex is built. We show here that this paradigm does not, in fact, hold and that CHD4 is a peripheral component of the NuRD complex. A complex lacking CHD4 that has HDAC activity can exist as a stable species. The addition of recombinant CHD4 to this nucleosome deacetylase complex reconstitutes a NuRD complex with nucleosome remodeling activity. These data contribute to our understanding of the architecture of the NuRD complex.
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Affiliation(s)
- Jason K K Low
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Sarah R Webb
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Ana P G Silva
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Hinnerk Saathoff
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Daniel P Ryan
- the Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Mario Torrado
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Mattias Brofelth
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Benjamin L Parker
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Nicholas E Shepherd
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
| | - Joel P Mackay
- From the School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia and
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17
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Kadoch C, Copeland RA, Keilhack H. PRC2 and SWI/SNF Chromatin Remodeling Complexes in Health and Disease. Biochemistry 2016; 55:1600-14. [DOI: 10.1021/acs.biochem.5b01191] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Cigall Kadoch
- Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Robert A. Copeland
- Epizyme Inc., 400 Technology
Square, 4th floor, Cambridge, Massachusetts 02139, United States
| | - Heike Keilhack
- Epizyme Inc., 400 Technology
Square, 4th floor, Cambridge, Massachusetts 02139, United States
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18
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Tosi A, Haas C, Herzog F, Gilmozzi A, Berninghausen O, Ungewickell C, Gerhold CB, Lakomek K, Aebersold R, Beckmann R, Hopfner KP. Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell 2013; 154:1207-19. [PMID: 24034245 DOI: 10.1016/j.cell.2013.08.016] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/05/2013] [Accepted: 08/12/2013] [Indexed: 11/16/2022]
Abstract
INO80/SWR1 family chromatin remodelers are complexes composed of >15 subunits and molecular masses exceeding 1 MDa. Their important role in transcription and genome maintenance is exchanging the histone variants H2A and H2A.Z. We report the architecture of S. cerevisiae INO80 using an integrative approach of electron microscopy, crosslinking and mass spectrometry. INO80 has an embryo-shaped head-neck-body-foot architecture and shows dynamic open and closed conformations. We can assign an Rvb1/Rvb2 heterododecamer to the head in close contact with the Ino80 Snf2 domain, Ies2, and the Arp5 module at the neck. The high-affinity nucleosome-binding Nhp10 module localizes to the body, whereas the module that contains actin, Arp4, and Arp8 maps to the foot. Structural and biochemical analyses indicate that the nucleosome is bound at the concave surface near the neck, flanked by the Rvb1/2 and Arp8 modules. Our analysis establishes a structural and functional framework for this family of large remodelers.
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Affiliation(s)
- Alessandro Tosi
- Department of Biochemistry, Ludwig-Maximilian University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilian University, 81377 Munich, Germany
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19
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Leschziner AE. Electron microscopy studies of nucleosome remodelers. Curr Opin Struct Biol 2011; 21:709-18. [PMID: 22040801 DOI: 10.1016/j.sbi.2011.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 10/01/2011] [Accepted: 10/11/2011] [Indexed: 11/26/2022]
Abstract
ATP-dependent chromatin remodeling complexes, or remodelers, are large protein assemblies that use the energy from ATP hydrolysis to non-covalently modify the structure of nucleosomes, playing a central role in the regulation of chromatin dynamics. Our understanding of the mechanism and regulation of this remodeling activity and the diversity of products that chromatin remodelers can generate remains limited, partly because very little structural data are available on these challenging samples. Electron microscopy (EM) and single-particle approaches have made inroads into the structural characterization of a number of remodeling complexes. Here I will review the work done to date, focusing on functional insights we have gained from these structures.
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Affiliation(s)
- Andres E Leschziner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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20
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Abstract
Chromatin remodelling is the ATP-dependent change in nucleosome organisation driven by Snf2 family ATPases. The biochemistry of this process depends on the behaviours of ATP-dependent motor proteins and their dynamic nucleosome substrates, which brings significant technical and conceptual challenges. Steady progress has been made in characterising the polypeptides of which these enzymes are comprised. Divergence in the sequences of different subfamilies of Snf2-related proteins suggests that the motors are adapted for different functions. Recently, structural insights have suggested that the Snf2 ATPase acts as a context-sensitive DNA translocase. This may have arisen as a means to enable efficient access to DNA in the high density of the eukaryotic nucleus. How the enzymes engage nucleosomes and how the network of noncovalent interactions within the nucleosome respond to the force applied remains unclear, and it remains prudent to recognise the potential for both DNA distortions and dynamics within the underlying histone octamer structure.
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Affiliation(s)
- Andrew Flaus
- Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
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21
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Hargreaves DC, Crabtree GR. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res 2011; 21:396-420. [PMID: 21358755 DOI: 10.1038/cr.2011.32] [Citation(s) in RCA: 614] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Macromolecular assemblies that regulate chromatin structure using the energy of ATP hydrolysis have critical roles in development, cancer, and stem cell biology. The ATPases of this family are encoded by 27 human genes and are usually associated with several other proteins that are stable, non-exchangeable subunits. One fundamental mechanism used by these complexes is thought to be the movement or exchange of nucleosomes to regulate transcription. However, recent genetic studies indicate that chromatin remodelers may also be involved in regulating other aspects of chromatin structure during many cellular processes. The SWI/SNF family in particular appears to have undergone a substantial change in subunit composition and mechanism coincident with the evolutionary advent of multicellularity and the appearance of linking histones. The differential usage of this greater diversity of mammalian BAF subunits is essential for the development of specific cell fates, including the progression from pluripotency to multipotency to committed neurons. Recent human genetic screens have revealed that BRG1, ARID1A, BAF155, and hSNF5 are frequently mutated in tumors, indicating that BAF complexes also play a critical role in the initiation or progression of cancer. The mechanistic bases underlying the genetic requirements for BAF and other chromatin remodelers in development and cancer are relatively unexplored and will be a focus of this review.
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Affiliation(s)
- Diana C Hargreaves
- Howard Hughes Medical Institute, Beckman Center B211, 279 Campus Drive, Mailcode 5323, Stanford University School of Medicine, Stanford, CA 94305-5323, USA
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22
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Krajewski WA, Vassiliev OL. The Saccharomyces cerevisiae Swi/Snf Complex Can Catalyze Formation of Dimeric Nucleosome Structures in Vitro. Biochemistry 2010; 49:6531-40. [DOI: 10.1021/bi1006157] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
| | - Oleg L. Vassiliev
- Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
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23
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Tang L, Nogales E, Ciferri C. Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 102:122-8. [PMID: 20493208 PMCID: PMC2924208 DOI: 10.1016/j.pbiomolbio.2010.05.001] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 05/08/2010] [Indexed: 01/03/2023]
Abstract
ATP-dependent chromatin remodeling complexes are specialized protein machinery able to restructure the nucleosome to make its DNA accessible during transcription, replication and DNA repair. During the past few years structural biologists have defined the architecture and dynamics of some of these complexes using electron microscopy, shedding light on the mechanisms of action of these important assemblies. In this paper we review the existing structural information on the SWI/SNF family of the ATP-dependent chromatin remodeling complexes, and discuss their mechanistic implications.
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Affiliation(s)
- Liling Tang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Chongqing 400044, China
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24
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Charlop-Powers Z, Zeng L, Zhang Q, Zhou MM. Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2. Cell Res 2010; 20:529-38. [PMID: 20368734 PMCID: PMC2921579 DOI: 10.1038/cr.2010.43] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Polybromo (PB) protein functions as a key component of the human PBAF chromatin remodeling complex in regulation of gene transcription. PB is made up of modular domains including six bromodomains that are known as acetyl-lysine binding domains. However, histone-binding specificity of the bromodomains of PB has remained elusive. In this study, we report biochemical characterization of all six PB bromodomains' binding to a suite of lysine-acetylated peptides derived from known acetylation sites on human core histones. We demonstrate that bromodomain 2 of PB preferentially recognizes acetylated lysine 14 of histone H3 (H3K14ac), a post-translational mark known for gene transcriptional activation. We further describe the molecular basis of the selective H3K14ac recognition of bromodomain 2 by solving the protein structures in both the free and bound forms using X-ray crystallography and NMR, respectively.
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Affiliation(s)
- Zachary Charlop-Powers
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA
| | - Lei Zeng
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA
| | - Qiang Zhang
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, Box 1677, New York, NY 10029, USA
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25
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Chang EY, Ferreira H, Somers J, Nusinow DA, Owen-Hughes T, Narlikar GJ. MacroH2A allows ATP-dependent chromatin remodeling by SWI/SNF and ACF complexes but specifically reduces recruitment of SWI/SNF. Biochemistry 2008; 47:13726-32. [PMID: 19035833 PMCID: PMC3428728 DOI: 10.1021/bi8016944] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The variant histone macroH2A helps maintain X inactivation and gene silencing. Previous work implied that nucleosomes containing macroH2A cannot be remodeled by ISWI and SWI/SNF chromatin remodeling enzymes. Using approaches that prevent misassembly of macroH2A nucleosomes, we find that macroH2A nucleosomes are excellent substrates for both enzyme families. Interestingly, SWI/SNF, which is involved in gene activation, preferentially binds H2A nucleosomes over macroH2A nucleosomes, but ACF, an ISWI complex implicated in gene repression, shows no preference. Thus, macroH2A may help regulate the balance between activating and repressive remodeling complexes.
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26
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Hu M, Zhang YB, Qian L, Briñas RP, Kuznetsova L, Hainfeld JF. Three-dimensional structure of human chromatin accessibility complex hCHRAC by electron microscopy. J Struct Biol 2008; 164:263-9. [PMID: 18814851 DOI: 10.1016/j.jsb.2008.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 08/25/2008] [Accepted: 08/26/2008] [Indexed: 01/06/2023]
Abstract
ATP-dependent chromatin remodeling complexes modulate the dynamic assembly and remodeling of chromatin involved in DNA transcription, replication, and repair. There is little structural detail known about these important multiple-subunit enzymes that catalyze chromatin remodeling processes. Here we report a three-dimensional structure of the human chromatin accessibility complex, hCHRAC, using single particle reconstruction by negative stain electron microscopy. This structure shows an asymmetric 15x10x12nm disk shape with several lobes protruding out of its surfaces. Based on the factors of larger contact area, smaller steric hindrance, and direct involvement of hCHRAC in interactions with the nucleosome, we propose that four lobes on one side form a multiple-site contact surface 10nm in diameter for nucleosome binding. This work provides the first determination of the three-dimensional structure of the ISWI-family of chromatin remodeling complexes.
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Affiliation(s)
- Minghui Hu
- Biology Department, Brookhaven National Laboratory, Bldg. 463, Upton, NY 11973, USA
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27
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Abstract
The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. SWI/SNF interactions with nucleosomes were mapped by DNA footprinting and site-directed DNA and protein cross-linking when SWI/SNF was recruited by a transcription activator. SWI/SNF was found by DNA footprinting to contact tightly around one gyre of DNA spanning approximately 50 bp from the nucleosomal entry site to near the dyad axis. The DNA footprint is consistent with nucleosomes binding to an asymmetric trough of SWI/SNF that was revealed by the improved imaging of free SWI/SNF. The DNA site-directed cross-linking revealed that the catalytic subunit Swi2/Snf2 is associated with nucleosomes two helical turns from the dyad axis and that the Snf6 subunit is proximal to the transcription factor recruiting SWI/SNF. The highly conserved Snf5 subunit associates with the histone octamer and not with nucleosomal DNA. The model of the binding trough of SWI/SNF illustrates how nucleosomal DNA can be mobilized while SWI/SNF remains bound.
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28
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Racki LR, Narlikar GJ. ATP-dependent chromatin remodeling enzymes: two heads are not better, just different. Curr Opin Genet Dev 2008; 18:137-44. [PMID: 18339542 DOI: 10.1016/j.gde.2008.01.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 01/09/2008] [Accepted: 01/11/2008] [Indexed: 11/26/2022]
Abstract
ATP-dependent chromatin remodeling complexes enable rapid rearrangements in chromatin structure in response to developmental cues. The ATPase subunits of remodeling complexes share homology with the helicase motifs of DExx box helicases. Recent single-molecule experiments indicate that, like helicases, many of these complexes use ATP to translocate on DNA. Despite sharing this fundamental property, two key classes of remodeling complexes, the ISWI class and the SWI/SNF class, generate distinct remodeled products. SWI/SNF complexes generate nucleosomes with altered positions, nucleosomes with DNA loops and nucleosomes that are capable of exchanging histone dimers or octamers. In contrast, ISWI complexes generate nucleosomes with altered positions but in standard structures. Here, we draw analogies to monomeric and dimeric helicases and propose that ISWI and SWI/SNF complexes catalyze different outcomes in part because some ISWI complexes function as dimers while SWI/SNF complexes function as monomers.
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Affiliation(s)
- Lisa R Racki
- Department of Biochemistry and Biophysics, N412F, 600 16th Street, University of California, San Francisco, San Francisco, CA 94158, United States
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29
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Abstract
To accompany the Focus on Chromatin appearing in this issue of Nature Structural & Molecular Biology, a series of primers has been specially prepared that covers the wealth of knowledge in four areas of chromatin research. These areas include functions associated with covalent histone modifications, the enzymes that mediate these modifications, modules that recognize chromatin, and the ATP-dependent chromatin-remodeling complexes. In such a complex field, the information has inevitably been somewhat simplified. As an example, the correlation between modifications and functions are often context dependent. For instance, H3K9 methylation has been associated with transcriptional activation when present in the coding region of the gene, but has also been associated with repression. The reference list provides further reading and details, as do the Reviews and Perspective in this issue. Although there are many informative structures in this field, space constraints allowed only representative structures to be shown, followed by reference citations for related structures ('3D REF' column). The primers can be used as a stand-alone resource--feel free to tear them out of the issue or print out the PDF versions and modify or add to them yourself as new data emerge. The online versions of the primers contain hyperlinks to the Protein Data Bank as well as 3D view links that allow structural visualization.
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30
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Skiniotis G, Moazed D, Walz T. Acetylated histone tail peptides induce structural rearrangements in the RSC chromatin remodeling complex. J Biol Chem 2007; 282:20804-8. [PMID: 17535815 DOI: 10.1074/jbc.c700081200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational acetylation of histone tails is often required for the recruitment of ATP-dependent chromatin remodelers, which in turn mobilize nucleosomes on the chromatin fiber. Here we show that the lower lobe of the ATP-dependent chromatin remodeler RSC exists in a dynamic equilibrium and can be found extended away or retracted against the tripartite upper lobe of the complex. Extension of the lower lobe increases the size of a central cavity that has been proposed to be the nucleosome binding site. We show that the presence of acetylated histone 3 N-terminal tail peptides stabilizes the lower lobe of RSC in the retracted state, suggesting that domains recognizing the acetylated histone tails reside at the interface between the two lobes. Based on three-dimensional reconstructions, we propose a model for the interaction of RSC with acetylated nucleosomes.
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Affiliation(s)
- Georgios Skiniotis
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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31
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Llorca O. Electron microscopy reconstructions of DNA repair complexes. Curr Opin Struct Biol 2007; 17:215-20. [PMID: 17387012 DOI: 10.1016/j.sbi.2007.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 01/31/2007] [Accepted: 03/16/2007] [Indexed: 12/24/2022]
Abstract
Lesions in DNA compromise the integrity of the genome; their consequences can range from cell malfunction to malignant transformation. DNA damage is repaired by huge multisubunit macromolecular complexes of dynamic composition and conformation. Hence, single-particle electron microscopy has started to contribute significantly to resolving the DNA repair machinery. In many cases, the complexity of the task means that the work requires laborious purification, well-designed strategies for image processing and meticulous labelling of subunits; often, only negative staining is feasible. Recent electron microscopy studies have revealed that the association of DNA-PKcs with Ku70/Ku80 and DNA during non-homologous end joining induces conformational changes that activate the kinase and direct the formation of a synaptic complex. Also, rearrangements of Rad51 filaments and their association with Brca2 were found to regulate homologous recombination.
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Affiliation(s)
- Oscar Llorca
- Centro de Investigaciones Biológicas (CIB)/Centre for Biological Research, Consejo Superior de Investigaciones Científicas/Spanish National Research Council, Ramiro de Maeztu, Madrid, Spain
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32
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Leschziner AE, Saha A, Wittmeyer J, Zhang Y, Bustamante C, Cairns BR, Nogales E. Conformational flexibility in the chromatin remodeler RSC observed by electron microscopy and the orthogonal tilt reconstruction method. Proc Natl Acad Sci U S A 2007; 104:4913-8. [PMID: 17360331 PMCID: PMC1820885 DOI: 10.1073/pnas.0700706104] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Indexed: 11/18/2022] Open
Abstract
Chromatin remodeling complexes (remodelers) are large, multisubunit macromolecular assemblies that use ATP hydrolysis to alter the structure and positioning of nucleosomes. The mechanisms proposed for remodeler action on nucleosomes are diverse, and require structural evaluation and insights. Previous reconstructions of remodelers using electron microscopy revealed interesting features, but also significant discrepancies, prompting new approaches. Here, we use the orthogonal tilt reconstruction method, which is well suited for heterogeneous samples, to provide a reconstruction of the yeast RSC (remodel the structure of chromatin) complex. Two interesting features are revealed: first, we observe a deep central cavity within RSC, displaying a remarkable surface complementarity for the nucleosome. Second, we are able to visualize two distinct RSC conformers, revealing a major conformational change in a large protein "arm," which may shift to further envelop the nucleosome. We present a model of the RSC-nucleosome complex that rationalizes the single molecule results obtained by using optical tweezers and also discuss the mechanistic implications of our structures.
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Affiliation(s)
| | - Anjanabha Saha
- Department of Oncological Sciences, Huntsman Cancer Institute, and
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112; and
| | | | - Yongli Zhang
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Carlos Bustamante
- Departments of *Molecular and Cell Biology
- Chemistry, and
- **Physics, and
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Bradley R. Cairns
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112; and
| | - Eva Nogales
- Departments of *Molecular and Cell Biology
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112; and
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33
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Saha A, Wittmeyer J, Cairns BR. Mechanisms for nucleosome movement by ATP-dependent chromatin remodeling complexes. Results Probl Cell Differ 2006; 41:127-48. [PMID: 16909894 DOI: 10.1007/400_005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chromatin remodeling complexes (remodelers) are a set of diverse multi-protein machines that reposition and restructure nucleosomes. Remodelers are specialized, containing unique proteins that assist in targeting, interaction with modified nucleosomes, and performing specific chromatin tasks. However, all remodelers contain an ATPase domain that is highly similar to known DNA translocases/helicases, suggesting that DNA translocation is a property common to all remodelers. Here we examine the different reactions they perform in vitro, focusing on the SWI/SNF and the ISWI complexes, and explore how DNA translocation might be utilized to execute various remodeling processes.
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Affiliation(s)
- Anjanabha Saha
- Department of Oncological Sciences and 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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34
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Wang H, Bash R, Lindsay SM, Lohr D. Solution AFM studies of human Swi-Snf and its interactions with MMTV DNA and chromatin. Biophys J 2005; 89:3386-98. [PMID: 16100261 PMCID: PMC1366835 DOI: 10.1529/biophysj.105.065391] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ATP-dependent nucleosome remodeling complexes are crucial for relieving nucleosome repression during transcription, DNA replication, recombination, and repair. Remodeling complexes can carry out a variety of reactions on chromatin substrates but precisely how they do so remains a topic of active inquiry. Here, a novel recognition atomic force microscopy (AFM) approach is used to characterize human Swi-Snf (hSwi-Snf) nucleosome remodeling complexes in solution. This information is then used to locate hSwi-Snf complexes bound to mouse mammary tumor virus promoter nucleosomal arrays, a natural target of hSwi-Snf action, in solution topographic AFM images of surface-tethered arrays. By comparing the same individual chromatin arrays before and after hSwi-Snf activation, remodeling events on these arrays can be monitored in relation to the complexes bound to them. Remodeling is observed to be: inherently heterogeneous; nonprocessive; able to occur near and far from bound complexes; often associated with nucleosome height decreases. These height decreases frequently occur near sites of DNA release from chromatin. hSwi-Snf is usually incorporated into nucleosomal arrays, with multiple DNA strands entering into it from various directions, + or - ATP; these DNA paths can change after hSwi-Snf activation. hSwi-Snf appears to interact with naked mouse mammary tumor virus DNA somewhat differently than with chromatin and ATP activation of surface-bound DNA/hSwi-Snf produces no changes detectable by AFM.
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Affiliation(s)
- H Wang
- Arizona Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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35
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Saha A, Wittmeyer J, Cairns BR. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat Struct Mol Biol 2005; 12:747-55. [PMID: 16086025 DOI: 10.1038/nsmb973] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Accepted: 07/01/2005] [Indexed: 11/08/2022]
Abstract
The RSC chromatin remodeler contains Sth1, an ATP-dependent DNA translocase. On DNA substrates, RSC/Sth1 tracks along one strand of the duplex with a 3' --> 5' polarity and a tracking requirement of one base, properties that may enable directional DNA translocation on nucleosomes. The binding of RSC or Sth1 elicits a DNase I-hypersensitive site approximately two DNA turns from the nucleosomal dyad, and the binding of Sth1 requires intact DNA at this location. Results with various nucleosome substrates suggest that RSC/Sth1 remains at a fixed position on the histone octamer and that Sth1 conducts directional DNA translocation from a location about two turns from the nucleosomal dyad, drawing in DNA from one side of the nucleosome and pumping it toward the other. These studies suggest that nucleosome mobilization involves directional DNA translocation initiating from a fixed internal site on the nucleosome.
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Affiliation(s)
- Anjanabha Saha
- Howard Hughes Medical Institute and the Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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