Composition and Function of Mutant Swi/Snf Complexes

Dutta, Arnob; Sardiu, Mihaela E.; Gogol, Madelaine; Gilmore, Joshua M.; Zhang, Daoyong; Florens, Laurence; Abmayr, Susan M.; Washburn, Michael P.; Workman, Jerry L.

doi:10.1016/j.celrep.2017.01.058

Cited by 74 publications

(105 citation statements)

References 58 publications

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“…RSC was purified from Saccharomyces cerivisiae using a TAP-tag method as described 35,37 . A strain modified with a TAP tag at the C terminus of STH1 was obtained from GE Dharmacon and grown at 30 °C in YPD.…”

Section: Methodsmentioning

confidence: 99%

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement

Patel

Moore

Greber

et al. 2019

Preprint

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Eukaryotic DNA is packaged into nucleosome arrays, which are repositioned by chromatin remodeling complexes to control DNA accessibility 1,2 . 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 2-4 . 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 through the interactions between the N-terminus of Sth1 and the core. Our cryo-EM analysis also 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 Rsc8 SWRIM 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. MainEukaryotes have four major families of chromatin remodelers: SWI/SNF, ISWI, CHD, and INO80 2 . Each of these remodelers plays distinct roles based on how they select and affect target nucleosomes. Together, these remodelers give rise to the distinct chromatin landscapes observed in eukaryotic cells and determine how genetic information is organized, replicated, transcribed, and repaired 5 . In S. cerevisiae there are two members of the SWI/SNF family of chromatin remodelers: RSC and SWI/SNF 3,4 . RSC is essential for viability and is ten times more abundant than SWI/SNF 4 . While both complexes play a role in remodeling nucleosomes during transcription initiation, RSC is also involved in transcription-independent processes such as mitotic division, double stranded break repair, and telomere maintenance 6-12 .RSC is a ~1-MDa complex composed of 17 proteins, with two copies of Rsc8 and one copy of either Rsc1 or Rsc2 (Fig. S1) 4,13 . In order to determine the structure of RSC, we purified the complex from S. cerevisiae and performed cryo-EM analysis (Fig. S2). We find that RSC is composed of five main lobes, three that form a rigid core (head, body and arm) and two that are flexibly attached (leg and tail) ( Fig. 1a, b; Fig. S3, S4). We determined the structure of the core to ~3.1 Å and mapped 14 proteins within this region: Rsc1/2, Rsc3, Rsc4, Rsc6, Rsc8 (2 copies), Rsc9, Rsc30, Rsc58, Ldb7, Npl6, Htl1, Sfh1, and Sth1 (Fig. 1c, d, e). Our negative stain analysis of the yeast SWI/SNF complex shows that, like RSC, it has head, body, and arm regions that define a rigid core, and a flexible leg that occupies similar overall positions (Fig. S5). However, SWI/SNF lacks a tail lobe, indicating that while RSC and SWI/SNF share a conserved core architecture, ...

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Section: Methodsmentioning

confidence: 99%

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement

Patel

Moore

Greber

et al. 2019

Preprint

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“…While SWI3 has been shown to be important for scaffolding and assembling the entire SWI/ SNF complex (Yang et al, 2007), SNF5 is thought to play a vital role not only as a bridge between SNF2 and the rest of the SWI/SNF complex including the independent SWI subunit, but also in promoting binding of the SNF2 ATPase domain to nucleosomal DNA and enhances the catalytic and nucleosome remodeling activities of SWI/ SNF (Sen et al, 2017). This SNF5/SWI3 regulatory module is thus critical for the integrity of SWI/SNF and its loss differentially affects SNF2 occupancy at gene promoters (Dutta et al, 2017). SWI/SNF is able to bind to both DNA and nucleosomes; however, it does so without sequence specificity (Cote et al, 1994;Quinn et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

Trichoderma reesei XYR1 recruits SWI/SNF to facilitate cellulase gene expression

Cao

Zheng

Zhang

et al. 2019

Molecular Microbiology

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Summary Cellulase gene expression in Trichoderma reesei is highly responsive to environmental cues and is under stringent regulation by multiple transcription factors. XYR1 (Xylanase regulator 1) has been identified as the most important transcriptional activator of cellulase/hemicellulase gene expression although the precise transactivating mechanism remains largely elusive. Here we show that the activation domain of XYR1 interacts with the T. reesei homolog of the TrSNF12 subunit of SWI/SNF complex. Deletion of Trsnf12 markedly impaired the induced cellulase gene expression. Individual loss of other SWI/SNF subunits including the catalytic subunit also severely compromised cellulase gene expression and interfered with loss of histone H4 in the cbh1 and eg1 promoters upon cellulose induction. In addition, we find that the SWI/SNF occupancy on cellulase gene promoters strictly required XYR1 and TrSNF12 but TrSNF12 was dispensable for the XYR1 binding to these promoters. These data suggest a model in which XYR1 recruits SWI/SNF through direct interactions with TrSNF12 to remodel chromatin at cellulase gene promoters, thereby activating cellulase gene expression to initiate the cellulolytic response in T. reesei.

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“…Ino80 [31, 68, 69], Swr1 [30, 68], NuRD [35], SAGA [77], Tip60 [45], SWI/SNF [34, 78], and Sin3 [79, 80, 81, 82] are a few examples. Proteomic analysis of chromatin remodeling has provided key insights in to the content of these complexes and their important roles in regulating the genome.…”

Section: Expert Commentarymentioning

confidence: 99%

“…In addition to finding new interactions, deletion network analysis is important in detecting hub proteins, which are known to be essential for protein complex organization. Analysis of mutated Swi/Snf complexes is also emerging providing new insights regarding how these complexes may function in cancers [34, 78]. In addition, point mutations can have significant impacts on PPIs.…”

Section: Expert Commentarymentioning

confidence: 99%

“…C) Cancer-driving mutations, like the many found in SWI/SNF complexes, are being identified by proteomic approaches. For example, loss of SWI/SNF complex subunit SNF5 was identified as a cancer-driving mutation through XL-MS perturbation studies [34, 78]. D) Oncohistones, or mutated histones, like histone H3 Lysine-27 to methionine mutation exists in highly aggressive pediatric gliomas.…”

Section: Figurementioning

confidence: 99%

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Unravelling the biology of chromatin in health and cancer using proteomic approaches

Eubanks

Dayebgadoh

Liu

et al. 2017

Expert Review of Proteomics

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Introduction: Chromatin remodeling complexes play important roles in the control of genome regulation in both normal and diseased states, and are therefore critical components for the regulation of epigenetic states in cells. Given the role epigenetics plays in cancer, for example, chromatin remodeling complexes are routinely targeted for therapeutic intervention. Areas covered: Protein mass spectrometry and proteomics are powerful technologies used to study and understand chromatin remodeling. While impressive progress has been made in this area, there remain significant challenges in the application of proteomic technologies to the study of chromatin remodeling. As parts of large multisubunit complexes that can be heavily modified with dynamic post-translational modifications, challenges in the study of chromatin remodeling complexes include defining the content, determining the regulation, and studying the dynamics of the complexes under different cellular states. Expert Commentary: Important considerations in the study of chromatin remodeling complexes include the complexity of sample preparation, the choice of proteomic methods for the analysis of samples, and data analysis challenges. Continued research in these three areas promise to yield even greater insights into the biology of chromatin remodeling and epigenetics and the dynamics of these systems in human health and cancer.

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Composition and Function of Mutant Swi/Snf Complexes

Cited by 74 publications

References 58 publications

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement

Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement

Trichoderma reesei XYR1 recruits SWI/SNF to facilitate cellulase gene expression

Unravelling the biology of chromatin in health and cancer using proteomic approaches

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