Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex

Han, Yanping; Aa, Reyes; Malik, Shuja Shafi; He, Yuan

doi:10.1101/805184

Cited by 4 publications

(4 citation statements)

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“…It is important to note that this initial assembly process primarily involves evolutionarily conserved subunits and domains and is thus likely conserved for all SWI/SNF chromatin remodelers (Kadoch and Crabtree, 2015). This model is supported by the structural similarities we observe between the yeast SWI/SNF and RSC complexes (and in agreement with a recently reported structure of yeast SWI/SNF bound to a nucleosome by Han et al, 2019). In the case of RSC, assembly Figure 6.…”

Section: Model Of Rsc Core Assemblysupporting

confidence: 87%

“…During the submission of this manuscript the structure of SWI/SNF bound to a nucleosome was published by Han et al (2019). While at the time of final submission of this manuscript, the structure by Han et al has not been deposited yet, and a direct comparison could not be made, several clear similarities and differences are apparent.…”

Section: Author Contributionsmentioning

confidence: 99%

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Faculty Opinions recommendation of Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement.

Owen-Hughes

2020

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature

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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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Section: Model Of Rsc Core Assemblysupporting

confidence: 87%

Section: Author Contributionsmentioning

confidence: 99%

Faculty Opinions recommendation of Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement.

Owen-Hughes

2020

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature

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“…When our manuscript was under review, three related structures were reported, two structures of RSC-nucleosome complexes 29 , 30 and a structure of the yeast SWI/SNF-nucleosome complex 31 . Together, these structures provide a basis for understanding the multiple functions of SWI/SNF family remodelers in chromatin biology.…”

Section: Swi/snf Family and Cancermentioning

confidence: 99%

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Wagner

Dienemann

Wang

et al. 2020

Nature

120

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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 RSC 3 contains 16 subunits, including the ATP-dependent DNA translocase Sth1 4 , 5 . RSC removes nucleosomes from promoter regions 6 , 7 and positions the specialized +1 and –1 nucleosomes that flank NDRs 8 , 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 elements 8 , 10 , 11 that influence RSC functionality 12 . 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 activity 5 . 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 cancer 13 .

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“…When our manuscript was under review, three related structures were reported, two structures of RSC-nucleosome complexes 29,30 and a structure of the yeast SWI/SNFnucleosome complex 31 . Together, these structures provide a basis for understanding the multiple functions of SWI/SNF family remodelers in chromatin biology.…”

Section: Swi/snf Family and Cancermentioning

confidence: 99%

Faculty Opinions recommendation of Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome.

Owen-Hughes

2020

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature

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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 RSC 3 contains 16 subunits, including the ATPdependent DNA translocase Sth1 4,5 . RSC removes nucleosomes from promoter regions 6,7 and positions the specialized +1 and -1 nucleosomes that flank NDRs 8,9 . 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 elements 8,10,11 that influence RSC functionality 12 . 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 translocasenucleosome interactions to regulate RSC activity 5 . The RSC-nucleosome structure provides a Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

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Cryo-electron microscopy structure of a nucleosome-bound SWI/SNF chromatin remodeling complex

Cited by 4 publications

References 74 publications

Faculty Opinions recommendation of Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement.

Faculty Opinions recommendation of Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement.

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Faculty Opinions recommendation of Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome.

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