1. Structural Biology and Molecular Biophysics

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

  1. Avinash B Patel  Is a corresponding author
  2. Camille M Moore
  3. Basil J Greber
  4. Jie Luo
  5. Stefan A Zukin
  6. Jeff Ranish
  7. Eva Nogales  Is a corresponding author
  1. University of California, Berkeley, United States
  2. The Institute for Systems Biology, United States
  3. Lawrence Berkeley National Laboratory, United States
https://doi.org/10.7554/eLife.54449
Share this article
Cite this article
  1. Avinash B Patel
  2. Camille M Moore
  3. Basil J Greber
  4. Jie Luo
  5. Stefan A Zukin
  6. Jeff Ranish
  7. Eva Nogales
(2019)
Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement
eLife 8:e54449.
https://doi.org/10.7554/eLife.54449
  2. Download BibTeX
  3. Download .RIS

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.

Data availability

The cryo-EM maps and coordinate models have been deposited in the Electron Microscopy Data Bank with the accession codes EMD-21107 (RSC core), EMD-21105 (head lobe multibody), EMD-21103 (body lobe multibody), EMD-21098 (arm lobe multibody), EMD-21106 (head lobe classified), EMD-21102 (body lobe classified), EMD-21104 (arm lobe classified), EMD-21114 (RSC-NCP locked) and EMD-21110 (RSC-NCP swiveled) and in the Protein Data Bank with the accession codes PDB-6V8O (RSC core) and PDB-6V92 (RSC-NCP).

The following data sets were generated

Article and author information

Author details

  1. Avinash B Patel

    Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
    For correspondence
    patelab@berkeley.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9140-8375

  2. Camille M Moore

    Molecular and Cell Biology Department, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.

  3. Basil J Greber

    California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9379-7159

  4. Jie Luo

    The Institute for Systems Biology, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.

  5. Stefan A Zukin

    Chemistry Department, University of California, Berkeley, Berkeley, United States
    Competing interests
    The authors declare that no competing interests exist.

  6. Jeff Ranish

    The Institute for Systems Biology, Seattle, United States
    Competing interests
    The authors declare that no competing interests exist.

  7. Eva Nogales

    Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
    For correspondence
    enogales@lbl.gov
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9816-3681

Funding

National Institutes of Health (U24GM129547)

  • Eva Nogales

National Institute of General Medical Sciences (R01-GM63072)

  • Eva Nogales

National Institute of General Medical Sciences (R35-GM127018)

  • Eva Nogales

National Institute of General Medical Sciences (R01- GM110064)

  • Jeff Ranish

National Institute of General Medical Sciences (R01-HL133678)

  • Jeff Ranish

Howard Hughes Medical Institute

  • Eva Nogales

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Cynthia Wolberger, Johns Hopkins University School of Medicine, United States

Version history

  1. Received: December 16, 2019
  2. Accepted: December 23, 2019
  3. Accepted Manuscript published: December 30, 2019 (version 1)
  4. Version of Record published: January 14, 2020 (version 2)

Copyright

© 2019, Patel et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 5,651
    views
  • 841
    downloads
  • 51
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Avinash B Patel
  2. Camille M Moore
  3. Basil J Greber
  4. Jie Luo
  5. Stefan A Zukin
  6. Jeff Ranish
  7. Eva Nogales
(2019)
Architecture of the chromatin remodeler RSC and insights into its nucleosome engagement
eLife 8:e54449.
https://doi.org/10.7554/eLife.54449

Share this article

https://doi.org/10.7554/eLife.54449

Categories and tags

Research organism

Further reading

    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Effect of α-tubulin acetylation on the doublet microtubule structure

    Shun Kai Yang, Shintaroh Kubo ... Khanh Huy Bui
    Research Article

    Acetylation of α-tubulin at the lysine 40 residue (αK40) by αTAT1/MEC-17 acetyltransferase modulates microtubule properties and occurs in most eukaryotic cells. Previous literatures suggest that acetylated microtubules are more stable and damage resistant. αK40 acetylation is the only known microtubule luminal post-translational modification site. The luminal location suggests that the modification tunes the lateral interaction of protofilaments inside the microtubule. In this study, we examined the effect of tubulin acetylation on the doublet microtubule (DMT) in the cilia of Tetrahymena thermophila using a combination of cryo-electron microscopy, molecular dynamics, and mass spectrometry. We found that αK40 acetylation exerts a small-scale effect on the DMT structure and stability by influencing the lateral rotational angle. In addition, comparative mass spectrometry revealed a link between αK40 acetylation and phosphorylation in cilia.

    1. Structural Biology and Molecular Biophysics

    Structure-guided mutagenesis of OSCAs reveals differential activation to mechanical stimuli

    Sebastian Jojoa-Cruz, Adrienne E Dubin ... Andrew B Ward
    Research Advance

    The dimeric two-pore OSCA/TMEM63 family has recently been identified as mechanically activated ion channels. Previously, based on the unique features of the structure of OSCA1.2, we postulated the potential involvement of several structural elements in sensing membrane tension (Jojoa-Cruz et al., 2018). Interestingly, while OSCA1, 2, and 3 clades are activated by membrane stretch in cell-attached patches (i.e. they are stretch-activated channels), they differ in their ability to transduce membrane deformation induced by a blunt probe (poking). Here, in an effort to understand the domains contributing to mechanical signal transduction, we used cryo-electron microscopy to solve the structure of Arabidopsis thaliana (At) OSCA3.1, which, unlike AtOSCA1.2, only produced stretch- but not poke-activated currents in our initial characterization (Murthy et al., 2018). Mutagenesis and electrophysiological assessment of conserved and divergent putative mechanosensitive features of OSCA1.2 reveal a selective disruption of the macroscopic currents elicited by poking without considerable effects on stretch-activated currents (SAC). Our results support the involvement of the amphipathic helix and lipid-interacting residues in the membrane fenestration in the response to poking. Our findings position these two structural elements as potential sources of functional diversity within the family.

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Interplay between charge distribution and DNA in shaping HP1 paralog phase separation and localization

    Tien M Phan, Young C Kim ... Jeetain Mittal
    Research Article

    The heterochromatin protein 1 (HP1) family is a crucial component of heterochromatin with diverse functions in gene regulation, cell cycle control, and cell differentiation. In humans, there are three paralogs, HP1α, HP1β, and HP1γ, which exhibit remarkable similarities in their domain architecture and sequence properties. Nevertheless, these paralogs display distinct behaviors in liquid-liquid phase separation (LLPS), a process linked to heterochromatin formation. Here, we employ a coarse-grained simulation framework to uncover the sequence features responsible for the observed differences in LLPS. We highlight the significance of the net charge and charge patterning along the sequence in governing paralog LLPS propensities. We also show that both highly conserved folded and less-conserved disordered domains contribute to the observed differences. Furthermore, we explore the potential co-localization of different HP1 paralogs in multicomponent assemblies and the impact of DNA on this process. Importantly, our study reveals that DNA can significantly reshape the stability of a minimal condensate formed by HP1 paralogs due to competitive interactions of HP1α with HP1β and HP1γ versus DNA. In conclusion, our work highlights the physicochemical nature of interactions that govern the distinct phase-separation behaviors of HP1 paralogs and provides a molecular framework for understanding their role in chromatin organization.