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Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler

ABSTRACT: The SWR1 chromatin remodeling complex (SRCAP in humans) is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here we use cryo-EM to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical structure-function roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α -helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1 promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 towards the +1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE275429 | GEO | 2024/08/26

REPOSITORIES: GEO

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Stepwise histone replacement by SWR1 requires dual activation with histone H2A.Z and canonical nucleosome

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2010-10-12 | E-GEOD-24618 | biostudies-arrayexpress

Nucleosome free DNA- and acetyl histone-binding components recruit SWR1 to yeast promoters for H2A.Z replacement

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Recognition of inherently unstable H2A-nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange

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Histone acetylation readers Bdf1 and Yaf9 guide targeting of SWR1 remodeler to +1 nucleosome

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Stepwise histone replacement by SWR1 requires dual activation with histone H2A.Z and canonical nucleosome

2010-10-12 | GSE24618 | GEO

Nucleosome free DNA- and acetyl histone-binding components recruit SWR1 to yeast promoters for H2A.Z replacement

2013-09-16 | GSE49183 | GEO

In the absence of H2A.Z, the SWR1 histone replacement complex causes genetic instability, stress and genome transcription misregulation

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In the absence of H2A.Z, the SWR1 histone replacement complex causes genetic instability, stress and genome transcription misregulation

2011-05-18 | GSE21571 | GEO

Structural insights into histone exchange by human SRCAP complex

Project description:Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome-binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeFx-bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation (ChIP) sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C.

2024-02-10 | GSE249825 | GEO

Asymmetric nucleosomes flank promoters in the budding yeast genome

Project description:Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that nucleosomes at 5% of budding yeast nucleosome positions have asymmetric histone-DNA interactions. These asymmetric interactions are enriched at nucleosome positions that flank promoters. Micrococcal nuclease (MNase) sequence-based profiles of asymmetric nucleosome positions revealed a corresponding asymmetry in MNase protection near the dyad axis, suggesting that the loss of DNA contacts around H4S47 is accompanied by protection of the DNA from MNase. Chromatin immunoprecipitation mapping of selected nucleosome remodelers indicated that asymmetric nucleosomes are bound by the RSC chromatin remodeling complex, which is required for maintaining nucleosomes at asymmetric positions. These results imply that the asymmetric nucleosome-RSC complex is a metastable intermediate representing partial unwrapping and protection of nucleosomal DNA on one side of the dyad axis during chromatin remodeling. We have analyzed the chromatin landscape of the yeast genome using paired-end MNase-seq and the chromatin binding of yeast remodelers Swr1, Ino80 and RSC at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).

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