A comparative structural study of ATP-dependent chromatin remodeling complexes

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PROJECT SUMMARY Nucleosomes are the basic DNA packaging unit in eukaryotes. ATP-dependent nucleosome remodeling complexes (“remodelers”) use ATP hydrolysis to non-covalently alter their structure to regulate genome dynamics. Remodelers, conserved from yeast to humans, generate a wide range of products despite sharing a conserved catalytic subunit: a 3’-5’ dsDNA translocase that binds to the nucleosome and breaks histone-DNA contacts and alters the structure of nucleosomes by propelling DNA over their surface. Remodeler ATPases are flanked by accessory domains that define 4 subfamilies: ISWI, CHD, SWI/SNF and INO80. These subfamilies differ in complexity, ranging from single-subunit remodelers (ISWI and CDH), to large, multi-subunit 1MDa+ complexes (SWI/SNF and INO80). Different subfamilies catalyze different outcomes. “Orphan” remodelers, whose translocases do not belong to any of the 4 subfamilies despite their conserved ATPase domains, are less well characterized. The overarching goal of this proposal is to understand the mechanistic underpinnings of the functional diversity of remodelers. ISWI and CHD remodelers, among the smallest and best understood, have provided insights into how they regulate their translocases to produce their specific remodeling outcomes. Although conceptual models have been proposed to explain the functional specialization of SWI/SNF and INO80 remodelers a mechanistic understanding is missing. Even less is known about orphan remodelers. In this proposal, we will tackle model systems representing functions for which mechanistic understanding is lacking. For orphan remodelers, we will focus on Rad26, the S. cerevisiae ortholog of the Cockayne Syndrome protein B (CSB), a protein that has long been known for its role in Transcription Coupled DNA Repair, and that we recently showed uses its DNA translocation to help RNA Polymerase II overcome transcriptional obstacles. For the SWI/SNF remodelers, we will focus on the RSC complex, an abundant and essential remodeler from S. cerevisiae capable of both sliding and ejecting histone octamers. For the INO80 family, we will continue working on the SWR1 complex, which is unique in its ability to exchange histone dimers in a nucleosome without altering its position. We will use a combination of structural (cryo-electron microscopy) and biochemical approaches to understand how these different remodelers regulate their DNA translocases to produce their specialized remodeling outcomes. !