A comparative structural study of ATP-dependent chromatin remodeling complexes

ATP依赖性染色质重塑复合物的比较结构研究

基本信息

批准号：
10220986
负责人：
Andres Leschziner
金额：
$ 35.55万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2011
资助国家：
美国
起止时间：
2011-04-01 至 2023-07-31
项目状态：
已结题

项目摘要

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. !

项目概要核小体是真核生物中依赖 ATP 的核小体重塑的基本 DNA 包装单位。复合物（“重塑者”）利用 ATP 水解非共价改变其结构来调节基因组重塑者从酵母到人类都保守，尽管共享一个基因，但仍能产生各种各样的产品。保守催化亚基：3'-5' dsDNA 转位酶，与核小体结合并破坏组蛋白 DNA 通过将 DNA 推到核小体表面来接触并改变核小体的结构。重塑 ATP 酶的两侧是定义 4 个亚家族的辅助结构域：ISWI、CHD、SWI/SNF 这些亚家族的复杂性有所不同，从单亚基重塑因子（ISWI 和 CDH）到大型多亚基 1MDa+ 复合物（SWI/SNF 和 INO80）。 “孤儿”重塑者，其易位酶不属于 4 个亚科中的任何一个，尽管它们是保守的 ATPase 结构域的特征尚不明确，该提案的总体目标是了解 ATPase 结构域。 ISWI 和 CHD 重塑者功能多样性的机制基础。最小且最容易理解的，提供了关于它们如何调节易位酶以产生其尽管已经提出了概念模型来解释功能。对于 SWI/SNF 和 INO80 重塑器的专业化，人们所知甚少。关于孤儿改造者。在本提案中，我们将解决代表功能的模型系统，这些功能需要机械理解对于孤儿重塑者，我们将重点关注 Rad26，Cockayne 综合征的酿酒酵母直系同源物。蛋白 B (CSB) 是一种长期以来因其在转录偶联 DNA 修复中的作用而闻名的蛋白质，我们最近展示了利用其 DNA 易位来帮助 RNA 聚合酶 II 克服转录障碍。对于 SWI/SNF 重塑剂，我们将重点关注 RSC 复合体，这是来自 SWI/SNF 的丰富且重要的重塑剂。对于 INO80 家族，我们将继续研究能够滑动和弹出组蛋白八聚体的酿酒酵母。位于 SWR1 复合体上，该复合体的独特之处在于能够在核小体中交换组蛋白二聚体而不改变它的位置。我们将结合使用结构（冷冻电子显微镜）和生化方法来了解这些不同的重塑者如何调节其 DNA 易位酶以产生其专门的重塑成果。！