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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. !

项目摘要核小体是真核生物中最基本的DNA包装单位。ATP依赖性核小体重塑复合物（“重塑物”）利用ATP水解来非共价地改变它们的结构以调节基因组动力学重塑者，从酵母到人类，产生广泛的产品，尽管共享一个保守的催化亚单位：一种3 '-5'双链DNA转位酶，与核小体结合并破坏组蛋白-DNA 通过在核小体表面推进DNA来接触和改变核小体的结构。重塑ATP酶两侧是辅助结构域，定义了4个亚家族：ISWI，CHD，SWI/SNF INO 80这些亚家族的复杂性不同，从单亚基重塑（ISWI和CDH），大的多亚基1 MDa+复合物（SWI/SNF和INO 80）。不同的亚家族催化不同的结果。 “孤儿”重塑者，其易位酶不属于4个亚家族中的任何一个，尽管它们的保守性是 ATP酶结构域的特征较少。本提案的总体目标是了解重塑者功能多样性的机制基础。ISWI和CHD重塑者，最小的和最好的理解，提供了深入了解他们如何调节他们的易位酶，以产生他们的具体的重建结果。虽然已经提出了概念模型来解释功能性 SWI/SNF和INO 80重塑器的专业化，缺少对机械的理解。我们知道的就更少了关于孤儿改造者在这个提议中，我们将处理代表功能的模型系统，缺乏。对于孤儿重塑者，我们将重点关注Rad 26，S。Cockayne综合征的酿酒酵母直系同源物蛋白B（CS B），一种长期以来已知在转录偶联DNA修复中起作用的蛋白，我们最近展示了利用它的DNA易位来帮助RNA聚合酶II克服转录障碍。对于SWI/SNF改造者，我们将重点关注RSC复合体，这是S. 酿酒酵母能够滑动和弹出组蛋白八聚体。对于INO 80系列，我们将继续努力 SWR 1复合物，其独特之处在于其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）和生物化学方法，了解这些不同的重塑者如何调节他们的DNA移位酶，以产生他们的专门的重塑成果。 !