High Resolution Mapping of Functional Elements in the Yeast Genome

酵母基因组功能元件的高分辨率图谱

基本信息

批准号：
10259814
负责人：
B FRANKLIN PUGH
金额：
$ 40.1万
依托单位：
CORNELL UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-11 至 2023-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10259814
关键词：
Address Architecture Binding Biochemical Biological Models Biology Cell Differentiation process Cells ChIP-seq Chromatin Chromatin Remodeling Factor Complex CpG Islands Crude Extracts DNA DNA Sequence Diffuse Disease ENG gene Elements Functional disorder Funding Gene Expression Regulation Genes Genetic Transcription Genome Genomics Goals Health Histones Human In Vitro Individual Medical Methods Modeling Molecular Chaperones Nuclear Nucleosomes Pattern Physiological Play Positioning Attribute Proteins Regulation Regulator Genes Research Resolution Role Saccharomyces cerevisiae Saccharomycetales Shapes Site Specific qualifier value Structure System Testing Transcriptional Regulation Validation Work Yeasts cell behavior cell type chromatin remodeling complex biological systems embryonic stem cell epigenome experimental study genome-wide human DNA in vivo novel particle pluripotency promoter reconstitution yeast genome

项目摘要

The budding yeast Saccharomyces cerevisiae is used as model system to understand genomic mechanisms by which chromatin organization is established. The start sites of genes, or promoters, are typically encased in a nucleosome-free region, that is bookended with two well-positioned nucleosomes. This precise organization is standard for most genes, and plays into how these genes are regulated. Therefore a fundamental understanding of gene regulatory mechanisms requires a complete understanding of how such canonical nucleosome organization arises and guides the placement of the transcription machinery. The proposed work will take advantage of biochemical reconstitution of aspects of canonical nucleosome organization on a genomic scale. This will allow individual mechanistic contributions of chromatin organizing factors and their effectors to be explicitly defined. In particular, how ATP-dependent chromatin remodeler complexes recognize DNA features and sequence-specific organizing factors, will be addressed. The organization of chromatin directs the organized assembly of the transcription machinery. Biochemical reconstitution will be used to tease apart selected individual contributions of chromatin organization and activator/repressor binding towards assembly of the transcription machinery on a genomic scale. Chromatin is generally thought to be composed of nucleosome particles containing 2 copies of each of the four core histones. However, it is now becoming clear that various partially assembled nucleosomes or subnucleosomes exist in vivo, and these structures may play critical roles in chromatin dynamics. The existence of these substructures and the histone chaperones that are likely to be involved in their assembly and disassembly will be investigated on a genomic scale.

使用芽殖酵母酿酒酵母作为模型系统来了解基因组机制建立了哪种染色质组织。基因或启动子的起始位点通常被包裹在无核小体区域，由两个位置良好的核小体组成。这个精确的组织是大多数基因的标准，并影响这些基因的调节方式。因此一个基本的对基因调控机制的理解需要完全理解这些规范如何核小体组织产生并指导转录机器的放置。拟议的工作将利用典型核小体组织各方面的生化重建基因组规模。这将允许染色质组织因子及其各自的机制贡献明确定义效应器。特别是，ATP 依赖性染色质重塑复合物如何识别 DNA 特征和序列特异性组织因素将得到解决。染色质的组织指导转录机器的有组织的组装。生化重构将用来挑逗除了染色质组织和激活剂/阻遏物结合的选定个体贡献之外在基因组规模上组装转录机器。染色质通常被认为由以下组成核小体颗粒含有四个核心组蛋白各 2 个副本。不过，现在情况已经逐渐明朗体内存在各种部分组装的核小体或亚核小体，这些结构可能发挥作用在染色质动力学中发挥关键作用。这些亚结构和组蛋白伴侣的存在可能参与其组装和分解的分子将在基因组规模上进行研究。