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.

酿酒酵母的萌芽酵母菌被用作模型系统，以理解基因组机制建立了哪个染色质组织。基因或启动子的开始位点通常被包裹在一个无核小体区域，用两个固定良好的核小体预订。这个确切的组织是大多数基因的标准，并涉及这些基因的调节方式。因此是基本的对基因调节机制的理解需要完全理解这种规范核小体组织出现并指导转录机械的位置。拟议的工作将利用典型核小体组织各个方面的生化重构基因组量表。这将允许染色质组织因子及其其个人机械贡献效应器要明确定义。特别是，如何依赖ATP的染色质重塑材料识别将解决DNA特征和序列特异性组织因子。染色质的组织指导有组织的转录机械组装。生化重构将用于取笑与染色质组织和激活剂/阻遏物结合的选定个人贡献与转录机械的组装以基因组量表的形式。通常认为染色质是由包含四个核心组蛋白中每个副本的核小体颗粒。但是，现在变得清晰在体内存在各种部分组装的核小体或亚核小体，这些结构可能会发挥作用染色质动力学中的关键作用。这些子结构和组蛋白伴侣的存在可能会参与其组装和拆卸，将以基因组量表进行研究。