Biochemical, Genomic and Computational Analysis of Transcriptional Repression

转录抑制的生化、基因组和计算分析

• 批准号: 9365047
• 负责人: David N Arnosti
• 金额: $ 31.08万
• 依托单位: MICHIGAN STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2021-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9365047
• 关键词: AIDS diagnosis; Animals; Binding; Binding Proteins; Biochemical; Biochemical Process; Biological; Cells; Chromatin; Chromatin Structure; Complex; Computer Analysis; Computing Methodologies; DNA Sequence; Data; Data Set; Dependence; Development; Disease; Drosophila genome; Drosophila genus; Elements; Embryo; Enhancers; Eukaryota; Event; Evolution; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Gene Targeting; Genes; Genetic; Genetic Transcription; Genome; Genomics; High-Throughput Nucleotide Sequencing; Human; Knowledge; Laboratories; Link; Maps; Measures; Mediating; Methods; Molecular; Organism; Output; Pathway interactions; Physiological; Physiology; Play; Process; Property; Proteins; Recruitment Activity; Regulatory Element; Reporter; Repression; Repressor Proteins; Research; Role; Signal Transduction; Structure; Testing; Tissue-Specific Gene Expression; Tissues; Transcription Coactivator; Transcription Repressor/Corepressor; Transcriptional Regulation; Variant; Work; XCL1 gene; base; chromatin modification; cofactor; common rule; gene repression; genome-wide; in vivo; insight; mathematical model; mutant; novel; predictive tools; promoter; response; stoichiometry; tool; transcription factor; transcriptome sequencing

Project Summary Transcriptional repressors represent the necessary counterweight to transcriptional activators in metazoan development. The mechanisms of transcriptional repression have been intensively investigated, but we lack crucial insights into how repressors act at a mechanistic level across many targets in the genome. In particular, the coordinated recruiting of transcriptional co-repressors can generate diverse effects on chromatin structure and modification, and we still lack insights on the functional significance of many changes that can be measured in `omics studies. To develop key insights into eukaryotic transcriptional regulatory mechanisms, we use the natural setting of the Drosophila embryo to identify basic biochemical processes in a developmental setting, where differential gene expression is used to drive the developmental fate of particular cells and tissues. In this proposal, 1) we will use genome-wide methods developed in our laboratory to identify direct biochemical, chromatin-based processes that are directed by a set of five endogenous transcriptional regulators that repress through short-range and long-range mechanisms. 2) We will study the in vivo activity of wild-type and mutant repression complexes to identify the contributions of distinct transcriptional co-repressors Groucho and CtBP, testing their contributions to quantitative and/or qualitative effects in chromatin modifications and gene regulation. 3) To identify the cis-regulatory context in which transcriptional repressors act on different enhancers, we will quantitatively measure and mathematically model the output of specific enhancers to uncover the fundamental quantitative properties of specific classes of repressors interacting with activators – i.e. the common “rules” by which these proteins interact on many target genes. The three interrelated aims will provide predictive tools for interpretation of genomic cis regulatory content of the metazoan genome, providing essential underpinnings for studies of evolution and disease in higher eukaryotes.

项目摘要 转录抑制因子在后生动物中代表着对转录激活因子的必要制衡。 发展。转录抑制的机制已经被深入研究，但我们缺乏 对抑制子如何在基因组中的许多靶点上以机械性水平起作用的关键见解。特别是， 转录共抑制因子的协同募集可以对染色质结构产生不同的影响 和修改，我们仍然缺乏对许多可以被 在‘经济学研究’中测量的。为了发展对真核转录调控机制的关键见解，我们 利用果蝇胚胎的自然环境来识别发育中的基本生化过程 环境，其中差异基因表达被用来驱动特定细胞的发育命运和 纸巾。在这个提案中，1)我们将使用我们实验室开发的全基因组方法来鉴定直接 生化的，基于染色质的过程，由一组五种内源性转录指导 通过短期和远程机制进行抑制的监管机构。2)我们将研究其体内活性。 野生型和突变型抑制复合体识别不同转录共抑制因子的作用 Groucho和CtBP，测试他们对染色质的数量和/或质量效应的贡献 基因修饰和基因调控。3)确定转录抑制子的顺式调控环境 作用于不同的增强剂，我们将定量测量和数学建模特定的 揭示与之相互作用的特定类抑制物的基本定量性质的增强剂 激活剂--即这些蛋白质与许多靶基因相互作用的共同“规则”。三位一体 相互关联的AIMS将为解释基因组顺式调控内容提供预测工具 后生动物基因组，为高等进化和疾病研究提供必要的基础 真核生物。