Cooperation between transcription factors and its role in the regulation of rhythmic enhancer activity by the circadian clock

转录因子之间的合作及其在生物钟调节节律增强子活性中的作用

基本信息

批准号：
10650845
负责人：
Jerome Menet
金额：
$ 32.5万
依托单位：
TEXAS A&M UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-06-25 至 2026-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10650845
关键词：
ARNTL gene Address Affect Animals Binding Binding Sites Biological Biological Process Biology Cell Nucleus Chromatin Coupled DNA DNA Binding Data Data Set Enhancers Environment Etiology Event Excision Exposure to Frequencies Gene Expression Gene Expression Regulation Genes Genetic Transcription Goals High Fat Diet Histones Hour Inflammatory Response Knowledge Label Literature Liver Location Mammals Mediating Methods Methyltransferase Modality Modeling Mus NF-kappa B Nucleosomes Organ Pathologic Pathway interactions Periodicity Physiological Positioning Attribute Post-Translational Protein Processing Process Regulation Regulator Genes Regulatory Element Reporting Research Role Techniques Testing Tissues Transcriptional Activation Transcriptional Regulation Variant chromatin immunoprecipitation circadian circadian pacemaker circadian regulation experimental study feeding genome-wide in vivo insight novel permissiveness programs recruit single molecule transcription factor transcriptome

项目摘要

SUMMARY Transcription activation relies on the cooperative activity of multiple transcription factors (TFs) that bind cis- regulatory elements (CREs) near their target genes. Although techniques like chromatin immunoprecipitation coupled to sequencing helped uncover the genome-wide location of binding sites for many TFs in different spe- cies and tissues, it still remains unclear how TFs cooperate to compete with histones, bind DNA, regulate CRE activity, and drive transcription activation. In this proposal, we will address this knowledge gap by exploiting the circadian regulation of gene expression by the TF CLOCK:BMAL1. Recent reports from our lab and the litera- ture indicate that the circadian regulation of transcription by CLOCK:BMAL1 relies on the interaction between CLOCK:BMAL1 and other TFs rather than on core clock genes only. CLOCK:BMAL1 rhythmic DNA binding promotes the rhythmic removal of nucleosomes at its CREs, strongly suggesting that CLOCK:BMAL1 gener- ates a permissive chromatin landscape that facilitates the rhythmic recruitment of other TFs at its CREs. This cooperation between CLOCK:BMAL1 and other TFs may explain why less than a third of CLOCK:BMAL1 tar- gets are rhythmically expressed under normal condition, and how their rhythmic transcription can be repro- grammed when animals are exposed to a new environment. This proposal builds upon these findings and the proposed experiments will determine if CLOCK:BMAL1 promotes the formation of partially unwrapped nucleo- somes (Aim 1), the modalities of CLOCK:BMAL1 cooperation with other TFs by using a method of single-mole- cule footprinting (Aim 2), and if high-fat diet alters the cooperativity between CLOCK:BMAL1 and other TFs to reprogram CRE transcriptional activity (Aim 3). Results from these experiments are expected to uncover novel and important mechanisms that control the rhythmic expression of thousands of genes, and to provide a new conceptual framework for how biological functions are coordinated between tissues. They are also expected to provide insights into the mechanisms that underlie the role of TF cooperativity in the control of CRE activity that can be widely relevant to fields beyond the circadian field.

概括转录激活依赖于结合顺式-的多个转录因子（TF）的协同活性其靶基因附近的调控元件（CRE）。尽管染色质免疫沉淀等技术与测序相结合有助于揭示不同物种中许多 TF 结合位点的全基因组位置。细胞和组织中，转录因子如何合作与组蛋白竞争、结合 DNA、调节 CRE 仍不清楚活性，并驱动转录激活。在本提案中，我们将通过利用 TF CLOCK:BMAL1 对基因表达的昼夜节律调节。我们实验室和文献的最新报告确实表明 CLOCK:BMAL1 对转录的昼夜节律调节依赖于 CLOCK：BMAL1 和其他 TF，而不仅仅是核心时钟基因。时钟：BMAL1 节律性 DNA 结合促进其 CRE 处核小体的有节奏去除，强烈表明 CLOCK:BMAL1 基因形成了一个宽松的染色质景观，有助于在其 CRE 上有节奏地招募其他 TF。这 CLOCK:BMAL1 和其他 TF 之间的合作可以解释为什么只有不到三分之一的 CLOCK:BMAL1 tar- gets在正常情况下有节律地表达，以及它们的节律性转录如何能够重现当动物暴露于新环境时会发生变化。该提案建立在这些发现和拟议的实验将确定 CLOCK:BMAL1 是否促进部分展开核的形成 somes（目标 1），CLOCK:BMAL1 通过使用单分子方法与其他 TF 合作的方式核心足迹（目标 2），并且如果高脂肪饮食改变了 CLOCK:BMAL1 和其他 TF 之间的协作性重新编程 CRE 转录活性（目标 3）。这些实验的结果预计会发现新的以及控制数千个基因节律表达的重要机制，并提供新的组织之间如何协调生物功能的概念框架。他们还预计深入了解 TF 协同性在控制 CRE 活动中的作用机制可以与昼夜节律领域以外的领域广泛相关。