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

总结 转录激活依赖于多个转录因子（TF）的协同活性，这些转录因子结合顺式- 调控元件（克雷斯）在其靶基因附近。虽然像染色质免疫沉淀这样的技术 结合测序有助于揭示不同物种中许多TF结合位点的全基因组位置， 然而，在细胞和组织中，TF如何与组蛋白竞争，结合DNA，调节CRE， 活性，并驱动转录激活。在本提案中，我们将通过利用 TF CLOCK：BMAL 1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- 结果表明，CLOCK：BMAL 1对转录的昼夜调节依赖于CLOCK：BMAL 1和BMAL 2之间的相互作用。 时钟：BMAL 1和其他TF，而不仅仅是核心时钟基因。时钟：BMAL 1节律性DNA结合 促进核小体在其克雷斯的节律性去除，强烈表明CLOCK：BMAL 1基因- 提供了一个宽松的染色质景观，促进了其他TF在其克雷斯的节律性募集。这 CLOCK：BMAL 1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：BMAL 1焦油， gets在正常情况下是有节奏地表达的，以及它们的节奏转录是如何被再现的， 当动物暴露在一个新的环境中时，这项建议是基于这些调查结果和 提出的实验将确定CLOCK：BMAL 1是否促进部分未包裹的核的形成， 一些（目的1），时钟的模式：BMAL 1与其他TF合作，通过使用单摩尔的方法， Cule足迹（目标2），如果高脂饮食改变了CLOCK：BMAL 1和其他TF之间的协同性， 重编程CRE转录活性（Aim 3）。这些实验的结果有望揭示新的 和重要的机制，控制成千上万的基因的节律表达，并提供一个新的 组织之间生物功能如何协调的概念框架。他们还预计， 提供深入了解TF协同性在控制CRE活性中的作用机制， 可以广泛地与昼夜节律领域之外的领域相关。

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.