Genomic strategies to identify novel gene regulatory mechanisms by ligand-activated transcriptional enhancers

通过配体激活转录增强子识别新基因调控机制的基因组策略

基本信息

批准号：
10546446
负责人：
Sreejith Janardhanan Nair
金额：
$ 11.7万
依托单位：
GEORGETOWN 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：
2022-02-01 至 2025-01-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10546446
关键词：
3-Dimensional Acute Architecture Binding Biochemical Biological Biological Assay Cell Communication Cell Nucleus Chromatin Communication Complex DNA DNA Sequence Data Disease Distant Elements Endocrine Enhancers Environment Estradiol Estrogen Receptor alpha Eukaryotic Cell Event Foundations Future Gene Activation Gene Expression Gene Expression Regulation Genes Genetic Enhancer Element Genetic Transcription Genome engineering Genomic approach Genomics Goals Grant Health Hi-C Hormonal Hormones Immunoprecipitation Ligands Light Liquid substance MCF7 cell Mediating Modeling Molecular Names Nuclear Hormone Receptors Nuclear RNA Nuclear Receptors Outcome Phase Physical activity Physical condensation Physiology Play Prevalence Process Proteins RNA RNA purification Receptor Signaling Regulation Regulator Genes Reporting Research Research Proposals Resources Ribonucleoproteins Role Signal Induction Signal Transduction System Testing Thermodynamics Tissues Transcriptional Activation Untranslated RNA Validation Work crosslink design experimental study genome wide association study genome-wide genomic locus hormonal signals imaging study in vivo live cell imaging loss of function macromolecule multidisciplinary novel physical process physical property programs promoter recruit response scaffold screening therapeutic target transcription factor

项目摘要

PROJECT SUMMARY Eukaryotic cells interact with cellular environment through transcription regulatory programs activated by various endocrine ligands. Gene regulation by estrogen receptor alpha (ER), a class of nuclear hormone receptor, has been an important paradigm in understanding ligand-induced transcriptional programs. In response to the ligand -estradiol (E2), ER binds predominantly to the transcriptional enhancers, which are regulatory DNA sequence that control the gene expression from distant genomic loci. E2 stimulation also led to rapid reorganization of three-dimensional chromatin architecture and enhancer cooperativity. Biochemical and genomic studies in the past decade have identified many coregulators of ER, and also have largely resolved the composition of ER- bound enhancer complex. However, multidisciplinary studies over the past few years have challenged the conventional models in ligand-induced activation of transcriptional enhancers and the mechanism of enhancer- promoter communication. Live-cell imaging studies have revealed that in response to acute hormonal signaling, ER form distinct compartments inside the cell nucleus that concentrate transcription machinery at robust E2 activated transcriptional enhancers. Compositionally, these “nuclear receptor condensates” are ribonucleoprotein complexes composed of not only proteins, but also non-coding enhancer RNA (eRNA) that contribute to the physical properties and activity. However, the contribution of other RNA species in ligand- induced enhancer condensate assembly and chromatin architecture is not yet understood. The proposed study will focus on identifying new RNA coregulators of ER that facilitate ribonucleoprotein condensate assembly and regulated enhancer cooperativity. The central objective of AIM I will be to identify and characterize new lncRNAs that contribute to enhancer complex assembly and gene regulation using biochemical, genomics and genome engineering. The focus of AIM II will be to understand the prevalence and functional role of ligand-induced spatial enhancer cooperativity. Preliminary studies have identified few protein candidates that might be playing a mechanistic role in this long-distance enhancer cooperativity. The contribution of these proteins, and the lncRNAs identified from the screening strategy implemented in AIM I, in long distance enhancer cooperativity will also be examined. These studies promise to unravel new RNA regulators of enhancer assembly and will pave the way towards a new understanding of ribonucleoprotein interactome in the regulation of various endocrine signaling programs. Importantly, completion of this proposal will generate the data and resources necessary to design a larger study focusing on the in vivo relevance and disease condition contributed by these new molecular players by altering hormonal signaling programs.

项目概要真核细胞通过各种激活的转录调控程序与细胞环境相互作用。雌激素受体α (ERα)（一类核激素受体）对内分泌配体进行基因调节。是理解配体诱导的转录程序的重要范例。 -雌二醇 (E2)，ER 主要与转录增强子结合，转录增强子是调节性 DNA 序列控制来自遥远基因组位点的基因表达的E2刺激也导致了快速重组。三维染色质结构和增强子协同性研究。过去十年已经鉴定了许多 ERα 的核心调节因子，并且在很大程度上解决了 ERα-的组成问题。然而，过去几年的多学科研究对结合增强子复合物提出了挑战。配体诱导转录增强子激活的常规模型和增强子的机制活细胞成像研究表明，响应急性激素信号传导， ER 在细胞核内形成不同的区室，将转录机制集中在强大的 E2 处从成分上看，这些“核受体凝聚物”是核糖核蛋白复合物不仅由蛋白质组成，还由非编码增强子 RNA (eRNA) 组成，然而，其他 RNA 种类在配体中的贡献。诱导的增强子凝聚体组装和染色质结构尚不清楚。将专注于识别 ERα 的新 RNA 共调节因子，以促进核糖核蛋白凝聚物的组装和 AIM I 的中心目标是识别和表征新的 lncRNA。利用生物化学、基因组学和基因组有助于增强子复合物组装和基因调控 AIM II 的重点是了解配体诱导的空间的普遍性和功能作用。初步研究已经确定了一些可能发挥协同作用的候选蛋白质。这些蛋白质在这种长距离增强子协同作用中的作用以及作用。从 AIM I 中实施的长距离增强子协同筛选策略中鉴定出的 lncRNA 这些研究有望揭示增强子组装的新 RNA 调节因子。为对核糖核蛋白相互作用组在各种调节中的新认识铺平道路重要的是，该提案的完成将产生数据和资源。有必要设计一项更大规模的研究，重点关注这些因素造成的体内相关性和疾病状况通过改变荷尔蒙信号传导程序来产生新的分子参与者。