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Regulation of long distance enhancer-promoter interactions by promoter-proximal elements

启动子-近端元件对长距离增强子-启动子相互作用的调节

基本信息

批准号：
10688129
负责人：
Angelike Stathopoulos
金额：
$ 36.21万
依托单位：
CALIFORNIA INSTITUTE OF TECHNOLOGY
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：
2022-08-19 至 2027-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10688129
关键词：
3-Dimensional Affect Architecture Binding Binding Proteins Biological Assay Cell Differentiation process Cells Chromatin Clustered Regularly Interspaced Short Palindromic Repeats Code Complex Coupled Cues DNA DNA Binding Data Development Disease Distal Drosophila genus Drosophila melanogaster Dysplasia Elements Embryo Enhancers Eukaryotic Cell Event Gene Expression Gene Expression Regulation Genes Genome Genomics Homeostasis Human Hybrids Image Link Maintenance Molecular Molecular Conformation Mutagenesis Mutation Organism Ovary Pathway interactions Pattern Phenotype RNA Interference Regulation Reporter Research Role Stretching System Techniques Testing Time Tissues Untranslated RNA chromatin immunoprecipitation combinatorial fly genetic analysis genomic locus imaging approach improved in vivo insight mutant novel strategies promoter response transcription factor whole genome

项目摘要

SUMMARY Tight regulation of gene expression in space and time is necessary for development and homeostasis in multicellular organisms. Regions of the genome outside gene coding sequences (cis-regulatory modules, or CRMs/enhancers) serve as assembly platforms for transcription factors that facilitate gene expression in response to cellular or environmental cues. Although many genes are regulated by multiple CRMs, mechanisms that coordinate the action of these CRMs and that regulate their local chromatin dynamics are poorly understood. In the fruit fly Drosophila melanogaster, expression of the transcription factor Brinker (Brk) is activated in the early embryo by two distal CRMs, one 5’ and one 3’ to the brk gene. Initially thought to be redundant, these CRMs were found to drive sequential, partially overlapping patterns of expression along the embryonic dorso-ventral axis. Further, these CRMs depend on a promoter-proximal element (PPE) that appears to facilitate the sequential, long-range interaction of each CRM with the promoter. We have additional evidence that the brk PPE is required for brk expression in several other tissues. We hypothesize that this PPE located upstream of the brk gene in Drosophila represents a general mechanism for coordinating multiple cis-regulatory modules’ (CRMs’) interaction with the promoter, and that this coordination of local chromatin dynamics is important for proper gene expression, development and maintenance of homeostasis. To test this hypothesis, we propose the following experimental directions: Aim 1 will test the idea that the brk PPE manages chromatin conformation at the brk gene locus; Aim 2 will identify molecular effectors supporting brk PPE action; and Aim 3 will investigate a role for one PPE-binding protein Odd paired (Opa) in supporting global CRM-promoter interactions at other loci in addition to brk. Many genes across diverse taxa are regulated by multiple CRMs – including so-called super, stretch or shadow enhancers – yet we know very little about how these various regulatory contributions are coordinated during normal development. Insights will come from the study of already well-characterized genes such as brk, whose expression depends on CRM coordination by a promoter proximal element; as well as through whole genome assays of chromatin conformation to uncover the mechanisms regulating CRM/enhancer-promoter interactions, in general. New experimental approaches, which permit targeted manipulation and direct observation of chromatin in live, differentiated cells of an intact organism, combined with tried-and-true techniques for the analysis of genetic and developmental phenomena in Drosophila can provide a link between CRM-promoter interaction and the contributions of transcription factor binding to the regulation of gene expression. Because many genes, pathways and regulatory mechanisms are shared between Drosophila and higher organisms, improved understanding of how gene regulation is coordinated at complex loci in flies is likely to inform new approaches to understand these phenomena in wild-type as well as disease-relevant human contexts.

总结