A Global Genomic Enhancer Strategy for Repressive Transcriptional Programs

University Of California, San Diego, La Jolla CA

Investigators

Abstract

PROJECT SUMMARY ABSTRACT The functional specialization, healthy life, and proper disposal of cells in all metazoans require precise genomic transcriptional responses to developmental and environmental signals. These responses are largely mediated by enhancers, regulatory DNA elements that contain specific recognition sequences required for binding of transcription factors. An ideal model for investigating the actions of enhancers and transcription factors on transcriptional programs is Estrogen receptor (ER?), which is activated by binding of the sex hormone 17?- estradiol (E2) and interacts with ~7000 possible enhancers in the human genome. A major unanswered question, exemplified by the transcriptional programs directed by ER? is how a DNA binding transcription factor, binding to regulatory enhancers, concurrently regulate global programs of gene activation and repression. While the key role of short-range enhancer-promoter interactions in transcriptional regulation is well established, the detailed influence of enhancer:promoter chromosomal architecture on the putative enhancer- dependent regulatory repressive network remains poorly understood. To uncover the links between such chromosomal structure and regulation of gene transcriptional programs, I hypothesize that E2/ER? binds to a massive number of robust, active enhancers, causing recruitment of coactivators but dismissal of Pol II from these enhancers, causing the failure of eRNA transcription and the resultant repression of coding target gene transcription. To investigate this hypothesis systematically, I propose to develop and apply appropriate powerful contemporary global genomic technologies, including 5C, 3D-DSL, Hi-C, GRO-seq, RNA-seq, and ATAC-seq., and the requisite bioinformatic pipelines for analyzing data. By providing critical mechanistic insights into the regulation of transcriptional programs relevant to most organ systems, the proposed research may help to advance the design of new modalities to address questions of development, homeostasis, metabolism, and aging. In so doing, I will not only gain critical scholarship in central global genomic and molecular biological issues, but I also will become proficient in the use of rapidly-emerging advanced bioinformatic and statistical methods for the analysis of large experimental data sets. This NRSA Individual Postdoctoral Fellowship will therefore empower me to acquire invaluable knowledge, training, and experience, while making an important contribution to biomedical science, critical to my goal of becoming a particularly effective independent investigator, dedicated to making transformative discoveries regarding fundamental questions in genomic biology.