Our research interests focus on the similarities and differences in chromatin structure among different cell types and how chromatin remodeling factors that modulate these differences regulate cell fate. The long- term goals of our laboratory are to comprehensively understand the functions, targets, regulation, and mechanisms of action of non-coding RNAs (ncRNAs) and chromatin regulatory factors with critical functions in gene regulatory networks. Approximately 75% of the mammalian genome is transcribed. While coding regions account for only ~2% of the genome, the remaining intergenic and intragenic transcription generates a large collection of non- coding RNAs (ncRNAs). Two regions rich with non-coding transcription are active enhancers (where ncRNAs are generated bi-directionally) and promoters (where ncRNAs are generated in the antisense orientation from protein-coding genes). While a few individual ncRNAs have been shown to function in gene activation, their activities in gene regulation have not been systematically addressed. Recently, we showed that esBAF, a nucleosome remodeling complex that binds enhancers and promoters, is necessary for repression of numerous ncRNAs throughout the genome in ES cells. Upon depletion of esBAF, nucleosome occupancy flanking regions of open chromatin was reduced, resulting in elevated ncRNA transcription. Based on these studies, we are in a unique position to build a network of ncRNA regulation by nucleosome remodeling factors in ES cells. Specifically, we will determine (1) how esBAF regulates higher order chromatin structure, (2) the functions of enhancer-specific ncRNAs (eRNAs) in enhancer looping and gene regulation, (3) the mechanisms underlying regulation of mRNAs by ncRNAs, and (4) the network of nucleosome remodeling complexes regulating ncRNA expression. These studies will enhance our understanding of the chromatin-centered regulation of ncRNAs. Over the next five years, our laboratory will identify nucleosome remodelers that regulate ncRNA expression, explore the role of nucleosome remodeling factors in regulating higher order chromatin structure at the level of enhancer-promoter looping, and determine the function of two uncharacterized classes of ncRNAs in ES cells. The proposed research is significant because it will uncover fundamental mechanisms that choreograph the interplay of chromatin dynamics with ncRNA function, consequently providing a crucial step in understanding ES cell fate decisions.
The majority of mammalian genomes are transcribed, generating a large number of RNAs that are not translated to proteins, known as non-coding RNAs (ncRNAs) and we found that a specific chromatin regulator, esBAF, is responsible for repressing the expression of many of these ncRNAs in embryonic stem (ES) cells. We now propose to further examine the regulation and function of these ncRNAs, specifically focusing on those generated antisense to protein-coding RNAs and those generated at regions that regulate protein-coding RNA expression (called enhancer regions). Together, these studies will uncover mechanisms of the gene regulatory network in ES cells by examining ncRNA regulation and the function of enhancer transcription, which will ultimately lead to a deeper understanding of ES cells and potential targets for therapeutics.