Benjamin Patty - Hainer Lab
Cell identity is driven by the activity of gene regulatory elements (GREs) known as promoters and enhancers. The activity of GREs is tightly coupled to genomic architecture, regulated in part by an important family of factors known as nucleosome remodelers. In parallel, these GREs drive cell-type specific patterns of non-protein coding RNAs (ncRNAs), such as upstream antisense RNAs (uaRNAs) and enhancer RNAs (eRNAs). Our previous work identified the nucleosome remodeler esBAF as the first global regulator of eRNA and uaRNA expression in a mammalian system. Apart from esBAF, eukaryotes possess a high diversity of nucleosome remodelers that localize to enhancers and promoters and serve critical roles in protein coding RNA expression, but their mechanisms of action in eRNA and uaRNA regulation remain largely undefined. Given the broad diversity of remodelers in eukaryotic systems and the diverse mechanisms by which they modulate chromatin architecture at GREs, we anticipate that many of these remodelers regulate expression of eRNAs and uaRNAs. To test this, we are individually screening 32 chromatin remodelers for eRNA and uaRNA regulatory roles in murine embryonic stem cells using RNA interference followed by nascent transcription profiling with the goal of building a network for ncRNA regulation. De novo transcriptome annotation and epigenetic profiling have characterized thousands of putative eRNAs and uaRNAs throughout the murine genome. Preliminary transcriptome analyses have identified thousands of ncRNAs misregulated in the absence of specific remodeler activity, including esBAF, Chd4, and INO80. Future work will characterize the remaining nucleosome remodelers to identify novel contributors of ncRNA regulation in eukaryotes and we will then focus on characterizing chromatin structure upon a subset of remodeler depletions to define the mechanisms of nucleosome-based regulation of ncRNAs at GREs.
Friday, December 17th, 2021
A219B Langley Hall
12:00 PM