BIOCHEMISTRY, MOLECULAR & CELL BIOLOGY FIELD SEMINAR

Yiyang Jin

Lis Lab & Yu Lab

Monday, [March 11th, 2024]

12:15 PM | Warren Hall 175

Investigating Mechanisms of Enhancer-Promoter Specificity in Humans

Transcription is a vital process that regulates proper gene expression, and various DNA elements in the genome work cooperatively to control the transcription process. Two key DNA sequence elements involved in transcription regulation are promoters and enhancers. Promoters are proximal to each gene specifying the transcription start sites and contributing to the regulation of that gene. Enhancers interact with and regulate their target promoters from a distance in an orientation independent manner. Previous studies have shown that different enhancers can activate the same promoter at varying degrees, and remarkable specificity has been observed between different types of promoters and enhancers across different organisms. We hypothesize that the specificity between enhancer-promoter interactions arise as a result of the mechanism enhancers use to activate promoters: promoters lacking certain parts of the transcription machinery cannot efficiently go through the rate-limiting steps of transcription, including Pol II recruitment and pause release, and they can only be activated by those enhancers that can provide these missing parts to them. To test this hypothesis, I established a high throughput chromatin-based enhancer activity assay based on FACS and genomic DNA sequencing to test how different enhancers can activate promoters with different pause-release patterns (PRO-seq pause release patterns reflect the promoters’ intrinsic ability to go through the two rate-limiting steps). Based on preliminary results, I confirmed that promoters with different pause release patterns show different preference towards different enhancers, and the transcription machinery recruited by the enhancers play an important role in shaping this specificity. Using GRO-seq assay, I can capture how a particular enhancer can alter the pause release pattern of an individual promoter. This allows me to further confirm the hypothesis that enhancer promoter specificity arise as enhancers help promoters to go through the two rate-limiting steps of transcription by supplying required transcription machinery to them.

Committee: Dr. John Lis, Dr. Haiyuan Yu, Dr. Frank Pugh