PhD Proposal Seminar – Tiegh Taylor (Mitchell Lab)

Uncovering the Sequence Basis to Long-Range Enhancer-Promoter Interactions

Abstract

Enhancer elements are notoriously difficult to predict, both by experimental methods identifying overlapping transcription factor binding and active histone modification, but also by computational methods based on sequence alone. Enhancers regulate their cognate genes over large distances, however, the closest gene in linear distance is frequently not the closest gene in 3D space, adding to the difficulty of accurately linking enhancer-promoter pairs. Precise spatiotemporal control of gene transcription is imperative during development, vital to this process is the precise activation or decommissioning of enhancers. I propose to identify both the elements in mouse embryonic stem cells which poise an enhancer for activation in a differentiated cell type; as well as the signals which control the chromatin structure around them. To do this, I am in the process of creating an enhancer activity and chromatin interaction anchor strength reporter assay. This will be used to assay synthetic sequences based on poised enhancers, high confidence predicted enhancers, and target binding sites for architectural proteins. These sequences will be examined in both embryonic stem cells, and cells undergoing differentiation into an endothelial lineage. The signals and sequences that direct enhancers to their cognate genes across tissues remain elusive, but through my research I propose to develop a method to empirically assay them to understand the sequence basis of chromatin architecture.