PhD Proposal Exam – Gurdeep Singh (Mitchell lab)

PhD Proposal Exam

Monday April 25^th, 2:10 pm – Ramsay Wright Building, Rm. RW432

Gurdeep Singh (Mitchell lab)

“Identifying Tissue Specific Transcriptional Regulatory Elements in Mammalian Genomes“

Abstract

The non-coding region in mammalian genomes ranges between 97-99% and much of its function is yet unknown. Enhancers are one of the major components of the complex non-coding genome which regulate gene expression in a tissue specific manner. These regulatory elements are challenging to identify and characterize their function because of their variable locations, tissue-specific on-off status and inefficiency of indirect methods leading to thousands of inactive enhancer-like regions. STARR-seq is a genome-wide active enhancer identification and strength validation method, primarily explored on the Drosophila genome so far. My analysis suggests that regions bound with higher number of transcription factors (TFs) from a specific set, have higher enrichment of enhancer features, H3K27ac & p300 and drive higher expression of target genes. I hypothesize that identification of a positive set of tissue-specific enhancers by STARR-seq will lead to the identification of a high confidence set of tissue-specific TFs and features for better enhancer prediction modeling. The proposed objectives to address my hypothesis are first, to optimize the STARR-seq method for enhancer identification in mouse embryonic stem cell (mES); second, to apply it in a genome-wide manner to identify positive enhancers active in 3 cell types namely mES, mouse trophoblast stem cells (mTS) and mouse embryonic fibroblasts (mEFs); and third, to use these positive enhancers to identify the set of TFs binding them using available ChIP-seq and TF binding motif data. Furthermore, ChIP-seq of suspected novel TFs involved in mES pluripotency will be performed to upgrade the mES specific TF set for determining MTLs.  My preliminary data from a mammalian STARR-seq experiment in mES using mouse 38 BACs suggests that it gives higher background signal as compared to Drosophila STARR-seq. This is because of strong basal activity of SCP1 promoter used in mammalian STARR-seq and hence will be replaced with minimal promoter for STARR-seq optimization. The identification of active enhancers and novel TFs in general is essential to further our understanding of genome function across diverse cell types and to better understand development, disease and species evolution.

Ramsay Wright is a wheelchair accessible building.