Discipline: Biological Sciences
Subcategory: Cell and Molecular Biology
Room: Exhibit Hall
Laure Ouoba - Bronx Community College
Co-Author(s): Mykel Barret, Adib Ummy, Dr. Emerson.
Proper retinal development requires precise spatiotemporal regulation of gene transcription. Interactions between enhancers and transcription factors mediate the regulation of gene transcription. The ThrbICR enhancer, which is active in developing photoreceptors and ganglion cells, drives the expression of Thrb, a gene implicated in regulating opsin expression in the mature retina. ThrbICR contains “CANNTG” motifs which likely enable its activation by bHLH transcription factors, such as NeuroD1. Previous studies have shown that point mutations in transcription factor binding sites sometimes alter transcriptional output. To test the hypothesis that different species possess variant transcription factor binding sites in ThrbICR that affect its ability to drive transcription, a bioinformatic analysis was conducted. Phylogenetic footprinting, performed on BLAT alignments of ThrbICR, reveals that it contains five putative bHLH binding sites that exhibit nucleotide divergence between species. For example, at one of these loci, the Chinese softshell turtle, shrew, pika, armadillo, naked mole rat, and platypus genomes contain “CACCCG” “CATGTG,” “TACCTG,” “AACCTG,” “CATCTG,” and “CATCCA” sequences, respectively, which deviate from the “CANNTG” motif produced from in vitro HT- SELEX assays. These sequence variants likely alter the activity of the ThrbICR by perturbing TF-DNA binding affinity. Our data will be used to design mutagenesis experiments that will test the functional consequences of these transcription factor binding site variations in vivo. The information produced by this research can be used to inspire the development of new therapies for retinal disease, particularly those aimed at controlling the expression of delivered therapeutic genes.
Funder Acknowledgement(s): This research project was supported by the National Science Foundation [CAREER 1453044; & AGS-1950629 (REU)]; National Institutes of Health, Maximizing Access to Research Careers: Undergraduate Student Training in Academic Research (MARC U-STAR) Program [project 2T34GM007639-36A]; National Oceanic and Atmospheric Administration [Grant# 16SEC481008 (Summer Bridge)]; and Pinkerton Foundation (HIRES). The statements contained within are not the opinions of the funding agency or U.S. government. but reflect solely the authors' opinions.
Faculty Advisor: Mykel Barrett, firstname.lastname@example.org
Role: BLAT aligned orthologous enhancers Cleaned sequence data Cistromic analysis Consensus motif retrieval from JASPAR database