Correlating Regulatory Region and Genetic Evolution
Authors: Chinmay P. Rele; Laura K. Reed
Affiliation: The University of Alabama
Keywords: f. speciation; a. core promoters and general transcription factors
Understanding change at an evolutionary scale is primarily done through accession protein and gene evolution; however, understanding how the regulation of those loci occurs would paint a clearer picture of how the proteome and genome interacts with the environment. The regulatory regions of genes are highly variable and important, for the timing of gene expression. Understanding the dynamics between the regulatory regions of an organism with its relevant effects in the genome, transcriptome, and proteome, can inform us of how the evolution of one plays a role on the other. We are studying the evolution of the regulatory regions of Insulin-like peptides (Ilps) and how their evolution correlates with other characteristics of the genes. Ilp is a good gene family to examine due to high duplication rates, and different mutation rates of those duplicates that occur within the Drosophila phylogeny. In this study, we use the hand-curated gene models of genes within the Insulin Signaling Pathway of 28 Drosophila species generated by The Genomics Education Partnership, including the Ilp paralogs. We are using these annotations to anchor the genomic region, extract genomic regions upstream of the start codon, and run Multiple Sequence Alignments. We intend to correlate features within these islands of conservation with genomic features to be able to find an association between regulatory regions and the genes they regulate. The patterns identified within these islands of conservation upstream of genes are likely cis-regulatory elements, or regions where regulatory elements exist that affect the regulation of the gene. Patterns such as indels (insertions/deletions), sequence motifs, as well as overall conservation found in these islands upstream of the gene can be correlated with the metrics of the genes directly downstream, such as ratio of nonsynonymous to synonymous mutations dN/dS, intron size, indel abundance, isoform number, and expression patterns (among other genetic characteristics). We expect to see positive correlation between the evolution of this upstream regulatory region and the evolution of features of the cis-regulated genes. Understanding the evolutionary patterns of these upstream regions is paramount in understanding how regulation of genes occurs.