Computational Prediction and Comparative Analysis of Dorsal Ventral Patterning Gene Enhancers in Drosophila and Tribolium

Abstract

Developmental processes in any organism are dependent on gene regulation and their expression. The gene regulatory network controlling axes formation in insects has undergone drastic evolutionary changes. Development and morphology of insects are distinguished by their anterior-posterior (AP) and dorsal-ventral (DV) patterning. This is accomplished through a specific gene regulatory mechanism and target gene expression. Multiple sequence-specific DNA binding proteins and co-regulators regulate gene expression. However, the ultimate goal of this transcriptional machinery is transcriptional initiation. Enhancers play a significant role in the transcriptional process. These enhancers are cis-regulatory modules/elements, non-coding DNA sequences containing multiple activator and repressor binding sites range from 200 bp to more than 1 kb in length and upstream to the promoter or within the first intron of the regulatory gene. To understand how changes in gene expression in different lineages can lead to novel phenotypes, a complete analysis of enhancer mechanism and evolution is required. Understanding enhancers and their evolution is crucial to know how variations in gene expression in different lineages can lead to different phenotypes. In Drosophila embryos, DV patterning is mediated by a dorsal protein gradient which further activates twist and snail, the important regulators of DV patterning in Drosophila. Tribolium, in addition to Drosophila, has emerged as a promising organism for studying these developmental phases in depth. To look at evolved features of DV patterning in different insect species, this study was designed to annotate ten DV genes (zerknullt (zen), single-minded (sim), ventral nervous system defective (vnd), bunched (bun), brinker (brk), intermediate neuroblasts defective (ind), short gastrulation (sog), tailup (tup), sna (snail) and rhomboid (rho)) enhancers in Tribolium and compare them to orthologous gene enhancers in Drosophila. Bioinformatics tools (Cluster-Buster and MCAST) were used to s