Comparative Analysis of Computationally Predicted Homeobox Promoters of Humans, Chimpanzees, Mice and Rats

Abstract

Homeobox genes are conserved sequences in different eukaryotic organisms known to direct the anterior-posterior axis of the body plan. Promoter regions at the beginning of the Hox sequence jumpstarts the transcription process, which result in the expression of genes. CpG islands found within the promoter regions can cause the inactivation or silencing of these promoters. This study aims to compare the locations of the promoter regions and the CpG islands of Homeo sapiens sapiens (human), Pan troglodytes (chimpanzee), Mus musculus (mouse), and Rattus norvegicus (brown rat) and relate them to the possible influence in the specification of the mammalian body plan. The sequences of each gene in Hox clusters A-D of the considered mammals were retrieved from Ensembl Genome Browser and ran on First Exon Finder (First EF), predicting the possible locations of the promoter regions and CpG islands. The sequences of the predicted promoters were confirmed via BLAST and identified using the Eukaryotic Promoter Database (EPD). The significance of the locations was computed using Kruskal-Wallis, a non-parametric statistical test. Among the four clusters, only the promoter locations in cluster B showed significant difference. HOX B genes have been linked with the control of the genes that target the development of axial morphology, particularly of the vertebral column bones. The magnitude of variation between the body plans of closely-related species can then be attributed to the promoter location and number, which promoters are present, and the inactivation of genes via CpG methylation.