Identification and characterization of developmental, tissue, and evolutionary transcription start sites in Bos taurus indicus

To further the understanding of the evolution of transcriptional regulation, we profiled genomewide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution across sub-species. Of all SNPs located in significant differentially used TSS clusters across sub-species, 472 SNPs were identified to have significant shifts in allele frequency across sub-species. Given Bos indicus cattle are more adapted to heat, we also specifically investigated TSSs for heat shock proteins (HSPs). In spleen and muscle, a higher TSS expression was observed across tissues in the genes in the top 25th percentile of highly expressed housekeeping Bos indicus than Bos taurus for all HSP genes tested. Lower TSS diversity was observed in Bos indicus than Bos taurus for all HSP genes tested. Lower TSS diversity was observed across tissues in the genes in the top 25th percentile of highly expressed housekeeping genes providing strong evidence in support of imprecise transcriptional initiation events.