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 genome-wide transcriptional start sites (TSSs) in two sub-species, Bos taurus taurus and Bos taurus indicus, that diverged approximately 500,000 years ago. Evolutionarily divergent TSSs were observed in more than half of the genes expressed across the sub-species, ranging from extreme cases in which a TSS was observed only in one sub-species to intermediate situations in which a corresponding TSS had been translocated by > 50 nucleotides, to situations where the number of TSS differed between the sub-species. Fetal and adult stages not only had their own regulatory profile of active and inactive genes but also their own pattern of TSSs. Given indicus are more adapted to heat, we also specifically investigated TSSs for heat shock proteins. More variation was observed in number of TSSs for heat shock proteins in indicus than taurus. This study confirmed that most genes are regulated in a tissue-specific manner.