Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend

It is vital to understand the conservation and evolution of gene promoter sequences in order to understand environmental adaptation. The level of promoter conservation varies greatly between housekeeping (HK) and tissue-specific (TS) genes, denoting differences in the strength of the evolutionary constraints. Here, we analyzed promoter conservation and evolution to exploit differential regulation between HK and TS genes. The analysis of conserved elements showed CpG islands, short tandem repeats and G-quadruplex sequences are highly enriched in HK promoters relative to TS promoters. In addition, the type and density of regulatory motifs in TS promoters are much higher than HK promoters, indicating that TS genes show more complex regulatory patterns than HK genes. Moreover, the evolutionary dynamics of promoters showed similar evolutionary trend to coding sequences. HK promoters suffer more stringent selective pressure in the long-term evolutionary process. HK genes tend to show increased upstream sequence conservation due to stringent selection pressures acting on the promoter regions. The specificity of TS gene expression may be due to complex regulatory motifs acting in different tissues or conditions. The results from this study can be used to deepen our understanding of adaptive evolution.