Repressor elements provide insights into tissue development and phenotypes in the pig

Repressor elements play important roles in economic phenotypes of the pig, however, these elements remain poorly characterized. Here, we used H3K27me3, ATAC-seq and RNA-seq data derived from six tissues from three embryonic layers to identify 2 034 super repressor elements (SREs) and 22 223 typical repressor elements (TREs) in the pig genome. Among the identified repressor elements, many are shared by mesodermal and ectodermal tissues. SREs tightly regulate their target genes (within a specific genomic region, SREs act on a small number of target genes with strong effects) while the regulation by TREs is looser (TREs act on a wider range of target genes with weaker effects). Furthermore, in neuronal tissues, repressor element regulated genes start to be repressed during the stage of differentiation of stem cells to progenitor cells. Many regulatory elements were found to cooperate with each other (and have additive effects) to regulate the expression of KLF4. This study provides the first comprehensive pig repressor element map and should be a crucial reference for future studies on REs.