Repressor elements significantly influence economically relevant phenotypes in pigs; however, their precise roles and characteristics are inadequately understood. In the present study, we employed H3K27me3 profiling, assay for transposase-accessible chromatin with highthroughput sequencing (ATAC-seq), and RNA sequencing (RNA-seq) data across six tissues derived from three embryonic layers to identify and map 2 034 super repressor elements (SREs) and 22 223 typical repressor elements (TREs) in the pig genome. Notably, many repressor elements were conserved across mesodermal and ectodermal tissues. SREs exhibited tight regulation of their target genes, affecting a limited number of genes within a specific genomic region with pronounced effects, while TREs exerted broader but weaker regulation over a wider range of target genes. Furthermore, in neuronal tissues, genes regulated by repressor elements started to be repressed during the differentiation of stem cells into progenitor cells. Notably, analysis showed that many repressor elements exhibited cooperative and additive effects on the modulation of KLF4 expression. This research provides the first comprehensive map of pig repressor elements, serving as an essential reference for future studies on repressor elements.
抑制元件在猪的经济表型中发挥着重要的作用。然而，这些元件还未得到充分表征。在该研究中，我们使用来自三个胚层的六种组织的H3K27me3、ATAC-seq和RNA-seq数据，在猪基因组中鉴定出2 034个超级抑制元件 (SREs) 和22 223个典型抑制元件 (TREs)。在已确定的抑制元件中，许多是中胚层和外胚层组织共有的。SREs对靶基因的调控紧实(在特定的基因组区域内，SREs作用于少数靶基因，且效果较强)，而TREs的调控较为松散（作用范围较广，但效果较弱）。此外，在神经组织中，在干细胞分化为前体细胞的阶段，抑制元件靶基因的表达开始受到抑制。最后，我们还发现许多调控元件通过相互配合 (加性效应) 来调控KLF4的表达。该研究第一次呈现了全面的家猪抑制元件图谱，为未来抑制元件的研究提供了重要参考。.
Keywords: KLF4; Pig; Regulatory model; Repressor elements; Silencer; Super repressor elements; Tissue development.