Fig. 1: Cis-regulatory element landscape of the pig genome.

LW, ES, and MS represent Large White, Enshi Black, and Meishan breeds, respectively. a Summary of cis-regulatory elements (enhancers and promoters) identified in various tissues of four pig breeds. b Genome browser views of ChIP-seq, ATAC-seq, and RNA-seq data at the AGL and FRRS1 loci in tissues of LW pig. The numbers in the brackets located in the respective ChIP-seq, ATAC-seq, and RNA-seq tracks indicate their signal intensities. c A bar plot showing the percentage of cis-regulatory elements annotated in the pig genome. The percentage of enhancers (or promoters) in the black bracket were in genomic regions of open chromatin. “Other” indicates the proportion of open chromatin regions that did not overlap with enhancers or promoters. d Percentages of cis-regulatory elements newly identified in this study (salmon) and recovered by UCSC TSSs or published data (blue) from pig pluripotent stem cells²⁴ and liver tissue²⁵. e Overview of Hi-C heatmap matrix (left) and a simulated structure of 3D chromatin (right) in pig skeletal muscle. A Lorentzian objective method²⁷ and GenomeFlow v2.0²⁸ were used for modeling.