Fig. 3

Cis-regulatory elements analysis. A Loop affected the expressions of genes of different types. B Average read coverage around transcription start sites (TSSs). C Volcano plot of differentially accessible regions (DARs). D Distribution of DAR. E P-P and E-P were the top two most frequent interaction categories during muscle development. F Pearson’s correlation between anchored elements. G E as well as P/O/N raised the expressions of target genes. Gene up-regulation was broadly accompanied by enhancer number increase. H Aggregate peak analysis (APA) of stage-specific loops. I and J The stage-specific loops elevated the expression levels of their anchored genes in both CFM and CAM. K An identified E-P loop putatively functions in cattle muscle development, supported by the evidence from VISTA (mm1359) and MGI (ZFP36L1). CFM, fetal cattle muscle; CAM, adult cattle muscle. ^*P <0.05