Fig. 5

Construction of potential trait-affecting eRNA-mediated gene regulatory networks (eGRN) by integrating multi-omics data. a Schematic diagram of the eGRN construction method. Motif scanning and expression correlation between transcription factors (TF) and eRNA expression levels were used to predict upstream TF of eRNAs. The distance between eRNAs and genes and the expression correlation between their expression levels were used to predict downstream target genes of eRNAs, topologically associated domain (TAD) structure was further used to filter out eRNAs and genes that were not in a same TAD. Genome-wide association study (GWAS) data were used to further filter for trait-associated hub eRNAs that harbor DNA variants that are associated with pig economic traits. b Heat maps showing the globally correlated changes of the expression of eRNAs and target genes. c eGRN for muscle- and fat-related traits. The color of a TF represents the number of its downstream regulatory eRNAs, where a darker color indicates a larger number of regulatory eRNAs. d Differential expression of eRNA target genes between ES and Duroc pigs (ES vs Duroc) in fat-related eGRN