Fig. 1

Identification and regulatory characteristics of eRNAs. a A heatmap revealed enhancer intensity dynamics in muscle and adipose tissues between Enshi Black (ES) and Duroc pigs. Enhancer intensity was calculated by normalized H3K27ac ChIP-seq signals. b Overlap of detectable eRNAs between different tissues and breeds. The bar chart in light green displays the number of detectable eRNAs for each tissue, the blue diagram illustrates the degree of overlap between detected eRNAs across different tissues and breeds. c Heatmap displaying the calculated Euclidean distances between samples based on the variance-stabilizing transformation of the eRNA expression matrix. d Pearson correlation between eRNA expression and enhancer activity in Duroc muscle tissue. e Comparison of eRNA expression levels within and outside of super-enhancers. Statistical significance was assessed using the two-sided unpaired Wilcoxon test (**P < 2.2e−16). f Proportion of detectable unidirectional- and bidirectional-transcribed eRNA per tissue. g Expression levels of unidirectional- and bidirectional-transcribed eRNAs in each tissue. Statistical significance was assessed using the two-sided unpaired Wilcoxon test (**P < 2.2e−16). h GC content of unidirectional- and bidirectional-transcribed eRNA sequences in each tissue. Statistical significance was assessed using the Student’s t-test (**P < 2.2e−16). i Deep learning model distinguishes transcriptional directions of eRNAs