Fig. 7
From: Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation
Enhancers mediate Hdac3-regulated RNA polymerase recruitment to the promoter-proximal region. a The distribution of transcriptional changes in promoter-proximal (top) and gene-body (bottom) regions for the closest active genes associated with upregulated enhancers and other active genes. b The fold improvement of each enhancer-gene association method and combinative strategy. The fold improvement is calculated based on the fraction of genes with upregulated promoter-proximal density in the comparison gene set (e.g., enhancer-closest genes) over that in the whole gene set. Eup: upregulated enhancers; 50Â kb: 50Â kb distance; 4D: 4DGenome; 4D_liver: enhancer-gene interactions in liver in 4DGenome. c H3K9ac enrichment around the 582 upregulated enhancers in WT (gray) and Hdac3-deleted livers (black) and enrichment around the top 50 enhancers ranked based on functional activity score (blue), binding affinity score (green), and the combined score (orange). d IGV snapshot of WT and Hdac3-KO PRO-seq, HDAC3 ChIP-seq peaks, and RNA-seq of the enhancer and Fscn1. The transcription of the enhancer was elevated, while the expression in both promoter-proximal and gene-body regions of the Fscn1 gene (chr5:142,960,355 - 142,973,189) was upregulated upon Hdac3 deletion