Journal: BMC Genomics

Article Title: Genome-wide enhancer-gene regulatory maps of liver reveal novel regulatory mechanisms underlying NAFLD pathogenesis

doi: 10.1186/s12864-025-11668-w

Figure Lengend Snippet: Study overview. Left: Construction of the ABC enhancer-gene maps of liver. The epigenomic data, including ATAC-seq, DNase-seq, H3K27ac ChIP-seq and HiC-seq data were from 15 liver biosamples. The bar chart represents the characteristics of ABC maps. Middle: We integrated the constructed ABC regulatory maps of liver and the NAFLD GWASs. Manhattan plots show the genome-wide association statistics of the discovery and replication cohorts, and the validated ABC SNPs. Right: The characterization of ABC SNPs and target genes, with the graphic summary of connecting rs2017869 within the non-coding region to NAFLD pathogenesis. Heatmaps show the characterization of ABC SNPs. Bar chart of pathway enrichment analyses and drug-gene interaction network represent the characterization of ABC genes. ABC, Activity-by-Contact; ATAC-seq, assay for transposase-accessible chromatin using sequencing; DNase-seq, DNase I hypersensitive sites sequencing; H3K27ac ChIP-seq, H3K27ac chromatin immunoprecipitation sequencing; Hi-C, high-throughput chromosome conformation capture; NAFLD, non-alcoholic fatty liver disease; GWAS, genome-wide association study; SNP, single nucleotide polymorphism; GGT1 , gamma-glutamyltransferase 1

Article Snippet: To construct Activity-by-Contact (ABC) maps for liver tissues and cell lines, we curated published epigenomic data, including DNase I hypersensitive sites sequencing (DNase-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), H3K27ac chromatin immunoprecipitation sequencing (H3K27ac ChIP-seq) and high-throughput chromosome conformation capture (Hi-C) data from ENCODE [ ] and the Roadmap Epigenomics Project [ ].

Techniques: ChIP-sequencing, Construct, GWAS, Activity Assay, Sequencing, Hi-C, High Throughput Screening Assay