Remodeling characteristics of H3K27me3-marked silencer in gastric intestinal metaplasia and its transcriptional regulatory mechanism

Objective To systemically characterize the genome-wide distribution of H3K27me3-marked silencers in gastric intestinal metaplasia (IM) tissues and to elucidate a novel epigenetic regulatory mechanism of IM. Methods Gastric antrum mucosa samples were collected from 22 healthy individuals and 39 patients with IM. The modification of H3K27me3 and the transcriptome characteristics were detected by Cleavage Under Targets and Tagmentation (CUT&Tag) sequencing and RNA sequencing, respectively. Various bioinformatics tools, such as Ngsplot, ChIPseeker, MAnorm2, GGBiPlot, edgeR, Homer and others were applied for analyzing the silencer signal and its regulation on gene expression of IM tissues. Results CUT&Tag sequencing and RNA sequencing data were of great quality, and there was no significance in the whole-genome distribution of H3K27me3 modification between normal gastric mucosa and IM tissues. Genome-scale distribution of H3K27me3-marked silencers was also portrayed, which revealed weakened silencer signal intensity in IM tissues (P < 0.05). Principal component analysis (PCA) showed that the silencer characteristics in IM were greatly different from those in normal tissues, indicating extensive silencer remodeling in the IM tissues. Combined with RNA sequencing analysis, silencer remodeling was closely associated with the increased expression of CDX1 and other IM-related genes, as well as with the possible activation of IM-related metabolic pathways. In addition, loss of silencer signal recruited various transcription factors such as ATOH1 (P < 0.01) and ONECUT2 (P < 0.01) to form a regulatory network, which were highly expressed in IM tissues, regulating the expression of CDX1 and other key genes of IM, and affecting cell biological processes like coll fate commitment. Conclusion Integration analysis of epigenetic and transcriptomic sequencing data discovers silencer remodeling as a hallmark epigenetic feature in gastric IM tissues. Loss-of-function in silencer loci may recruit IM-regulatory transcription factors such as ATOH1 and ONECUT2, which may generate a network to impact on the expression of key genes and the metabolism of IM cells.