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.

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.

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.

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.

To profile the genome-wide distribution of H3K27ac-marked enhancers in gastric intestinal metaplasia（IM）tissues and to investigate the potential regulatory mechanism of enhancers on IM.

IM tissues from 41 patients and normal gastric mucosa from 21 healthy individuals were collected for analysis using Cleavage Under Targets and Tagmentation（CUT&Tag）sequencing and RNA sequencing. The number and signal intensity of H3K27ac modifications in the 2 tissues were compared to reveal the reprogramming characteristics of the enhancers in the IM tissues. Meanwhile, the underlying regulatory mechanism of enhancer-associated transcription factors on the expression of IM-related genes were investigated.

As compared with normal gastric mucosa, the number and signal intensity of H3K27ac modifications were significantly elevated in the IM tissues, and the reprogramming areas were mainly located in the enhancers. The enhancers with greatly increased activity accounted for 92.4% of all variant enhancer loci in IM, which improved the expression of many intestinal epithelium-related genes, leading to altered phenotypes and biological properties of metaplastic mucous cells. The binding motifs of 14 transcription factors including CDX2 were identified by enrichment analysis in the enhancer loci. These transcription factors were up-regulated in the IM tissues and thus constituted a transcriptional regulatory network, and may play an important role in enhancer activating IM-related genes.

Through integration analysis of epigenetic and transcriptomic sequencing, enhancer reprogramming is identified as a critical epigenetic modification feature in gastric IM. Multiple transcription factors like CDX2 might be recruited to the enhancer loci, and then generate a regulatory network to synergistically up-regulate the expression of IM-related genes.