Reprogramming characteristics of H3K27ac-marked enhancer in gastric intestinal metaplasia and its transcriptional regulatory mechanism

Objective 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. Methods 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. Results 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. Conclusion 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.