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

Linyu WU; Wenkang LIU; Bo YU; Zhaole CHU; Biying LIU; Xianfeng LI; Dongfeng CHEN; Tao WANG; Bin WANG

doi:10.16016/j.2097-0927.202210068

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

Basic Medicine | 更新时间：2026-01-09

- Remodeling characteristics of H3K27me3-marked silencer in gastric intestinal metaplasia and its transcriptional regulatory mechanism
- Journal of Army Medical University Vol. 45, Issue 6, Pages: 510-518(2023)
- 作者机构：
  
  400042 重庆，陆军特色医学中心消化内科，消化系统肿瘤精准防治重庆市重点实验室
- 作者简介：
- 基金信息：
  
  the National Natural Science Foundation for Excellent Young Scientists of China(81822032);the Natural Science Foundation for Distinguished Young Scholars of Chongqing(CSTC2019JCYJJQX0027)
- DOI：10.16016/j.2097-0927.202210068
  CLC： R394-33;R394.3;R735.2
- Received：11 October 2022，
  
  Revised：2023-01-12，
  
  Published：30 March 2023
- 稿件说明：
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Linyu WU, Wenkang LIU, Bo YU, et al. Remodeling characteristics of H3K27me3-marked silencer in gastric intestinal metaplasia and its transcriptional regulatory mechanism[J]. Journal of Army Medical University, 2023, 45(6): 510-518.
DOI：

Linyu WU, Wenkang LIU, Bo YU, et al. Remodeling characteristics of H3K27me3-marked silencer in gastric intestinal metaplasia and its transcriptional regulatory mechanism[J]. Journal of Army Medical University, 2023, 45(6): 510-518. DOI： 10.16016/j.2097-0927.202210068.

摘要

目的

绘制胃黏膜肠上皮化生(intestinal metaplasia

IM)(简称肠化)组织中沉默子(组蛋白H3K27me3修饰为标记)的全基因组分布图谱，揭示肠化发生的表观调控新机制。

方法

在陆军特色医学中心消化内科收集22例人正常胃窦黏膜及39例人胃窦肠化黏膜，采用低起始量细胞的染色质靶向捕获(Cleavage Under Targets and Tagmentation，CUT&Tag)测序技术检测基因组H3K27me3修饰情况，RNA测序检测转录组特征。利用Ngsplot、ChIPseeker、MAnorm2、ggbiplot、edgeR、Homer等工具分析沉默子信号及其对肠化组织基因表达调控作用。

结果

H3K27me3的CUT

Tag测序数据质量较好，正常胃黏膜和肠化组织H3K27me3修饰的全基因组分布特征无明显差异。肠化组织沉默子信号强度显著降低(

0.05)。主成分分析发现，肠化组织的全局性沉默子特征与正常组织差异明显，表现为沉默子重塑。整合分析转录组数据发现，沉默子重塑可能是CDX1等肠化标志性基因表达增加、肠化相关信号通路激活的重要原因之一。沉默子信号丢失可能招募ATOH1 (

0.01) 和ONECUT2 (

0.01) 等转录因子形成网络，它们在肠化组织高表达，调控CDX1等肠化关键基因表达，影响营养物质代谢等细胞生物学过程。

结论

表观组、转录组学测序数据整合分析表明沉默子重塑是胃黏膜肠化的一种显著表观遗传特征，沉默子丢失区域可能招募ATOH1及ONECUT2等转录因子形成网络，调控肠化关键基因表达与肠化细胞的多种物质代谢过程。

Abstract

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 (

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 (

0.01) and ONECUT2 (

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.

关键词

Keywords

references

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