Whole genomic hot spot analysis of DNA base damage in non-small cell lung cancer cells based on ChIP-seq technique

Shixun LI; Yi CHENG; Nan DAI; Yanli XIONG; Mengxia LI

doi:10.16016/j.1000-5404.202010121

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Whole genomic hot spot analysis of DNA base damage in non-small cell lung cancer cells based on ChIP-seq technique

Basic Medicine | 更新时间：2026-01-09

- Whole genomic hot spot analysis of DNA base damage in non-small cell lung cancer cells based on ChIP-seq technique
- Journal of Third Military Medical University Vol. 43, Issue 7, Pages: 575-583(2021)
- 作者机构：
  
  400042 重庆，陆军军医大学(第三军医大学)大坪医院肿瘤科
- 作者简介：
- 基金信息：
  
  the General Program of National Natural Science Foundation of China(81871897)
- DOI：10.16016/j.1000-5404.202010121
  CLC： R394-33;R394.3;R734.2
- Received：20 October 2020，
  
  Revised：2021-01-11，
  
  Published：15 April 2021
- 稿件说明：
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Shixun LI, Yi CHENG, Nan DAI, et al. Whole genomic hot spot analysis of DNA base damage in non-small cell lung cancer cells based on ChIP-seq technique[J]. Journal of Third Military Medical University, 2021, 43(7): 575-583.
DOI：

Shixun LI, Yi CHENG, Nan DAI, et al. Whole genomic hot spot analysis of DNA base damage in non-small cell lung cancer cells based on ChIP-seq technique[J]. Journal of Third Military Medical University, 2021, 43(7): 575-583. DOI： 10.16016/j.1000-5404.202010121.

摘要

目的

建立可用于在全基因组水平分析DNA碱基损伤位点分布的方法，利用该方法分析非小细胞肺癌A549细胞株中DNA碱基损伤热点区域的分布规律。

方法

利用染色质免疫沉淀偶联测序(chromatin immunoprecipitation sequencing

ChIP-seq)技术对A549细胞中与脱嘌呤/脱嘧啶核酸内切酶1(apurinic/apyrimidinic endonuclease 1

APE1)和8-氧鸟嘌呤DNA糖化酶1(8-oxoguanine DNA glycosylase 1

OGG1)蛋白特异结合DNA片段进行序列鉴定，通过生物信息学的方法分析全基因组DNA碱基损伤热点分布规律。

结果

APE1和OGG1结合峰主要分布在基因启动子区，比例分别为41.70%和49.26%，APE1和OGG1结合峰于TSS上游2 000 bp区域内分别占比38.80%和39.80%，APE1与OGG1结合峰具有显著相关性(

=0.636 3，

0.01)。APE1和OGG1共同结合峰相关基因数有25 038个，其中与肿瘤发生直接相关的有641个。

结论

建立在全基因组水平分析DNA碱基损伤位点分布的方法；在非小细胞肺癌细胞中，DNA碱基损伤并非随机分布而主要分布于基因调控功能区，碱基损伤修复蛋白结合相关热点区域与肿瘤发生及肿瘤炎症微环境密切相关。

Abstract

Objective

To establish a method that can be used to analyze the distribution of DNA base damage sites at the genome-wide level

and use this method to analyze the distribution pattern of DNA base damage hotspots in non-small cell lung cancer cell line A549.

Methods

Chromatin immunoprecipitation sequencing(ChIP-seq)was used to perform immunoaffinity separation of specific binding DNA fragments with apurinic/apyrimidinic endonuclease 1(APE1)and 8-oxoguanine DNA glycosylase 1(OGG1)in A549 cells for sequence identification

and bioinformatics analysis was carried out to study the whole genome DNA base damage hotspots distribution.

Results

The binding peaks of APE1 and OGG1 were mainly distributed in the gene promoter region

with proportions of 41.70% and 49.26% respectively. The peaks of APE1 and OGG1 located in the 2 000 bp region upstream of TSS

accounting for 38.80% and 39.80%

respectively. The binding peaks of APE1 and OGG1 were significantly correlated(

=0.636 3

0.01). The number of APE1 and OGG1 associated genes with the same binding peak was 25 038

among which 641 were directly associated with tumorigenesis.

Conclusion

A genome-wide analysis method is established to analyze the distribution of DNA base damage sites. DNA base damage is not randomly distributed in lung cancer cells

but mainly distributed in gene regulatory region. Hot spots related to base damage repair protein binding may be closely associated with tumor genesis and tumor inflammatory microenvironment.

关键词

Keywords

references

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