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

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(r=0.636 3, P < 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.

Keywords

• chromatin immunoprecipitation sequencing
• non-small cell lung cancer
• dna base damage
• base excision-repair