Genome‑wide analysis of histone modifications by ChIP‑chip to identify silenced genes in gastric cancer

Zhu,Xinjiang; Liu,Jian; Xu,Xiaoyang; Zhang,Chundong; Dai,Dongqiu

doi:10.3892/or.2015.3824

Genome‑wide analysis of histone modifications by ChIP‑chip to identify silenced genes in gastric cancer

Authors:
- Xinjiang Zhu
- Jian Liu
- Xiaoyang Xu
- Chundong Zhang
- Dongqiu Dai
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Affiliations: Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, Liaoning 110032, P.R. China
Published online on: February 27, 2015 https://doi.org/10.3892/or.2015.3824
Pages: 2567-2574

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Abstract

The present study aimed to identify novel histone modification markers in gastric cancer (GC) by chromatin immunoprecipitation microarray (ChIP‑chip) analysis and to determine whether these markers were able to discriminate between normal and GC cells. We also tested for correlations with DNA methylation. We probed a human CpG island microarray with DNA from a GC cell line (MKN45) by chromatin immunoprecipitation (ChIP). ChIP‑reverse‑transcriptase quantitative polymerase chain reaction PCR (RT‑qPCR) was used to validate the microarray results. Additionally, mRNA expression levels and the DNA methylation of potential target genes were evaluated by RT‑qPCR and methylation‑specific PCR (MSP). The moults showed that 134 genes exhibited the highest signal‑to‑noise ratio of H3‑K9 trimethylation over acetylation and 46 genes exhibited the highest signal‑to‑noise ratio of H3‑K9 trimethylation over H3‑K4 trimethylation in MKN45 cells. The ChIP‑qPCR results agreed with those obtained from the ChIP‑chip analysis. Aberrant DNA methylation status and mRNA expression levels were also identified for selected genes (PSD, SMARCC1 and Vps37A) in the GC cell lines. The results suggest that CpG island microarray coupled with ChIP (ChIP‑chip) can identify novel targets of gene silencing in GC. Additionally, ChIP‑chip is the best approach for assessing the genome‑wide status of epigenetic regulation, which may allow for a broader genomic understanding compared to the knowledge that has been accumulated from single‑gene studies.

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