Research Papers:

Integrated bioinformatics analysis of chromatin regulator EZH2 in regulating mRNA and lncRNA expression by ChIP sequencing and RNA sequencing

Yuan Li, Mei Luo, Xuejiao Shi, Zhiliang Lu, Shouguo Sun, Jianbing Huang, Zhaoli Chen _ and Jie He

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Oncotarget. 2016; 7:81715-81726. https://doi.org/10.18632/oncotarget.13169

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Yuan Li1, Mei Luo2, Xuejiao Shi1, Zhiliang Lu1, Shouguo Sun1, Jianbing Huang1, Zhaoli Chen1, Jie He1

1Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China

2Central Laboratory, Beijing Luhe Hospital, Capital Medical University, Beijing, People’s Republic of China

Correspondence to:

Zhaoli Chen, email: [email protected]

Jie He, email: [email protected]

Keywords: EZH2, ChIP sequencing, RNA-sequencing, long noncoding RNA, cancer

Received: August 23, 2016     Accepted: October 24, 2016     Published: November 07, 2016


Enhancer of zeste homolog 2 (EZH2), a dynamic chromatin regulator in cancer, represents a potential therapeutic target showing early signs of promise in clinical trials. EZH2 ChIP sequencing data in 19 cell lines and RNA sequencing data in ten cancer types were downloaded from GEO and TCGA, respectively. Integrated ChIP sequencing analysis and co-expressing analysis were conducted and both mRNA and long noncoding RNA (lncRNA) targets were detected. We detected a median of 4,672 mRNA targets and 4,024 lncRNA targets regulated by EZH2 in 19 cell lines. 20 mRNA targets and 27 lncRNA targets were found in all 19 cell lines. These mRNA targets were enriched in pathways in cancer, Hippo, Wnt, MAPK and PI3K-Akt pathways. Co-expression analysis confirmed numerous targets, mRNA genes (RRAS, TGFBR2, NUF2 and PRC1) and lncRNA genes (lncRNA LINC00261, DIO3OS, RP11-307C12.11 and RP11-98D18.9) were potential targets and were significantly correlated with EZH2. We predicted genome-wide potential targets and the role of EZH2 in regulating as a transcriptional suppressor or activator which could pave the way for mechanism studies and the targeted therapy of EZH2 in cancer.

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