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2016 ; 7
(49
): 81715-81726
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Integrated bioinformatics analysis of chromatin regulator EZH2 in regulating mRNA
and lncRNA expression by ChIP sequencing and RNA sequencing
#MMPMID27835578
Li Y
; Luo M
; Shi X
; Lu Z
; Sun S
; Huang J
; Chen Z
; He J
Oncotarget
2016[Dec]; 7
(49
): 81715-81726
PMID27835578
show ga
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.
|*Chromatin Assembly and Disassembly
[MESH]
|*Chromatin Immunoprecipitation
[MESH]
|*Gene Expression Regulation, Neoplastic
[MESH]
|*Sequence Analysis, RNA
[MESH]
|Binding Sites
[MESH]
|Cell Line, Tumor
[MESH]
|Computational Biology/*methods
[MESH]
|Databases, Genetic
[MESH]
|Enhancer of Zeste Homolog 2 Protein/*genetics/metabolism
[MESH]