A genomic screen for long noncoding RNA genes epigenetically silenced in colorectal cancer

Long noncoding RNAs (lncRNAs) have emerged as key components in multiple cellular processes, although their physiological and pathological functions are not fully understood. To identify cancer-related lncRNAs, researchers at the Sapporo Medical University screened for those that are epigenetically silenced in colorectal cancer (CRC).

Through a genome-wide analysis of histone modifications in CRC cells, they found that the transcription start sites (TSSs) of 1,027 lncRNA genes acquired trimethylation of histone H3 lysine 4 (H3K4me3) after DNA demethylation. Integrative analysis of chromatin signatures and the DNA methylome revealed that the promoter CpG islands (CGIs) of 66 lncRNA genes contained cancer-specific methylation. By validating the expression and methylation of lncRNA genes in CRC cells, the researchers ultimately identified 20 lncRNAs, including ZNF582-AS1, as targets of epigenetic silencing in CRC. ZNF582-AS1 is frequently methylated in CRC cell lines (87.5%), primary CRCs (77.2%), colorectal adenomas (44.7%) and advanced adenomas (87.8%), suggesting that this methylation is an early event during colorectal tumorigenesis. Methylation of ZNF582-AS1 is associated with poor survival of CRC patients, and ectopic expression of ZNF582-AS1 suppressed colony formation by CRC cells. These findings offer insight into the association between epigenetic alterations and lncRNA dysregulation in cancer and suggest that ZNF582-AS1 may be a novel tumor-suppressive lncRNA.

Screen for epigenetically silenced lncRNA genes in CRC


(a) Workflow of the screen to identify lncRNAs silenced in association with aberrant CGI methylation in CRC. (b) Representative results of a ChIP-seq analysis in HCT116 and DKO2 cells. (c) Heat map showing the presence (blue) or absence (white) of histone modifications (H4K4me3, H3K79me2 and H3K27me3) at the TSS regions of lncRNA genes in HCT116 and DKO2 cells. The presence (green) or absence (white) of a CGI is also indicated on the right. (d) The fraction of TSSs with an H3K4me3 mark in HCT116 and DKO2 cells. Shown are the numbers of TSSs with the indicated H3K4me3 status in the two cell lines. (e) Heat maps showing the histone modifications at selected TSSs in CRC cells.

Kumegawa K, Maruyama R, Yamamoto E, Ashida M, Kitajima H, Tsuyada A, Niinuma T, Kai M, Yamano HO, Sugai T, Tokino T, Shinomura Y, Imai K, Suzuki H. (2016) A genomic screen for long noncoding RNA genes epigenetically silenced by aberrant DNA methylation in colorectal cancer. Sci Rep [Epub ahead of print]. [article]

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