Genome-wide screen for differentially methylated long noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as regulated by enhancer DNA methylation with prognostic relevance for human breast cancer

Abstract

The majority of long noncoding RNAs (lncRNAs) is still poorly characterized with respect to function, interactions with protein-coding genes, and mechanisms that regulate their expression. As for protein-coding RNAs, epigenetic deregulation of lncRNA expression by alterations in DNA methylation might contribute to carcinogenesis. To provide genome-wide information on lncRNAs aberrantly methylated in breast cancer we profiled tumors of the C3(1) SV40TAg mouse model by MCIp-seq (Methylated CpG Immunoprecipitation followed by sequencing). This approach detected 69 lncRNAs differentially methylated between tumor tissue and normal mammary glands, with 26 located in antisense orientation of a protein-coding gene. One of the hypomethylated lncRNAs, 1810019D21Rik (now called Esrp2-antisense (as)) was identified in proximity to the epithelial splicing regulatory protein 2 (Esrp2) that is significantly elevated in C3(1) tumors. ESRPs were shown previously to have a dual role in carcinogenesis. Both gain and loss have been associated with poor prognosis in human cancers, but the mechanisms regulating expression are not known. In-depth analyses indicate that coordinate overexpression of Esrp2 and Esrp2-as inversely correlates with DNA methylation. Luciferase reporter gene assays support co-expression of Esrp2 and the major short Esrp2-as variant from a bidirectional promoter, and transcriptional regulation by methylation of a proximal enhancer. Ultimately, this enhancer-based regulatory mechanism provides a novel explanation for tissue-specific expression differences and upregulation of Esrp2 during carcinogenesis. Knockdown of Esrp2-as reduced Esrp2 protein levels without affecting mRNA expression and resulted in an altered transcriptional profile associated with extracellular matrix (ECM), cell motility and reduced proliferation, whereas overexpression enhanced proliferation. Our findings not only hold true for the murine tumor model, but led to the identification of an unannotated human homolog of Esrp2-as which is significantly upregulated in human breast cancer and associated with poor prognosis.

Obesity-induced reduced expression of the lncRNA ROIT impairs insulin transcription by downregulation of Nkx6.1 methylation

“…2b). According to previous reports [29], qPCR analyses with primers detecting variants v1-4 or v1+2 revealed that all variants together had about 20-fold higher expression than the long variants v1+2 both in MIN6 cells and islets, suggesting that the short variant v4 represents the major transcript ( Fig. 2c).…”

Aberrant methylation‐mediated downregulation of long noncoding RNA C5orf66‐AS1 promotes the development of gastric cardia adenocarcinoma

“…Recent studies have demonstrated that aberrant DNA methylation of promoters may be an epigenetic regulator of lncRNA expression . In the present study, we found frequent hypermethylation of C5orf66‐AS1 in the three CpG islands, and the hypermethylation of the CpG sites around the transcription start site was more tumor specific and might be associated with the inactivation of C5orf66‐AS1.…”

ALKBH5 Inhibits Pancreatic Cancer Motility by Decreasing Long Non-Coding RNA KCNK15-AS1 Methylation

“…RNA m 6 A methylation is reversible and can be demethylated by ALKBH5 or FTO [17,18]. The m 6 A mRNA modification has been studied extensively; however, the importance of lncRNA methylation has remained elusive [19]. We found that KCNK15-AS1 underwent m 6 A methylation in pancreatic cells HPDE6-C7, MIA-PaCa-2, and BxPC-3.…”