CVm6A: A Visualization and Exploration Database for m6As in Cell Lines

Abstract

N6-methyladenosine (m6A) has been identified in various biological processes and plays important regulatory functions in diverse cells. However, there is still no visualization database for exploring global m6A patterns across cell lines. Here we collected all available MeRIP-Seq and m6A-CLIP-Seq datasets from public databases and identified 340,950 and 179,201 m6A peaks dependent on 23 human and eight mouse cell lines respectively. Those m6A peaks were further classified into mRNA and lncRNA groups. To better understand the potential function of m6A, we then mapped m6A peaks in different subcellular components and gene regions. Among those human m6A modification, 190,050 and 150,900 peaks were identified in cancer and non-cancer cells, respectively. Finally, all results were integrated and imported into a visualized cell-dependent m6A database CVm6A. We believe the specificity of CVm6A could significantly contribute to the research for the function and regulation of cell-dependent m6A modification in disease and development.

VIRMA-Dependent N6-Methyladenosine Modifications Regulate the Expression of Long Non-Coding RNAs CCAT1 and CCAT2 in Prostate Cancer

“…Although most of the m 6 A studies focused on its role in mRNA function, recent reports showed that m 6 A may also regulate ncRNAs functions [17]. Similarly to mRNAs, lncRNAs are also dynamically m 6 A methylated and the modification levels depend on the cell line, tissue type and growth conditions [41,42]. In this study, we focused on potentially m 6 A-regulated lncRNAs with impact on PCa.…”

A single N6-methyladenosine site in lncRNA HOTAIR regulates its function in breast cancer cells

“…To investigate the possibility that m6A regulates the function of HOTAIR in a mechanism similar to its regulation of lncRNA Xist, we investigated previous studies in human cells where m6A sites have been mapped genome wide. We searched the CVm6A database 25 to identify any previously mapped sites of m6A modification in HOTAIR. HOTAIR contains 3 m6A peaks mapped in HeLa cells, although the enrichment score is low for these sites ( Figure S1).…”

N6-methyladenine modification in noncoding RNAs and its function in cancer

“…The m6A methylation landscape of human lncRNAs is essentially different from that of mRNA. It is reported that the average enrichment scores of lncRNAs were similar to those of mRNA in cell lines, but the number of m6A peaks distributed in lncRNAs is significantly lower than those in mRNAs [ 53 ]. In human fetal tissue, lncRNAs were less methylated than mRNAs with an average of 21%.…”