RNA 5-methylcytosine modification is enriched and conserved at 5' UTRs in human and mouse

ABSTRACT: Compared with the well-studied 5-methylcytosine (m5C) in DNA, the role of m5C in mRNA remains elusive as existing studies of RNA m5C are largely confined to rRNA and tRNA. Using bisulfite sequencing (BS-Seq) approach, we profiled transcriptome-wide m5C and found that RNA m5C modification is enriched and conserved at 5’UTRs in human and mouse. Through a comparative analysis of the mRNA and DNA methylome, we demonstrate that like DNA methylation, RNA m5C methylation exhibits a strong clustering. Surprisingly, mRNA Cytosine-5 methylation inversely correlates with DNA methylation under CpG context, which suggests a synergic regulatory effect. Importantly, comparison of the global RNA m5C methylome of breast cancer cells with normal mammary epithelial cells revealed that breast cancer methylome is predominantly hypomethylated and several breast cancer-related genes are differentially methylated. Despite global hypomethylation, 5’UTR of differentially methylated genes contain higher percentage of m5C. Taken together, this study provides a first-in-depth characterization of transcriptome-wide m5C modification. Furthermore, our findings showing differential m5C methylation pattern in normal and cancer cells suggest a vital role m5C methylation may play in the post transcriptional regulation of key pro-tumorigenic genes. Sample Preparation and RNA Bisulfite Sequencing: MCF10A and MDA-MB-468 (MDA468) cells were obtained from ATCC. Cells were cultured and maintained in DMEM media as per ATCC instructions. For BS-Seq total RNA was isolated from MCF10A and MDA_MB-468 cells and was enriched for polyA+ RNA using poly-A selection kits. The purified RNA is subjected to sodium bisulfite treatment at 60 degrees for 8 hours. The bisulfite-treated RNA was then reverse transcribed was subjected to deep-sequencing using Illumina RNA-Seq protocol.

ORGANISM(S): Homo sapiens

PROVIDER: GSE84230 | GEO | 2017/07/11

SECONDARY ACCESSION(S): PRJNA328434

REPOSITORIES: GEO