Distinct 5-methylcytosine profiles in poly(A)RNA from mouse embryonic stem cells and the brain

Background: Recent work identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation and methylation of carbon 5 in cytosine (m5C). However, knowledge about prevalence and transcriptome-wide distribution of m5C is still extremely limited and thus, studies in different cell types, tissues and organisms are needed to gain insight into possible functions of this modification and interactions with other regulatory processes Results: We carried out an unbiased global analysis of m5C in total and nuclear poly(A)RNA of embryonic stem cells (ESCs) and brain of the mouse. We show that there are intriguing differences in these samples and cell compartments with respect to degree of methylation, functional classification of methylated transcripts and position bias within the transcript. Specifically, we observe a pronounced accumulation of m5C sites in the vicinity of the translational start codon, depletion in coding sequences and mixed patterns of enrichment in the 3’UTR. Degree and pattern of methylation distinguish transcripts modified in both ESCs and brain from those methylated in either one of the samples. Furthermore, we observed significant enrichment of m5C in the vicinity of the transcriptional start site in lncRNAs. We also present data regarding correlations between m5C and N6-methyladenosine, miRNA target sites and binding sites of RNA binding proteins. Conclusion: Our study presents the first comprehensive picture of cytosine methylation in the mouse epitranscriptome. These data can serve as a basis for future studies of function and biological significance of m5C in mRNA in mammals.