title: Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain.
abstract: Recent work has 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 the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes.
  
  
  
  We have carried out an unbiased global analysis of m5C in total and nuclear poly(A) RNA of mouse embryonic stem cells and murine brain. We show that there are intriguing differences in these samples and cell compartments with respect to the 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 embryonic stem cells and brain from those methylated in either one of the samples. We also analyze potential correlations between m5C and micro RNA target sites, binding sites of RNA binding proteins, and N6-methyladenosine.
  
  
  
  Our study presents the first comprehensive picture of cytosine methylation in the epitranscriptome of pluripotent and differentiated stages in the mouse. These data provide an invaluable resource for future studies of function and biological significance of m5C in mRNA in mammals.
authors.affiliation: Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Amort
authors.affiliation: Division of Bioinformatics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
authors.forename: Dietmar
authors.initials: D
authors.lastname: Rieder
authors.affiliation: Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Wille
authors.affiliation: Zymo Research corp, Irvine, CA, USA.
authors.forename: Daria
authors.initials: D
authors.lastname: Khokhlova-Cubberley
authors.affiliation: Department of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020, Innsbruck, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Riml
authors.affiliation: Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
authors.forename: Lukas
authors.initials: L
authors.lastname: Trixl
authors.affiliation: Zymo Research corp, Irvine, CA, USA.
authors.forename: Xi-Yu
authors.initials: XY
authors.lastname: Jia
authors.affiliation: Department of Organic Chemistry and Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020, Innsbruck, Austria.
authors.forename: Ronald
authors.initials: R
authors.lastname: Micura
authors.affiliation: Division of Molecular Biology, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria. alexandra.lusser@i-med.ac.at.
authors.forename: Alexandra
authors.identifier: 0000-0002-2226-9081
authors.initials: A
authors.lastname: Lusser
mesh_terms: D044503:5-Methylcytosine / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D001921:Brain / Q000378:metabolism*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D008745:Methylation; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D000066450:Mouse Embryonic Stem Cells / Q000378:metabolism*; D059372:Nucleotide Motifs; D009928:Organ Specificity / Q000235:genetics; D011485:Protein Binding; D034622:RNA Interference; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D044503:5-Methylcytosine
keywords: 5-Methylcytosine; Bisulfite sequencing; Embryonic stem cells; Epitranscriptome; Mouse brain; RNA binding proteins; RNA methylation; m5C; m6A; meRIP