We are analyzing https://link.springer.com/article/10.1186/s13059-016-1139-1.

Title:
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain | Genome Biology
Description:
Background 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. Results 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. Conclusion 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.
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Keywords {🔍}

rna, pubmed, brain, sites, polya, methylation, article, transcripts, google, scholar, methylated, total, escs, cas, additional, nuclear, cytosine, binding, file, analysis, cell, mcs, esc, central, mouse, utr, reads, enrichment, sample, data, cells, mrna, samples, bisulfite, fig, sequencing, distribution, figure, transcript, found, control, stem, candidate, table, number, expression, unique, gene, embryonic, revealed,

Topics {✒️}

dietmar rieder esc-2i/leukemia inhibitory factor alexandra lusser female 129s2/svpascrl mice distinct 5-methylcytosine profiles daria khokhlova-cubberley xi-yu jia embryonic stem cells transcriptome-wide target profiling article download pdf esdn es-derived neuronal 1-piperazineethanesulfonic acid [hepes]-koh 129s2/svpascrl-derived blastocysts auto-cross-linking setting meta-gene profiles quantitative real-time pcr n6-methyladenosine-dependent regulation nonsense-mediated rna decay transcriptome-wide cytosine methylation full size image nanodrop uv/vis spectrophotometer bisulfite-mediated cytosine modification author correspondence original author multi-cell type tissue high-throughput sequencing data pet-15b vector sequence immuno-northern blot detection 5-hydroxymethyl-uridine-modified rna transcriptome-wide manner posttranscriptional rna modification 10 mm tris-hcl ph 8 10 mm tris-hcl ph 7 5 mm tris-hcl ph 7 base-call quality score gov/geo/query/acc liquid chromatography-mass spectrometry regulate factor binding remove low-quality reads anti-5-methylcytosine antibody mirna-mediated transcript regulation mouse cell types/tissues rna binding proteins rna-binding proteins nsun2-mediated cytosine-5 methylation anti-m5c antibody sample protein-rna interactions respective cell type/tissue cell stem cell transcriptome-wide mapping

Questions {❓}

Grand challenge commentary: RNA epigenetics?
Gov/sra?

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         description: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.
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      headline:Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
      description: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.
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         Bioinformatics
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      name:Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria

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