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Series GSE83432 Query DataSets for GSE83432
Status Public on Dec 09, 2016
Title Distinct 5-methylcytosine profiles in poly(A)RNA from mouse embryonic stem cells and the brain
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary 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.
Overall design RNA was isolated from mouse embryonic stem cells (ESC) and brains as well as from the nuclei of the respective samples (in triplicates) and RNA-Bisulfite sequencing was performed.
Contributor(s) Amort T, Rieder D, Wille A, Khokhlova-Cubberley D, Riml C, Trixl L, Jia X, Micura R, Lusser A
Citation(s) 28077169
Submission date Jun 16, 2016
Last update date May 15, 2019
Contact name Alexandra Lusser
Phone +43 512 9003-70210
Organization name Biocenter Medical University Innsbruck
Department Molecular Biology
Street address Innrain 80
City Innsbruck
State/province Tyrol
ZIP/Postal code 6020
Country Austria
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (12)
GSM2202964 ESC RNA CN 1
GSM2202965 ESC RNA CN 2
GSM2202966 ESC RNA CN 3
BioProject PRJNA325895
SRA SRP076669

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Supplementary file Size Download File type/resource
GSE83432_Brain_nuclear.xlsx 872.2 Kb (ftp)(http) XLSX
GSE83432_Brain_nuclear_indReplicates.xlsx 22.7 Mb (ftp)(http) XLSX
GSE83432_Brain_total.xlsx 244.6 Kb (ftp)(http) XLSX
GSE83432_Brain_total_indReplicates.xlsx 4.0 Mb (ftp)(http) XLSX
GSE83432_ESC_nuclear.xlsx 1.3 Mb (ftp)(http) XLSX
GSE83432_ESC_nuclear_indReplicates.xlsx 14.9 Mb (ftp)(http) XLSX
GSE83432_ESC_total.xlsx 842.5 Kb (ftp)(http) XLSX
GSE83432_ESC_total_indReplicates.xlsx 7.8 Mb (ftp)(http) XLSX
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