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| Status |
Public on May 19, 2017 |
| Title |
Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs [Whole-transcriptome bisulfite sequencing] |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
(Cytosine-5) RNA methylation plays an important role in several biologically and pathologically relevant processes. However, owing to methodological limitations, the transcriptome-wide distribution of this mark has remained largely unknown. We have previously established RNA bisulfite sequencing as a method for the analysis of RNA (cytosine-5) methylation patterns at single-base resolution. Furthermore, next-generation sequencing has provided opportunities to establish transcriptome-wide maps of this modification. We have now established a computational approach that integrates tailored filtering and data-driven statistical modelling to eliminate many of the artifacts that are known to be associated with bisulfite sequencing. Using RNAs from mouse embryonic stem cells we have performed a comprehensive methylation analysis of mouse tRNAs, rRNAs and mRNAs. Our approach identified all known methylation marks in tRNA and two previously unknown but evolutionary conserved marks in 28S rRNA. Furthermore, the catalytic activities of the Dnmt2 tRNA methyltransferase could be resolved at single-base resolution. Of note, mRNAs were found to be very sparsely methylated or not methylated at all, which provides an important reference for further studies. Our approach can be used to profile (cytosine-5) RNA methylation patterns in many experimental contexts be important for understanding the function of (cytosine-5) RNA methylation in RNA biology and in human disease.
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| Overall design |
Whole-transcriptome bisulfite sequencing of wild type and Dnmt2-/- embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina
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| Contributor(s) |
Legrand C, Tuorto F, Lyko F |
| Citation(s) |
28684555 |
| |
| Submission date |
May 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Francesca Tuorto |
| E-mail(s) |
Francesca.Tuorto@medma.uni-heidelberg.de
|
| Organization name |
Deutsches Krebsforschungszentrum
|
| Department |
Division of Biochemistry Mannheim Institute for Innate Immunoscience (MI3)
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| Street address |
Ludolf-Krehl-Str. 13-17
|
| City |
Mannheim |
| ZIP/Postal code |
D-68167 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (16)
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| This SubSeries is part of SuperSeries: |
| GSE81825 |
Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs |
|
| Relations |
| BioProject |
PRJNA322645 |
| SRA |
SRP075648 |
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