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RNA bisulfite sequencing of 25S rRNA (C2278) in S. cerevisiae and of 28S rRNA (C3381) in C. elegans

ABSTRACT: RNA bisulfite sequencing of 25S rRNA (C2278) in S. cerevisiae and of 28S rRNA (C3381) in C. elegans

PROVIDER: PRJNA266730 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1646700.fastq.gz	Fastqsanger.gz
	SRR1646710.fastq.gz	Fastqsanger.gz
	SRR1646701.fastq.gz	Fastqsanger.gz
	SRR1646711.fastq.gz	Fastqsanger.gz
	SRR1646702.fastq.gz	Fastqsanger.gz

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RNA bisulfite sequencing of 25S rRNA (C2278) in S. cerevisiae and of 28S rRNA (C3381) in C. elegans

Project description:The RNA methyltransferase NSUN5 modulates the lifespans of yeast, worms and flies by re-programming the translation of specific subsets of mRNAs, which are associated with the cellular stress response. Here we show by RNA bisulfite sequencing that Rcm1 specifically methylates C2278 of yeast 25S rRNA and nsun-5 C3381 of C. elegans 28S rRNA.

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Project description:(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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