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Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

ABSTRACT: Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

PROVIDER: PRJNA322635 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3583360_1.fastq.gz	Fastqsanger.gz
	SRR3583360_2.fastq.gz	Fastqsanger.gz
	SRR3583370_1.fastq.gz	Fastqsanger.gz
	SRR3583370_2.fastq.gz	Fastqsanger.gz
	SRR3583361_1.fastq.gz	Fastqsanger.gz

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Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs [mRNA bisulfite sequencing]

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.

2017-05-19 | GSE81824 | GEO

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs [Whole-transcriptome bisulfite sequencing]

2017-05-19 | GSE81823 | GEO

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs.

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 previously established RNA bisulfite sequencing as a method for the analysis of RNA cytosine-5 methylation patterns at single-base resolution. More recently, next-generation sequencing has provided opportunities to establish transcriptome-wide maps of this modification. Here, we present a computational approach that integrates tailored filtering and data-driven statistical modeling to eliminate many of the artifacts that are known to be associated with bisulfite sequencing. By using RNAs from mouse embryonic stem cells, we 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. In addition, mRNAs were found to be very sparsely methylated or not methylated at all. Finally, the tRNA-specific activity of the DNMT2 methyltransferase could be resolved at single-base resolution, which provided important further validation. Our approach can be used to profile cytosine-5 RNA methylation patterns in many experimental contexts and will be important for understanding the function of cytosine-5 RNA methylation in RNA biology and in human disease.

| S-EPMC5580717 | biostudies-literature

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-05-19 | GSE81825 | GEO

Deep bisulfite amplicon sequencing and visualisation reveal diverse and heterogeneous DNA methylation patterns.

Project description:DNA methylation at a gene promoter region has the potential to regulate gene transcription. Their patterns are often complex with the region showing multiple allelic patterns in a sample. This complexity is commonly obscured when DNA methylation data is summarised as an average percentage value for each CpG site (or aggregated across CpG sites). The methylation state at adjacent CpG sites is therefore lost when data is summarised this way. Methylation patterns can only be characterised by clonal analysis. Deep sequencing provides the ability to investigate clonal DNA methylation patterns in unprecedented detail and scale, enabling the proper characterisation of the heterogeneity of methylation patterns. However, the sheer amount of sequencing data requires new synoptic approaches to visualise the distribution of allelic patterns. We have developed an analysis and visualisation software tool "Methpat", that extracts and displays clonal DNA methylation patterns from massively parallel sequencing data aligned using Bismark. We have performed multiplex bisulfite amplicon sequencing on a range of CpG island targets across a panel of human cell lines and primary tissues. Using Methpat, we demonstrate clonal diversity of epialleles analysed at specific gene promoter regions. We also describe the existence of DNA methylation within the mitochondrial genome. Multiplex bisulfite PCR and Next Generation sequencing of 35 samples

2015-11-23 | E-GEOD-67856 | biostudies-arrayexpress

High grade glioma methylation analysis using bisulfite and oxidative bisulfite-treatment

Project description:Bisulfite and oxidative bisulfite treated sample methylation analysis of IDH1 mutant and wild-type high grade human gliomas, to profile 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Genomic DNA isolated directly from fresh-frozen human high grade glioma specimens.

2020-10-06 | GSE104723 | GEO

Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data.

Project description:Bisulfite treatment of DNA followed by high-throughput sequencing (Bisulfite-seq) is an important method for studying DNA methylation and epigenetic gene regulation, yet current software tools do not adequately address single nucleotide polymorphisms (SNPs). Identifying SNPs is important for accurate quantification of methylation levels and for identification of allele-specific epigenetic events such as imprinting. We have developed a model-based bisulfite SNP caller, Bis-SNP, that results in substantially better SNP calls than existing methods, thereby improving methylation estimates. At an average 30× genomic coverage, Bis-SNP correctly identified 96% of SNPs using the default high-stringency settings. The open-source package is available at http://epigenome.usc.edu/publicationdata/bissnp2011.

| S-EPMC3491382 | biostudies-literature

Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Schistosoma mansoni]

Project description:Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation. Whole genome methylation analysis of S. mansoni. One sample was analyzed, containing DNA from adult male worms.

2013-05-06 | E-GEOD-39997 | biostudies-arrayexpress

Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns [Drosophila melanogaster]

Project description:Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation. Whole genome methylation analysis of D. melanogaster. Two samples were analyzed, one sample containing DNA from WT embryos, one sample containing DNA from Dnmt2-/- embryos.

2013-05-06 | E-GEOD-39996 | biostudies-arrayexpress

High grade glioma methylation analysis using bisulfite and oxidative bisulfite-treatment

Project description:High grade glioma methylation analysis using bisulfite and oxidative bisulfite-treatment

| PRJNA413641 | ENA