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Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA

ABSTRACT: Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA

PROVIDER: PRJNA896964 | ENA |

REPOSITORIES: ENA

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Optimized bisulfite sequencing reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [TAPS]

Project description:Optimized bisulfite sequencing reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [TAPS]

| PRJNA896966 | ENA

Optimized bisulfite sequencing reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [WGBS]

Project description:Optimized bisulfite sequencing reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [WGBS]

| PRJNA896967 | ENA

Optimized bisulfite sequencing reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [TAPS]

Project description:Whether 5mC exists in mitochondrial DNA is controversial, as data ranging from lack of 5mC to very extensive 5mC have been reported. By comprehensive bioinformatic analyses of published and our own data, we reveal that the observation of extensive and strand-biased mtDNA-5mC is artifact due to combinatorial effects of inefficient bisulfite conversion, extremely low sequencing reads in the L strand and interfering signals from nuclear mitochondrial DNA sequences (NUMTs).

2023-06-12 | GSE217114 | GEO

Optimized bisulfite sequencing reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [WGBS]

2023-06-12 | GSE217116 | GEO

Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA.

Project description:BackgroundDNA methylation is one of the best characterized epigenetic modifications in the mammalian nuclear genome and is known to play a significant role in various biological processes. Nonetheless, the presence of 5-methylcytosine (5mC) in mitochondrial DNA remains controversial, as data ranging from the lack of 5mC to very extensive 5mC have been reported.ResultsBy conducting comprehensive bioinformatic analyses of both published and our own data, we reveal that previous observations of extensive and strand-biased mtDNA-5mC are likely artifacts due to a combination of factors including inefficient bisulfite conversion, extremely low sequencing reads in the L strand, and interference from nuclear mitochondrial DNA sequences (NUMTs). To reduce false positive mtDNA-5mC signals, we establish an optimized procedure for library preparation and data analysis of bisulfite sequencing. Leveraging our modified workflow, we demonstrate an even distribution of 5mC signals across the mtDNA and an average methylation level ranging from 0.19% to 0.67% in both cell lines and primary cells, which is indistinguishable from the background noise.ConclusionsWe have developed a framework for analyzing mtDNA-5mC through bisulfite sequencing, which enables us to present multiple lines of evidence for the lack of extensive 5mC in mammalian mtDNA. We assert that the data available to date do not support the reported presence of mtDNA-5mC.

| S-EPMC10403921 | biostudies-literature

Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA

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

2023-06-12 | GSE217117 | GEO

Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster

Project description:This SuperSeries is composed of the following subset Series: GSE32362: Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (Illumina HumanMethylation450 BeadChip) GSE33129: Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (Illumina HiSeq2000 sequencing) Refer to individual Series

2012-05-02 | E-GEOD-33130 | biostudies-arrayexpress

Ultrafast Bisulfite Sequencing for Efficient and Accurate 5-Methylcytosine Detection in DNA and RNA

Project description:We present an ultrafast bisulfite sequencing (UBS-seq) method, which accelerates the bisulfite reaction by about 13-fold, resulting in minimal DNA damage and much lower background in all DNA sequences. This ultrafast BS protocol is also ideal for mapping of RNA 5-methylcytosine (m5C) because of much shorter reaction time and dramatically reduced RNA background. And allowed detection of m5C stoichiometry in highly structured RNA species.

2023-10-13 | GSE225614 | GEO

Single-base resolution methylome of 5-methylcytosine in mammalian transcriptome

Project description:Single-base resolution methylome of 5-methylcytosine in mammalian transcriptome

| PRJNA301456 | ENA

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

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