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

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

PROVIDER: PRJNA896967 | 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 analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA

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

| PRJNA896964 | ENA

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

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 | 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 reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA [TAPS]

2023-06-12 | GSE217114 | GEO

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

DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [WGBS]

Project description:DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [WGBS]

| PRJNA1124892 | ENA

Whole Genome Bisulfite Sequencing (WGBS) of the SH-SY5Y human neuroblastoma cell line

Project description:WGBS was performed on: 1) untreated SH-SY5Y human neuroblastoma cells (day 0) 2) vincristine-treated SH-SY5Y human neuroblastoma cells (7 days of treatment - day 7) 3) vincristine-treated SH-SY5Y human neuroblastoma cells (7 days of treatment followed by 7 days of recovery - day 14)

2022-10-01 | E-MTAB-11223 | biostudies-arrayexpress

NPC268 whole-genome bisulfite sequencing (WGBS)

Project description:NPC268 whole-genome bisulfite sequencing (WGBS)

| PRJNA976248 | ENA

BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS.

Project description:BACKGROUND:Whole genome bisulfite sequencing (WGBS) also known as BS-seq has been widely used to measure the methylation of whole genome at single-base resolution. One of the key steps in the assay is converting unmethylated cytosines into thymines (BS conversion). Incomplete conversion of unmethylated cytosines can introduce false positive methylation call. Developing a quick method to evaluate bisulfite conversion ratio (BCR) is benefit for both quality control and data analysis of WGBS. RESULTS:Here we provide a computational method named "BCREval" to estimate the unconverted rate (UCR) by using telomeric repetitive DNA as native spike-in control. We tested the method by using public WGBS data and found that it is very stable and most of BS conversion assays can achieve>?99.5% efficiency. The non-CpG DNA methylation at telomere fits a binomial model and may result from a random process with very low possibility (the ratio?<?0.4%). And the comparison between BCREval and Bismark (Krueger and Andrews, Bioinformatics 27:1571-1572, 2011), a widely used BCR evaluator, suggests that our algorithm is much faster and more efficient than the latter. CONCLUSION:Our method is a simple but robust method to QC and speculates BCR for WGBS experiments to make sure it achieves acceptable level. It is faster and more efficient than current tools and can be easily integrated into presented WGBS pipelines.

| S-EPMC6995172 | biostudies-literature

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