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Whole mitochondrial genome bisulfite sequencing (WmGBS) analysis for the mouse brain, liver, and embryonic stem cells

ABSTRACT: Whole mitochondrial genome bisulfite sequencing (WmGBS) analysis for the mouse brain, liver, and embryonic stem cells

PROVIDER: PRJNA408242 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6056870_1.fastq.gz	Fastqsanger.gz
	SRR6056870_2.fastq.gz	Fastqsanger.gz
	SRR6056880_1.fastq.gz	Fastqsanger.gz
	SRR6056880_2.fastq.gz	Fastqsanger.gz
	SRR6056861_1.fastq.gz	Fastqsanger.gz

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Whole mitochondrial genome bisulfite sequencing (WmGBS) analysis for the mouse brain, liver, and embryonic stem cells

Project description:Whilst 5-methylcytosine (5mC) is a major epigenetic mark in the nuclear DNA in mammals, whether or not mitochondrial DNA (mtDNA) receives 5mC modification remains controversial. Herein, we exhaustively analysed mouse mtDNA using three methods that are based upon different principles for detecting 5mC. Next-generation bisulfite sequencing did not give any significant signatures of methylation in mtDNAs of liver, brain and embryonic stem cells (ESCs). Also, treatment with methylated cytosine-sensitive endonuclease McrBC resulted in no substantial decrease of mtDNA band intensities in Southern hybridisation. Furthermore, mass spectrometric nucleoside analyses of highly purified liver mtDNA preparations did not detect 5-methyldeoxycytidine at the levels found in the nuclear DNA but at a range of only 0.3–0.5% of deoxycytidine. Taken together, we propose that 5mC is not present at any specific region(s) of mtDNA and that levels of the methylated cytosine are fairly low, provided the modification occurs. It is thus unlikely that 5mC plays a universal role in mtDNA gene expression or mitochondrial metabolism.

2018-04-11 | GSE104104 | GEO

Whole genome bisulfite sequencing of muscle, liver, brain tissues in cattle

Project description:Whole genome bisulfite sequencing of muscle, liver, brain tissues in cattle

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Whole genome bisulfite sequencing of muscle, liver, brain tissues in cattle

Project description:In this study, we generated whole genome bisulfite sequencing data 3 tissues in Holstein cattle. We analyzed the variations of DNA methylation among tissues.

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Genome-wide characterization of mitochondrial DNA methylation in human brain

Project description:Here, we present a novel approach to interrogate the mitochondrial DNA (mtDNA) methylome at single base resolution using targeted bisulfite sequencing. We applied this method to investigate mitochondrial DNA methylation patterns in post-mortem superior temporal gyrus and cerebellum brain tissue from seven human donors. We show that mitochondrial DNA methylation patterns are relatively low but conserved, with peaks in DNA methylation >5% at a number of sites and higher levels of methylation at non-CpG compared to CpG sites. We identify a number of loci that show differential DNA methylation patterns associated with age, sex and brain region. Finally we validate differences between cortical and cerebellar mitochondrial DNA methylation patterns using data previously generated using methylated DNA immunoprecipitation sequencing.

2022-12-20 | GSE189565 | GEO

Whole genome bisulfite sequencing of Ing1/Gadd45a double knockout and wildtype mouse embryonic fibroblasts

Project description:ING1b and GADD45a are nuclear proteins involved in the regulation of cell growth, apoptosis and DNA repair. We previously found that ING1b is essential to target GADD45a-mediated active DNA-demethylation via TET1 to specific loci. In order to study the physiological impact of ING1-GADD45a on DNA methylation in base-resolution genome-wide, we compared the methylation levels of wildtype mouse embryonic fibroblasts (MEFs) with Ing1/Gadd45a double-knockout MEFs via whole genome bisulfite sequencing.

2018-06-11 | GSE99601 | GEO

Ultra-deep whole genome bisulfite sequencing reveals a single methylation hotspot in human brain mitochondrial DNA.

Project description:While DNA methylation is established as a major regulator of gene expression in the nucleus, the existence of mitochondrial DNA (mtDNA) methylation remains controversial. Here, we characterized the mtDNA methylation landscape in the prefrontal cortex of neurological healthy individuals (n=26) and patients with Parkinson's disease (n=27), using a combination of whole-genome bisulphite sequencing (WGBS) and bisulphite-independent methods. Accurate mtDNA mapping from WGBS data required alignment to an mtDNA reference only, to avoid misalignment to nuclear mitochondrial pseudogenes. Once correctly aligned, WGBS data provided ultra-deep mtDNA coverage (16,723 ± 7,711) and revealed overall very low levels of cytosine methylation. The highest methylation levels (5.49 ± 0.97%) were found on CpG position m.545, located in the heavy-strand promoter 1 region. The m.545 methylation was validated using a combination of methylation-sensitive DNA digestion and quantitative PCR analysis. We detected no association between mtDNA methylation profile and Parkinson's disease. Interestingly, m.545 methylation correlated with the levels of mtDNA transcripts, suggesting a putative role in regulating mtDNA gene expression. In addition, we propose a robust framework for methylation analysis of mtDNA from WGBS data, which is less prone to false-positive findings due to misalignment of nuclear mitochondrial pseudogene sequences.

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Project description:Global changes in DNA methylation occur during mammalian development but may be more limited during differentiation of cell lineages. The extent and specific nature of methylation changes at the time when neural progenitor cells in the brain cease proliferation and commit to become differentiated cortical neurons remains unknown. Here, we have used whole genome bisulfite sequencing to quantitate a level of modified bisulfite-resistant cytosines (5-methylcytosine and 5-hydroxymethylcytosine) at base resolution in differentiating neurons and their progenitors isolated from mouse brain at the peak of embryonic neurogenesis. We find that, during this transition, globally, modified cytosine pattern is very stable. Localized losses of modified cytosines (hypomethylation) were much more common than gains and were targeted frequently to intragenic enhancer regions marked by H3K27 acetylation. Most genes with intragenic clustered hypomethylated CpG sites were upregulated in neurons and encoded factors essential for neurogenesis. The hypomethylated regions were enriched in motifs recognized by the neuronal transcription factor NEUROD2 which become activated in differentiated neurons. NEUROD2 binding coincided with 80% of the hypomethylated intragenic enhancer regions. The data suggest that in developing neurons, the limited reorganization of the DNA methylome reflects the engagement of intragenic enhancers by NEUROD2 in parallel with activation of neuronal function-related genes.

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Whole-genome bisulfite sequencing across 27 developmental stages in Sus scrofa skeletal muscle

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