Methodology for Accurate Detection of Mitochondrial DNA Methylation
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Methodology for Accurate Detection of Mitochondrial DNA Methylation. / Mechta, Mie; Ingerslev, Lars Roed; Barrès, Romain.
In: Journal of Visualized Experiments, Vol. 135, e57772, 2018.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Methodology for Accurate Detection of Mitochondrial DNA Methylation
AU - Mechta, Mie
AU - Ingerslev, Lars Roed
AU - Barrès, Romain
PY - 2018
Y1 - 2018
N2 - Quantification of DNA methylation can be achieved using bisulfite sequencing, which takes advantage of the property of sodium bisulfite to convert unmethylated cytosine into uracil, in a single-stranded DNA context. Bisulfite sequencing can be targeted (using PCR) or performed on the whole genome and provides absolute quantification of cytosine methylation at the single base-resolution. Given the distinct nature of nuclear- and mitochondrial DNA, notably in the secondary structure, adaptions of bisulfite sequencing methods for investigating cytosine methylation in mtDNA should be made. Secondary and tertiary structure of mtDNA can indeed lead to bisulfite sequencing artifacts leading to false-positives due to incomplete denaturation poor access of bisulfite to single-stranded DNA. Here, we describe a protocol using an enzymatic digestion of DNA with BamHI coupled with bioinformatic analysis pipeline to allow accurate quantification of cytosine methylation levels in mtDNA. In addition, we provide guidelines for designing the bisulfite sequencing primers specific to mtDNA, in order to avoid targeting undesirable NUclear MiTochondrial segments (NUMTs) inserted into the nuclear genome.
AB - Quantification of DNA methylation can be achieved using bisulfite sequencing, which takes advantage of the property of sodium bisulfite to convert unmethylated cytosine into uracil, in a single-stranded DNA context. Bisulfite sequencing can be targeted (using PCR) or performed on the whole genome and provides absolute quantification of cytosine methylation at the single base-resolution. Given the distinct nature of nuclear- and mitochondrial DNA, notably in the secondary structure, adaptions of bisulfite sequencing methods for investigating cytosine methylation in mtDNA should be made. Secondary and tertiary structure of mtDNA can indeed lead to bisulfite sequencing artifacts leading to false-positives due to incomplete denaturation poor access of bisulfite to single-stranded DNA. Here, we describe a protocol using an enzymatic digestion of DNA with BamHI coupled with bioinformatic analysis pipeline to allow accurate quantification of cytosine methylation levels in mtDNA. In addition, we provide guidelines for designing the bisulfite sequencing primers specific to mtDNA, in order to avoid targeting undesirable NUclear MiTochondrial segments (NUMTs) inserted into the nuclear genome.
KW - Bisulfite sequencing
KW - DNA methylation
KW - Epigenetics
KW - Genetics
KW - Issue 135
KW - Mitochondria
KW - Mitochondrial DNA
KW - Mitochondrial DNA methylation
KW - Mitoepigenetics
U2 - 10.3791/57772
DO - 10.3791/57772
M3 - Journal article
C2 - 29863674
AN - SCOPUS:85051027242
VL - 135
JO - Journal of Visualized Experiments
JF - Journal of Visualized Experiments
SN - 1940-087X
M1 - e57772
ER -
ID: 201301101