DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria

Shock, Lisa S.; Thakkar, Prashant V.; Peterson, Erica J.; Moran, Richard G.; Taylor, Shirley M.

doi:10.1073/pnas.1012311108

Cited by 555Epigenetics and DNA MethylationMitochondrial Function and PathologyRNA modifications and cancer

DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria

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Shock, Lisa S., Thakkar, Prashant V., Peterson, Erica J., Moran, Richard G., Taylor, Shirley M.·2011·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.1012311108PMC PMC3048134

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Abstract

Mitochondrial DNA (mtDNA) has been reported to contain 5-methylcytosine (5mC) at CpG dinucleotides, as in the nuclear genome, but neither the mechanism generating mtDNA methylation nor its functional significance is known. We now report the presence of 5-hydroxymethylcytosine (5hmC) as well as 5mC in mammalian mtDNA, suggesting that previous studies underestimated the level of cytosine modification in this genome. DNA methyltransferase 1 (DNMT1) translocates to the mitochondria, driven by a mitochondrial targeting sequence located immediately upstream of the commonly accepted translational start site. This targeting sequence is conserved across mammals, and the encoded peptide directs a heterologous protein to the mitochondria. DNMT1 is the only member of the three known catalytically active DNA methyltransferases targeted to the mitochondrion. Mitochondrial DNMT1 (mtDNMT1) binds to mtDNA, proving the presence of mtDNMT1 in the mitochondrial matrix. mtDNMT1 expression is up-regulated by NRF1 and PGC1α, transcription factors that activate expression of nuclear-encoded mitochondrial genes in response to hypoxia, and by loss of p53, a tumor suppressor known to regulate mitochondrial metabolism. Altered mtDNMT1 expression asymmetrically affects expression of transcripts from the heavy and light strands of mtDNA. Hence, mtDNMT1 appears to be responsible for mtDNA cytosine methylation, from which 5hmC is presumed to be derived, and its expression is controlled by factors that regulate mitochondrial function.

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Shock and colleagues reported in 2011 that human and mouse cell-line mtDNA contains 5-mC and 5-hmC cytosine residues together with DNMT1.
“However, in 2011, Shock and colleagues showed that both 5-mC and hydroxymethylated (5-hmC) cytosine residues, along with DNA methyltransferase 1 (DNMT1), are present in mtDNA from human and mouse cell lines100.”
From Mitochondrial and metabolic dysfunction in ageing and age-related diseases (2022) · cites this paper as [100]

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Authors: Shock, L. S., Thakkar, P. V., Peterson, E. J., Moran, R. G., & Taylor, S. M.
Affiliations: Department of Microbiology and Immunology,
Virginia Commonwealth University (US)
VCU Massey Comprehensive Cancer Center (US)
ORCID: Shock, Lisa S.
Thakkar, Prashant V.
Peterson, Erica J.
Taylor, Shirley M.
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 2011-02-14
Volume: 108
Issue: 9
Pages: 3630-3635
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.1012311108
PMC: PMC3048134
OpenAlex: W2150095915
Cited by: 555
References: 36
Citations by year: 2026: 24 · 2025: 35 · 2024: 29 · 2023: 33 · 2022: 42 · 2021: 39 · 2020: 43 · 2019: 30 · 2018: 41 · 2017: 56 · 2016: 38 · 2015: 47 · 2014: 30 · 2013: 34 · 2012: 24
FWCI: 12.64
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Cancer Institute (R01CA106630, CA106630, P30CA016059)
National Institute of Neurological Disorders and Stroke (P30NS047463)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords: mitochondrial DNA, DNMT1, 5-hydroxymethylcytosine, 5-methylcytosine, cytosine methylation, mitochondrial targeting sequence, NRF1, PGC-1α, p53, mitochondrial metabolism, hypoxia
MeSH terms: DNA (Cytosine-5-)-Methyltransferase 1, Amino Acid Sequence, Animals, Base Sequence, Cell Compartmentation, Cytosine, DNA (Cytosine-5-)-Methyltransferases, DNA, Mitochondrial, Humans, Mitochondria, Molecular Sequence Data, Protein Binding, Transcription, Genetic, Oxidative Stress, DNA Methylation, Protein Sorting Signals, 5-Methylcytosine, HCT116 Cells, Genes, Mitochondrial, Mice

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DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria

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