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| Status |
Public on Nov 09, 2018 |
| Title |
Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 in the mitochondrial genome |
| Organisms |
Escherichia coli; Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium |
| Experiment type |
Other
|
| Summary |
N6-methyldeoxyadenosine (6mA) is a well-characterized DNA modification in prokaryotes but reports on its presence and function in mammals have been controversial. To address this issue, we established the capacity of 6mA-Crosslinking-Exonuclease-sequencing (6mACE-seq) to detect genome-wide 6mA at single-nucleotide-resolution, demonstrating this by accurately mapping 6mA in synthesized DNA and bacterial genomes. Using 6mACE-seq, we generated a human-genome-wide 6mA map that accurately reproduced known 6mA enrichment at active retrotransposons and revealed mitochondrial chromosome-wide 6mA clusters asymmetrically enriched on the heavy-strand. We identified a novel putative 6mA-binding protein in single stranded DNA binding protein 1 (SSBP1), a mitochondrial DNA (mtDNA) replication factor known to coat the heavy-strand, linking 6mA with the regulation of mtDNA replication. Finally, we characterized AlkB homolog 1 (ALKBH1) as a mitochondrial protein with 6mA demethylase activity and showed that its loss decreases mitochondrial oxidative phosphorylation. Our results show that 6mA clusters play a previously unappreciated role in regulating human mitochondrial function, despite 6mA being an uncommon DNA modification in the human genome.
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| Overall design |
UV crosslinking, immunoprecipitation and exonuclease treatment with anti-6mA antibodies was used to map 6mA in DNA at single-nucleotide-resolution
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| Contributor(s) |
Goh WS |
| Citation(s) |
30412255 |
| Submission date |
Aug 27, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Wee Siong Sho Goh |
| E-mail(s) |
shogoh@szbl.ac.cn
|
| Organization name |
Shenzhen Bay Laboratory
|
| Department |
Institute of Molecular Physiology
|
| Lab |
Sho Goh Laboratory
|
| Street address |
Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518107 |
| Country |
China |
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| Platforms (4)
|
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL16085 |
Illumina MiSeq (Escherichia coli) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL23683 |
Illumina MiSeq (Salmonella enterica subsp. enterica serovar Typhimurium) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA488087 |
| SRA |
SRP158929 |
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