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| Status |
Public on Sep 01, 2018 |
| Title |
DNA is Methylated on N4-Cytosine in Eukaryotes |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
DNA methylation is a key mechanism for regulation of DNA repair, DNA replication, and gene expression. In bacteria, DNA is modified by methylation on C5-cytosine (5mC), N6-adenine (6mA) and N4-cytosine (4mC). Metazoans were thought to only use 5mC to regulate gene expression until the recent discovery of N6-adenine methylation in DNA of diverse metazoan species, including mammals. Here we show by dot blot, immunoprecipitation with 4mC-specific antibodies, and ultra-high performance liquid chromatography coupled with triple-quadrupole mass spectrometry that 4mC also occurs in most eukaryotes. We further characterize 4mC sites on a near genome-wide scale by single molecule real time (SMRT) sequencing in the nematode C. elegans. In C. elegans, 4mC is found in all chromosomes but is relatively sparse on the X chromosome. 4mC is relatively enriched on introns, depleted on exons, and co-localizes with 6mA. In human cells, 4mC is anti-correlated with 5mC. Moreover, 4mC modifications are associated with increased gene expression. Transfection of human cells with a 4mC-modified luciferase reporter plasmid increases luciferase expression as compared to the unmethylated plasmid. These data suggest that 4mC promotes gene transcription, playing an opposing role to 5mC, which generally represses transcription. Thus 4mC modification of DNA is a previously unrecognized mechanism of gene regulation in eukaryotes, providing evidence for a complex epigenetic DNA code.
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| Overall design |
C. elegans L4 stage wildtype SMRTseq data
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| Contributor(s) |
Wang J, O'Brown Z, Boulias K, Zhang L, Shibuya H, Burger S, Feroe A, Yu M, He C, Liu T, Greer EL |
| Citation(s) |
31159718 |
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| Submission date |
Sep 16, 2016 |
| Last update date |
Jun 16, 2019 |
| Contact name |
Jie Wang |
| E-mail(s) |
Jie.Wang@Roswellpark.org
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| Organization name |
Roswell Park Comprehensive Cancer Center
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| Department |
Department of Biostatistics and Bioinformatics
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| Street address |
Elm and Carlton Streets
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| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14263 |
| Country |
USA |
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| Platforms (1) |
| GPL19919 |
PacBio RS II (Caenorhabditis elegans) |
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| Samples (1) |
| GSM2318501 |
whole L4 stage wildtype C. elegans gDNA |
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| Relations |
| BioProject |
PRJNA343175 |
| SRA |
SRP089990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE86993_RAW.tar |
360.0 Kb |
(http)(custom) |
TAR (of GFF) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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