|
| Status |
Public on Apr 15, 2010 |
| Title |
Genome-wide evolutionary analysis of eukaryotic DNA methylation |
| Organisms |
Volvox carteri; Physcomitrium patens; Oryza sativa; Phycomyces blakesleeanus; Coprinopsis cinerea; Tribolium castaneum; Bombyx mori; Drosophila melanogaster; Apis mellifera; Ciona intestinalis; Laccaria bicolor; Uncinocarpus reesii; Nematostella vectensis; Selaginella moellendorffii; Tetraodon nigroviridis; Postia placenta; Chlorella variabilis |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. We show that methylation of plant transposons in the CHG context extends to green algae, and present evidence for RNA-directed DNA methylation of fungal genes. We also show that antagonism between DNA methylation and histone H2A.Z is conserved between plants and animals. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.
Keywords: Epigenetics
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| Overall design |
Examination of DNA methylation and transcription in plant, animal, and fungal genomes, and examination of how H2A.Z deposition relates to both methylation and transcription in puffer fish. Descriptions of the Samples' raw and processed data (provided as supplementary files) can be found in GSE19824_README.txt at the foot of this record.
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| |
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| Contributor(s) |
Zemach A, McDaniel IE, Silva P, Zilberman D |
| Citation(s) |
20395474 |
| |
| Submission date |
Jan 11, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshiro Nishimura |
| E-mail(s) |
tnish@berkeley.edu
|
| Phone |
5106429550
|
| Organization name |
University of California at Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
Daniel Zilberman
|
| Street address |
211 Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
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| Platforms (17)
|
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
| GPL9151 |
Illumina Genome Analyzer II (Bombyx mori) |
| GPL9316 |
Illumina Genome Analyzer II (Oryza sativa) |
| GPL9909 |
Illumina Genome Analyzer II (Apis mellifera) |
| GPL9911 |
Illumina Genome Analyzer II (Ciona intestinalis) |
| GPL9912 |
Illumina Genome Analyzer II (Coprinopsis cinerea) |
| GPL9913 |
Illumina Genome Analyzer II (Laccaria bicolor) |
| GPL9914 |
Illumina Genome Analyzer II (Nematostella vectensis) |
| GPL9915 |
Illumina Genome Analyzer II (Phycomyces blakesleeanus) |
| GPL9916 |
Illumina Genome Analyzer II (Physcomitrella patens) |
| GPL9917 |
Illumina Genome Analyzer II (Postia placenta) |
| GPL9918 |
Illumina Genome Analyzer II (Selaginella moellendorffii) |
| GPL9919 |
Illumina Genome Analyzer II (Tetraodon nigroviridis) |
| GPL9920 |
Illumina Genome Analyzer II (Tribolium castaneum) |
| GPL9921 |
Illumina Genome Analyzer II (Uncinocarpus reesii) |
| GPL9922 |
Illumina Genome Analyzer II (Volvox carteri) |
| GPL15029 |
Illumina Genome Analyzer II (Chlorella variabilis) |
|
| Samples (33)
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| Relations |
| BioProject |
PRJNA122153 |
| SRA |
SRP002417 |
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