|
| Status |
Public on Apr 09, 2010 |
| Title |
Conservation and divergence of methylation patterning in plants and animals |
| Organisms |
Chlamydomonas reinhardtii; Populus trichocarpa; Arabidopsis thaliana; Oryza sativa; Apis mellifera; Ciona intestinalis; Danio rerio; Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. While DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here, we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most of the organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honeybee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, we demonstrate that the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.
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| Overall design |
Comparison of methylation across eight eukaryotic organisms
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| |
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| Contributor(s) |
Feng S, Cokus SJ, Zhang X, Chen P, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE |
| Citation(s) |
20395551 |
| Submission date |
Mar 31, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
matteo Pellegrini |
| E-mail(s) |
matteop@mcdb.ucla.edu
|
| Phone |
310-825-0012
|
| Organization name |
UCLA
|
| Department |
MCD Biology
|
| Lab |
Matteo Pellegrini
|
| Street address |
621 Charles Young Drive South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
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| Platforms (9)
|
| GPL9062 |
Illumina Genome Analyzer (Arabidopsis thaliana) |
| GPL9100 |
Illumina Genome Analyzer II (Chlamydomonas reinhardtii) |
| GPL9147 |
Illumina Genome Analyzer (Oryza sativa) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
| GPL9311 |
Illumina Genome Analyzer (Ciona intestinalis) |
| GPL9909 |
Illumina Genome Analyzer II (Apis mellifera) |
| GPL10164 |
Illumina Genome Analyzer (Danio rerio) |
| GPL10284 |
Illumina Genome Analyzer (Populus trichocarpa) |
|
| Samples (14)
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| Relations |
| SRA |
SRP002239 |
| BioProject |
PRJNA126633 |
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