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Series GSE21152 Query DataSets for GSE21152
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.
Overall design Comparison of methylation across eight eukaryotic organisms
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
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
Platforms (9)
GPL9062 Illumina Genome Analyzer (Arabidopsis thaliana)
GPL9100 Illumina Genome Analyzer II (Chlamydomonas reinhardtii)
GPL9147 Illumina Genome Analyzer (Oryza sativa)
Samples (14)
GSM530098 Ath_wildtype_shoots_bisulfite
GSM530099 Ath_wildtype_flowers_bisulfite
GSM530100 Ath_vim1vim2vim3_flowers_bisulfite
SRA SRP002239
BioProject PRJNA126633

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Supplementary file Size Download File type/resource
GSE21152_RAW.tar 313.8 Mb (http)(custom) TAR (of TXT)
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Processed data provided as supplementary file
Raw data are available in SRA

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