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| Status |
Public on Jun 12, 2009 |
| Title |
Extensive demethylation of repetitive elements during seed development underlies gene imprinting |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by genome tiling array
Methylation profiling by high throughput sequencing
|
| Summary |
DNA methylation is an epigenetic mark associated with transposable element silencing and gene imprinting in flowering plants and mammals. In plants, imprinting occurs in the endosperm, which nourishes the embryo during seed development. We have profiled Arabidopsis DNA methylation genome-wide in the embryo and endosperm. Large-scale methylation changes accompany endosperm development and endosperm-specific gene expression. Transposable element fragments are extensively demethylated in the endosperm. We discovered new imprinted genes by identifying candidate genes associated with the top differentially methylated regions. Our data suggest that imprinting in plants evolved from genome defense against transposable elements.
Keywords: Affinity-purification on microarray
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| Overall design |
All experiments were done using two channels per chip. Immunoprecipitated methylated DNA (IP) was compared to control genomic DNA (input). Both the IP and input represent Cy5 and Cy3 labeled Illumina GA libraries.
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| |
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| Contributor(s) |
Gehring M, Henikoff S |
| Citation(s) |
19520961 |
| |
| Submission date |
Jan 26, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL3371 |
FHCRC Arabidopsis Tiling Array |
| GPL9062 |
Illumina Genome Analyzer (Arabidopsis thaliana) |
|
| Samples (10)
|
| GSM364540 |
Embryo DNA methylation IP/total DNA (MGE_220227) |
| GSM364541 |
Endosperm DNA methylation IP/total DNA (MGE_220242) |
| GSM364542 |
dme-2 endosperm DNA methylation IP/total DNA (MGd_220241) |
|
| Relations |
| SRA |
SRP000779 |
| BioProject |
PRJNA111577 |
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