GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE38935 Query DataSets for GSE38935
Status Public on Sep 21, 2012
Title Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes
Organism Arabidopsis thaliana
Experiment type Methylation profiling by high throughput sequencing
Summary The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation prior to fertilization, but the targeting preferences and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell, and preferentially targets small, AT-rich and nucleosome-depleted transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA-directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes, thereby assuring stable silencing of transposable elements across generations
Overall design Examination of DNA methylation in Arabidopsis endosperm, embryo, and pollen
Contributor(s) Nishimura T, Zilberman D
Citation(s) 22984074
Submission date Jun 26, 2012
Last update date Nov 24, 2020
Contact name Toshiro Nishimura
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
Platforms (2)
GPL11221 Illumina Genome Analyzer IIx (Arabidopsis thaliana)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
Samples (10)
GSM952438 at-embryo-col_wt_x_ler_wt
GSM952439 at-embryo-ler_wt_x_col_wt
GSM952440 at-endosperm-col_dme_x_ler_wt
SRA SRP013933
BioProject PRJNA169395

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38935_RAW.tar 4.2 Gb (http)(custom) TAR (of GFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap