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Series GSE89789 Query DataSets for GSE89789
Status Public on Nov 30, 2016
Title DNA demethylation is initiated in the central cells of Arabidopsis and rice
Organisms Arabidopsis thaliana; Oryza sativa
Experiment type Methylation profiling by high throughput sequencing
Summary Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extra-embryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell prior to fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Downregulation of the MET1 DNA methyltransferase has also been proposed to contribute to demethylation in the central cell. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice, as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared to non-sexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm.
 
Overall design Examination of DNA methylation in Arabidopsis central cell, and rice egg and central cell
 
Contributor(s) Park K, Kim MY, Vickers M, Park J, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S
Citation(s) 27956642
Submission date Nov 13, 2016
Last update date May 15, 2019
Contact name Xiaoqi Feng
E-mail(s) xiaoqi.feng@jic.ac.uk
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Xiaoqi Feng
Street address Norwich Research Park
City Norwich
State/province Norfolk
ZIP/Postal code NR4 7UH
Country United Kingdom
 
Platforms (2)
GPL21087 Illumina NextSeq 500 (Oryza sativa)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (5)
GSM2388871 EC Rice
GSM2388872 CC Rice
GSM2388873 CC Wt Rep 1
Relations
BioProject PRJNA353305
SRA SRP093292

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

Supplementary file Size Download File type/resource
GSE89789_RAW.tar 2.3 Gb (http)(custom) TAR (of GFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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