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Series GSE9925 Query DataSets for GSE9925
Status Public on Jan 04, 2008
Title Global mapping of epigenetic modifications of histone H3 Lysine 4 di- and trimethylation in Rice
Organism Oryza sativa
Experiment type Genome binding/occupancy profiling by genome tiling array
Methylation profiling by genome tiling array
Summary We present high-resolution maps of DNA methylation and H3K4 di- and tri-methylation of two entire chromosomes and two fully sequenced centromeres in rice shoots and cultured cells. Most transposable elements have highly methylated DNA but no H3K4 methylation whereas over half of protein-coding genes have both methylated DNA and di- and/or tri-methylated H3K4. Methylation of DNA but not H3K4 correlates with suppressed transcription. In contrast, if both DNA and H3K4 are methylated transcription is only slightly reduced. Transcriptional activity was positively correlated with H3K4Me3/H3K4Me2 within the gene body: genes with predominantly H3K4Me3 were actively transcribed whereas genes with predominantly H3K4Me2 were transcribed at moderate levels. Both H3K4Me2 and H3K4Me3 exhibited two peaks in long rice genes; a minor peak correlated with putative transcription start sites and a major peak downstream, implying possible roles in transcriptional initiation and elongation.
Keywords: whole genome profiling, DNA methylation, ChIP
 
Overall design Plant Materials and Growth Conditions
All plants used in this study were rice strain Oryza sativa ssp japonica cv Nipponbare. Dehusked seeds were surface sterilized and sown on solidified Murashige and Skoog medium with 3.0% sucrose. Plants were grown in chambers at 28°C with continuous white light for 7 days, and the entire shoots were harvested. Suspension cultured cells were derived from the same rice strain and maintained as described previously (Su et al., 2007).

Isolation of epigenetically modified genomic DNA fragments
Methylated DNA was isolated from total genomic DNA prepared using the Plant DNeasy Mini Kit (QIAGEN) by the McrBC-digestion method (Lippman et al., 2004). DNA bearing modified was isolated by chromatin immunoprecipitation (ChIP) with antibodies that specifically recognize H3K4Me2, H3K4Me3 and CenH3.

Tiling Microarray Design, Hybridization, Scanning and Data analysis
Tiling probes were selected by the NASA Oligonucleotide Selection Algorithm (NOPSA) (Stolc et al., 2005). Microarrays were hybridized with Cy3 or Cy5 labeled DNA for 16-20 hours at 50°C, then washed each 10 min at room temperature. Hybridization images were generated by a GenePix 4200A scanner (Axon). Raw data was sequentially processed by LOESS normalization and Quantile normalization.
 
Contributor(s) Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, Li S, Deng X
Citation(s) 18263775
Submission date Dec 17, 2007
Last update date Oct 14, 2015
Contact name Hang He
E-mail(s) hehang@gmail.com
Organization name Yale University
Department MCDB
Lab Deng Xing-Wang
Street address 165 Prospect St
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platforms (2)
GPL6285 Yale University MCDB Rice japonica NimbleGen 390K Oligo Array version1
GPL6286 Yale University MCDB Rice japonica NimbleGen 390K Oligo Array for H3K4Me2 and H3K4Me3 version1
Samples (32)
GSM251113 DNAmeth_MethylatedDNA_532_CC replicate1
GSM251116 DNAmeth_Genomic_635_CC replicate1
GSM251118 DNAmeth_MethylatedDNA_532_CC replicate2
Relations
BioProject PRJNA103927

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
GSE9925_RAW.tar 511.8 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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