|
| Status |
Public on Oct 10, 2017 |
| Title |
DNA demethylation activates genes in seed maternal integument development in rice (Oryza sativa L.) |
| Organism |
Oryza sativa |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development. Bisulfite sanger sequencing and qRT-PCR of six differentially methylated genes revealed extensive occurrence of DNA hypomethylation triggered by double fertilization at IAP compared with IBP, suggesting that DNA demethylation might be a key mechanism to activate numerous maternal controlling genes. These results presented here not only greatly expanded the rice methylome dataset, but also shed novel insight into the regulatory roles of DNA methylation in rice seed maternal integument development.
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| Overall design |
The global DNA methylomic profiling of seed integument before and after pollination of rice were generated by whole-genome deep bisulfite deep sequencing, in triplicate, using IlluminaHiSeqTM 2500.
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| Contributor(s) |
Wang Y, Lin H, Zhang J |
| Citation(s) |
29031162 |
| |
| Submission date |
Feb 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian zhang |
| E-mail(s) |
zhangjian@caas.cn
|
| Phone |
+86 13656661382
|
| Organization name |
China National Rice Research Institute
|
| Department |
State Key Lab of Rice Biology
|
| Lab |
Rice Reproductive Developmental Biology Group
|
| Street address |
28 shuidaosuo road,Fuyang, Hangzhou
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
311400 |
| Country |
China |
| |
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| Platforms (1) |
| GPL13160 |
Illumina HiSeq 2000 (Oryza sativa) |
|
| Samples (6)
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| Relations |
| BioProject |
PRJNA376108 |
| SRA |
SRP100418 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95107_RAW.tar |
5.1 Gb |
(http)(custom) |
TAR (of BIGWIG) |
| GSE95107_methylgene_Downstream_1K.Hyper.IBP.vs.IAP.txt.gz |
3.0 Mb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_Downstream_1K.Hypo.IBP.vs.IAP.txt.gz |
706.2 Kb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_UTR3.Hyper.IBP.vs.IAP.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_UTR3.Hypo.IBP.vs.IAP.txt.gz |
459.1 Kb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_UTR5.Hyper.IBP.vs.IAP.txt.gz |
769.1 Kb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_UTR5.Hypo.IBP.vs.IAP.txt.gz |
522.4 Kb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_Upstream_2K.Hyper.IBP.vs.IAP.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_Upstream_2K.Hypo.IBP.vs.IAP.txt.gz |
714.1 Kb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_exon.Hyper.IBP.vs.IAP.txt.gz |
13.9 Mb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_exon.Hypo.IBP.vs.IAP.txt.gz |
5.4 Mb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_gene.Hyper.IBP.vs.IAP.txt.gz |
2.9 Mb |
(ftp)(http) |
TXT |
| GSE95107_methylgene_gene.Hypo.IBP.vs.IAP.txt.gz |
702.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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