|
| Status |
Public on May 01, 2013 |
| Title |
Imprinted expression of genes and small RNA is triggered by localized demethylation of the maternal genome in rice endosperm |
| Organism |
Oryza sativa |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
We report that rice endosperm shows a specific hypomethylation of DNA in the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini, and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small Class II (cut and paste) transposable elements, those in endosperm are much more uniformly derived, including sequences from other TE classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that demethylation of maternal endosperm DNA is conserved in flowering plants.
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| Overall design |
Examination of DNA methylation and small RNA expression in the seeds of two cultivars from the japonica subspecies of Oryza sativa L.
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| |
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| Contributor(s) |
Rodrigues J, Ruan R, Nishimura T, Ronald P, Fischer R, Zilberman D |
| Citation(s) |
23613580 |
| |
| Submission date |
Mar 05, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshiro Nishimura |
| E-mail(s) |
tnish@berkeley.edu
|
| 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) |
| GPL13160 |
Illumina HiSeq 2000 (Oryza sativa) |
| GPL15432 |
Illumina Genome Analyzer IIx (Oryza sativa) |
|
| Samples (16)
|
| GSM1093498 |
Oryza Sativa L Root Cultivar Nipponbare RRF |
| GSM1093499 |
Oryza Sativa L Root Cultivar Nipponbare RRG |
| GSM1093500 |
Oryza Sativa L Shoot Cultivar Nipponbare RSF |
| GSM1093501 |
Oryza Sativa L Shoot Cultivar Nipponbare RSG |
| GSM1093502 |
Oryza Sativa L Endosperm Cultivar Nipponbare NNA |
| GSM1093503 |
Oryza Sativa L Embryo Cultivar Nipponbare NEA |
| GSM1093504 |
Oryza Sativa L Endosperm Cultivar Kitaake KNA |
| GSM1093505 |
Oryza Sativa L Embryo Cultivar Kitaake KEA |
| GSM1093506 |
Oryza Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare KNEB1 |
| GSM1093507 |
Oryza Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare KNNB1 |
| GSM1093508 |
Oryza Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare NKES2 |
| GSM1093509 |
Oryza Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare NKNS2 |
| GSM1093510 |
Oryza Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare KNES1 |
| GSM1093511 |
Oryza Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare KNNS1 |
| GSM1093512 |
Oryza Sativa L Embryo F1 Cultivar Kitaake x Cultivar Nipponbare NKEB2 |
| GSM1093513 |
Oryza Sativa L Endosperm F1 Cultivar Kitaake x Cultivar Nipponbare NKNB2 |
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| Relations |
| BioProject |
PRJNA192671 |
| SRA |
SRP019243 |
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