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| Status |
Public on Mar 30, 2012 |
| Title |
DCL4-Dependent Clusters of PhasiRNAs in Rice. |
| Organism |
Oryza sativa |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
The osdcl4-1 mutant exhibits much severer developmental defects than dcl4 in Arabidopsis, suggesting that Os DCL4 may process broader substrates in rice. By deep sequencing of small RNAs from different tissues of wild types and osdcl4-1, we revealed that 21-nucleotide siRNAs were largely dependent on Os DCL4. Besides several tasiRNA loci reported in Arabidopsis and rice, over one thousand 21-nucleotide and several dozen 24-nucleotide phased siRNA (phasiRNA) clusters were identified in panicles but not in seedlings and grains. Further analyses identified two conserved 22-nucleotide motifs among the cleavage sites of the 21- and 24- phasiRNA loci, and the cleavage sites of over 90% of 21- and 24-nucleotide phasing clusters were confirmed by PARE/degradome analysis from 93-11 panicles. MiR2118 and miR2275, expressed specifically in panicles, were predicted to trigger cleavages at 21- and 24-nucleotide phasiRNA clusters, respectively. The triggers of phasiRNAs are more dependent on Os DCL4 than Os DCL1. Furthermore, the processing of 21-nucleotide phasiRNAs was largely Os DCL4-dependent, whereas the processing of 24-nucleotide phasiRNAs was slightly affected by Os DCL4, but not by Os DCL3a and Os DCL1. Our results revealed distinct roles of Os DCL4 in a novel 21- and 24-nucleotide phasiRNA biogenesis pathway in rice.
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| Overall design |
Six small RNA libraries were constructed from seedlings and panicles of 93-11 (a wild-type Indica rice variety) and osdcl4-1, as well as those from Nipponbare panicles and seedlings (a wild-type Japonica rice variety).
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| Contributor(s) |
Li P, Song X, Zhai J, Zhou M, Ma L, Liu B, Jeong D, Nakano M, Cao S, Liu C, Chu C, Wang X, Green PJ, Meyers BC, Cao X |
| Citation(s) |
21973320 |
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| Submission date |
Jul 06, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
xiaofeng cao |
| E-mail(s) |
xfcao@genetics.ac.cn
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| Phone |
86-10-64869203
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| Organization name |
Institute of Genetics and Developmental Biology
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| Department |
State Key Laboratory of Plant Genomics
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| Street address |
West Lincui Road, Chaoyang District
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platforms (1) |
| GPL9147 |
Illumina Genome Analyzer (Oryza sativa) |
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| Samples (6)
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| GSM562942 |
Oryza sativa L. ssp. indica 93-11 seedlings sRNA |
| GSM562943 |
Oryza sativa L. ssp. indica 93-11 panicles sRNA |
| GSM562944 |
Oryza sativa L. ssp. indica osdcl4-1 seedlings sRNA |
| GSM562945 |
Oryza sativa L. ssp. indica osdcl4-1 panicles sRNA |
| GSM562946 |
Oryza sativa L. ssp. japonica Nipponbare seedlings sRNA |
| GSM562947 |
Oryza sativa L. ssp. japonica Nipponbare panicles sRNA |
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| Relations |
| SRA |
SRP002899 |
| BioProject |
PRJNA128249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE22763_RAW.tar |
662.9 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE22763_readme.txt.gz |
183 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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