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E-GEOD-22763 - DCL4-Dependent Clusters of PhasiRNAs in Rice

Status
Released on 29 March 2012, last updated on 2 June 2014
Organism
Oryza sativa
Samples (6)
Protocols (4)
Description
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. 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).
Experiment type
RNA-seq of non coding RNA 
Contacts
xiaofeng cao <xfcao@genetics.ac.cn>, Bin Liu, Blake C Meyers, Chengcai Chu, Chunyan Liu, Dong-Hoon Jeong, Jixian Zhai, Lijia Ma, Mayumi Nakano, Ming Zhou, Pamela J Green, Pingchuan Li, Shouyun Cao, Xianwei Song, Xiaofeng Cao, Xiu-jie Wang
Citation
Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Song X, Li P, Zhai J, Zhou M, Ma L, Liu B, Jeong DH, Nakano M, Cao S, Liu C, Chu C, Wang XJ, Green PJ, Meyers BC, Cao X. , PMID:21973320
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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