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Roles of Dicer-like Proteins in Rice Phased Small RNA Biogenesis

The Dicer and Dicer-like (DCL) proteins are core components involved in the biogenesis of small RNAs, and are evolutionarily conserved in a diverse set of eukaryotes. Higher plants have evolved multiple DCL proteins to produce and regulate different classes of small RNAs with specialized molecular functions. In rice, numerous genomic clusters are targeted by one of two miRNAs, miR2118 and miR2275, to produce secondary siRNAs of either 21- or 24-nucleotide in a phased manner. The biogenesis requirements or the functions of the phased small RNAs are completely unknown.


To gain insight into the biogenesis and possible functions of the phased small RNAs, scientists in Dr. Xiaofeng Cao’s group from the Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, revealed multiple DCLs involving the biogenesis of these siRNAs using deep-sequencing combined with genetic approaches. Besides processing of trans-acting siRNAs as previously reported, OsDCL4 was founded to be required for 21-nucleotide phased small RNA biogenesis; OsDCL3b, whose function was previously unknown, acts specifically in the processing of 24-nucleotide phased small RNAs. Both sizes phased small RNAs were further confirmed to be the secondary small RNAs which are triggered the initial cleavages by OsDCL1-dependent miR2118 and miR2275, respectively. Expression analysis showed that the trigger miRNAs for 21- and 24-nucleotide phased small RNAs are mainly or exclusively accumulated in rice and maize stamens, suggesting that both sizes of phased small RNAs are preferentially present and play roles in the male reproductive organs.


This work with Dr. Xianwei Song, Pingchuan Li, Jixian Zhai and Ming Zhou as the first author has been online published on The Plant Journal (DOI: 10.1111/j.1365-313X.2011.04805.x). This research was supported by grants from National Basic Research Program of China, National Natural Science Foundation of China, Department of Agriculture of China, the 863 project.



Xiaofeng Cao, Ph.D.

Institute of Genetics and Developmetnal Biology, Chinese Academy of Sciences, Beijing, China.


(Image by Xianwei Song etc.)


Figure. A model of 21- and 24-nucleotide phased small RNA biogenesis in rice.


The trigger precursors are processed by OsDCL1 into 22-nucleotide mature miR2118 and miR2275. The 22-nucleotide triggers can initiate the cleavage of 21- and 24-nucleotide phased small RNA primary transcripts generated by RNA polymerase II (Pol II). Unknown RDR protein(s) may act on the cleavage transcripts to synthesize the second strand to form double-stranded RNAs as substrates for DCLs. OsDCL4 produces 21-nucleotide phased small RNAs and OsDCL3b is responsible for 24-nucleotide phased small maturation.