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Roles of DCL4 and DCL3b in rice phased small RNA biogenesis
Author(s) -
Song Xianwei,
Li Pingchuan,
Zhai Jixian,
Zhou Ming,
Ma Lijia,
Liu Bin,
Jeong DongHoon,
Nakano Mayumi,
Cao Shouyun,
Liu Chunyan,
Chu Chengcai,
Wang XiuJie,
Green Pamela J.,
Meyers Blake C.,
Cao Xiaofeng
Publication year - 2012
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2011.04805.x
Subject(s) - small rna , trans acting sirna , biology , small interfering rna , rna , small nucleolar rna , dicer , rna silencing , argonaute , microrna , genetics , long non coding rna , microbiology and biotechnology , computational biology , rna interference , gene
Summary Higher plants have evolved multiple proteins in the RNase III family to produce and regulate different classes of small RNAs with specialized molecular functions. In rice ( Oryza sativa ), numerous genomic clusters are targeted by one of two microRNAs (miRNAs), miR2118 and miR2275, to produce secondary small interfering RNAs (siRNAs) of either 21 or 24 nucleotides in a phased manner. The biogenesis requirements or the functions of the phased small RNAs are completely unknown. Here we examine the rice Dicer‐Like (DCL) family, including OsDCL1, ‐3a, ‐3b and ‐4. By deep sequencing of small RNAs from different tissues of the wild type and osdcl4‐1 , we revealed that the processing of 21‐nucleotide siRNAs, including trans‐acting siRNAs (tasiRNA) and over 1000 phased small RNA loci, was largely dependent on OsDCL4. Surprisingly, the processing of 24‐nucleotide phased small RNA requires the DCL3 homolog OsDCL3b rather than OsDCL3a, suggesting functional divergence within DCL3 family. RNA ligase‐mediated 5′ rapid amplification of cDNA ends and parallel analysis of RNA ends (PARE)/degradome analysis confirmed that most of the 21‐ and 24‐nucleotide phased small RNA clusters were initiated from the target sites of miR2118 and miR2275, respectively. Furthermore, the accumulation of the two triggering miRNAs requires OsDCL1 activity. Finally, we show that phased small RNAs are preferentially produced in the male reproductive organs and are likely to be conserved in monocots. Our results revealed significant roles of OsDCL4, OsDCL3b and OsDCL1 in the 21‐ and 24‐nucleotide phased small RNA biogenesis pathway in rice.