Transcriptome-wide identification of microRNA targets in rice

被引:344
作者
Li, Yong-Fang [1 ]
Zheng, Yun [2 ]
Addo-Quaye, Charles [3 ]
Zhang, Li [1 ]
Saini, Ajay [1 ]
Jagadeeswaran, Guru [1 ]
Axtell, Michael J. [3 ,4 ]
Zhang, Weixiong [2 ,5 ]
Sunkar, Ramanjulu [1 ]
机构
[1] Oklahoma State Univ, Dept Biochem & Mol Biol, Stillwater, OK 74078 USA
[2] Washington Univ, Dept Comp Sci & Engn, St Louis, MO 63130 USA
[3] Penn State Univ, Dept Biol, University Pk, PA 16802 USA
[4] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
[5] Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA
基金
美国国家科学基金会;
关键词
degradome; miRNAs; miRNA targets; post-transcriptional gene regulation; rice; STRESS-RESPONSIVE MICRORNAS; SMALL RNAS; TRANSLATIONAL INHIBITION; SUPEROXIDE-DISMUTASE; REGULATORY ROLES; SIRNA BIOGENESIS; MESSENGER-RNAS; ARABIDOPSIS; EXPRESSION; GENES;
D O I
10.1111/j.1365-313X.2010.04187.x
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. Currently, miRBase (version 13) lists 142 and 353 miRNAs from Arabidopsis and rice (Oryza sativa), respectively. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. In contrast with the well-characterized miRNA targets that are cleaved in Arabidopsis, only a few such targets have been confirmed in rice. To identify small RNA targets in rice, we applied the 'degradome sequencing' approach, which globally identifies the remnants of small RNA-directed target cleavage by sequencing the 5' ends of uncapped RNAs. One hundred and sixty targets of 53 miRNA families (24 conserved and 29 rice-specific) and five targets of TAS3-small interfering RNAs (siRNAs) were identified. Surprisingly, an additional conserved target for miR398, which has not been reported so far, has been validated. Besides conserved homologous transcripts, 23 non-conserved genes for nine conserved miRNAs and 56 genes for 29 rice-specific miRNAs were also identified as targets. Besides miRNA targets, the rice degradome contained fragments derived from MIRNA precursors. A closer inspection of these fragments revealed a unique pattern distinct from siRNA-producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants.
引用
收藏
页码:742 / 759
页数:18
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