Degradome sequencing reveals endogenous small
RNA targets in rice ( Oryza sativa L. ssp . indica )

doi:10.1007/s11515-010-0007-8

Front. Biol.

2010, Vol. 5

Issue (1) : 67-90 https://doi.org/10.1007/s11515-010-0007-8

Research articles

Degradome sequencing reveals endogenous small RNA targets in rice ( Oryza sativa L. ssp . indica )

Ming ZHOU¹,Lianfeng GU¹,Pingchuan LI¹,Xianwei SONG¹,Liya WEI¹,Zhiyu CHEN¹,Xiaofeng CAO², ³,

1.State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China；Graduate School of the Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China; 2.State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; 3.2010-03-15 9:36:58;

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Abstract MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA (sRNA) targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). One hundred and seventy-seven transcripts targeted by a total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORs (ARFs) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5′ rapid amplification of cDNA ends (RLM 5′-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.

Keywords Degradome miRNA ta-siRNA small RNA targets rice

Issue Date: 01 February 2010

Cite this article:

Ming ZHOU,Lianfeng GU,Pingchuan LI, et al. Degradome sequencing reveals endogenous small RNA targets in rice ( Oryza sativa L. ssp . indica )[J]. Front. Biol., 2010, 5(1): 67-90.

URL:

https://academic.hep.com.cn/fib/EN/10.1007/s11515-010-0007-8
https://academic.hep.com.cn/fib/EN/Y2010/V5/I1/67

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