Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome-wide identification of small RNA targets in rice


ABSTRACT: MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. Most miRNA targets in Arabidopsis are validated, but those in rice are yet to be characterized. To identify transcriptome-wide small RNA targets in rice, we generated 20-nt small cDNA library and obtained nearly 40 million reads. Sequence analysis yielded 11,552,007 unique reads that can be perfectly mapped to the rice genome. Sequence analysis not only found homologous targets for conserved miRNAs but also many novel targets. Besides miRNA atregts, 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. Keywords: high throughout sequencing of rice degradome Identify transcriptome-wide small RNA targets in rice

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Ramanjulu Sunkar 

PROVIDER: E-GEOD-17398 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptome-wide identification of microRNA targets in rice.

Li Yong-Fang YF   Zheng Yun Y   Addo-Quaye Charles C   Zhang Li L   Saini Ajay A   Jagadeeswaran Guru G   Axtell Michael J MJ   Zhang Weixiong W   Sunkar Ramanjulu R  

The Plant journal : for cell and molecular biology 20100226 5


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 targ  ...[more]

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