Abstract: The production of small RNAs (sRNAs) from phased positions set by microRNA-directed cleavage of trans-acting-siRNA-producing locus (TAS) transcript has been characterized extensively; however, the production of sRNAs from non-phased positions remains unknown. We report three cis-cleavages that occurred in TAS3 transcripts in Vitis vinifera, by combining high-throughput sRNA deep sequencing information with evolutional conservation and genome-wide RNA degradome analysis. The three cis-cleavages can be deciphered to generate an orderly cleavage cascade, and can also produce distinct phasing patterns. Each of the patterns, either upstream or downstream of the cis-cleaved position, had a set of sRNAs arranged in 21-nucleotide increments. Part of the cascading cis-cleavages was also conserved in Arabidopsis thaliana. Our results will enhance the understanding of the production of sRNAs from non-phased positions that are not set by microRNA-directed cleavage.
Keywords: trans-acting siRNA; cis-cleavage; ta-siRNA-producing locus; miRNA
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Zhang, C.; Li, G.; Wang, J.; Zhu, S.; Li, H. Cascading cis-Cleavage on Transcript from trans-Acting siRNA-Producing Locus 3. Int. J. Mol. Sci. 2013, 14, 14689-14699.
Zhang C, Li G, Wang J, Zhu S, Li H. Cascading cis-Cleavage on Transcript from trans-Acting siRNA-Producing Locus 3. International Journal of Molecular Sciences. 2013; 14(7):14689-14699.
Zhang, Changqing; Li, Guangping; Wang, Jin; Zhu, Shinong; Li, Hailing. 2013. "Cascading cis-Cleavage on Transcript from trans-Acting siRNA-Producing Locus 3." Int. J. Mol. Sci. 14, no. 7: 14689-14699.