Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice
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ORIGINAL PAPER
Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice Fangqian Ou-Yang & Qing-Jun Luo & Yue Zhang & Casey R. Richardson & Yingwen Jiang & Christopher D. Rock
Received: 10 October 2012 / Revised: 23 January 2013 / Accepted: 4 February 2013 / Published online: 19 February 2013 # Springer-Verlag Berlin Heidelberg 2013
Abstract microRNAs (miRNAs) are a class of small RNAs (sRNAs) of ∼21 nucleotides (nt) in length processed from foldback hairpins by DICER-LIKE1 (DCL1) or DCL4. They regulate the expression of target mRNAs by base pairing through RNA-induced silencing complex (RISC). In the RISC, ARGONAUTE1 (AGO1) is the key protein that cleaves miRNA targets at position ten of a miRNA:target duplex. The authenticity of many annotated rice miRNA hairpins is under debate because of their homology to repeat sequences. Some of them, like miR1884b, have been removed from the current release of miRBase based on incomplete information. In this study, we investigated the association of transposable element Fangqian Ou-Yang and Qing-Jun Luo contributed equally to this work. Electronic supplementary material The online version of this article (doi:10.1007/s10142-013-0313-8) contains supplementary material, which is available to authorized users. F. Ou-Yang : Q.-J. Luo : C. R. Richardson : Y. Jiang : C. D. Rock (*) Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA e-mail: [email protected] Y. Zhang Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA Present Address: F. Ou-Yang Division of Biostatistics, University of Texas Health Science Center School of Public Health, 1200 Herman Pressler, Houston, TX 77030, USA Present Address: Q.-J. Luo : Y. Zhang Department of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
(TE)-derived miRNAs with typical miRNA pathways (DCL1/4- and AGO1-dependent) using publicly available deep sequencing datasets. Seven miRNA hairpins with 13 unique sRNAs were specifically enriched in AGO1 immunoprecipitation samples and relatively reduced in DCL1/4 knockdown genotypes. Interestingly, these species are ∼21-nt long, instead of 24-nt as annotated in miRBase and the literature. Their expression profiles meet current criteria for functional annotation of miRNAs. In addition, diagnostic cleavage tags were found in degradome datasets for predicted target mRNAs. Most of these miRNA hairpins share significant homology with miniature inverted-repeat transposable elements, one type of abundant DNA transposons in rice. Finally, the root-specific production of a 24-nt miRNA-like sRNA was confirmed by RNA blot for a novel EST that maps to the 3′-UTR of a candidate pseudogene showing extensive sequence homology to miR1884b hairpin. Our data are consistent with the hypothesis that TEs can serve as a driving force for the evolution of some MIRNAs, where co-opting of DICER-LIKE1/4 processing and integration into AGO1 could exapt transcribed TEass
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