NDLI: Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice

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Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice

Content Provider	Springer Nature Link
Author	Ou Yang, Fangqian Luo, Qing Jun Zhang, Yue Richardson, Casey R. Jiang, Yingwen Rock, Christopher D.
Copyright Year	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 (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 TE-associated hairpins into typical miRNA pathways.
Starting Page	207
Ending Page	216
Page Count	10
File Format	PDF
ISSN	1438793X
Journal	Functional & Integrative Genomics
Volume Number	13
Issue Number	2
e-ISSN	14387948
Language	English
Publisher	Springer-Verlag
Publisher Date	2013-02-19
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	MicroRNA Transposable element Repeat-associated small RNA ARGONAUTE DICER-LIKE Cell Biology Plant Genetics & Genomics Microbial Genetics and Genomics Biochemistry Bioinformatics Animal Genetics and Genomics
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice