TY - JOUR
T1 - Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice
AU - Ou-Yang, Fangqian
AU - Luo, Qing Jun
AU - Zhang, Yue
AU - Richardson, Casey R.
AU - Jiang, Yingwen
AU - Rock, Christopher D.
N1 - Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2013/6
Y1 - 2013/6
N2 - 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.
AB - 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.
KW - ARGONAUTE
KW - DICER-LIKE
KW - MicroRNA
KW - Repeat-associated small RNA
KW - Transposable element
UR - http://www.scopus.com/inward/record.url?scp=84878765666&partnerID=8YFLogxK
U2 - 10.1007/s10142-013-0313-8
DO - 10.1007/s10142-013-0313-8
M3 - Article
C2 - 23420033
AN - SCOPUS:84878765666
VL - 13
SP - 207
EP - 216
JO - Functional and Integrative Genomics
JF - Functional and Integrative Genomics
SN - 1438-793X
IS - 2
ER -