Regulation of rice root development by a retrotransposon acting as a microRNA sponge
- Sainsbury Laboratory, United Kingdom
- The Sainsbury Laboratory, United Kingdom
Abstract
It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.
Data availability
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rice whole transcriptome surveyed by RNA-Seq and Paired-end technologyPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE16631).
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RNA-sequencing Reveals Previously Unannotated Protein-coding and miRNA-coding Genes Expressed in Aleurone Cells of Rice SeedPublicly available at the NCBI Gene Expression Omnibus (accession no: SRP028376).
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Rapid diversification of five Oryza AA genomes associated with rice adaptationPublicly available at the NCBI Gene Expression Omnibus (accession no: PRJNA264480).
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Rapid diversification of five Oryza AA genomes associated with rice adaptationPublicly available at the NCBI Gene Expression Omnibus (accession no: PRJNA264485).
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Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domesticationPublicly available at the DNA Data Bank of Japan (accession no: SRP070627).
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Transcriptome Analysis of Rice Root Heterosis by RNA-SeqPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE41797).
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A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profilingPublicly available at the NCBI Gene Expression Omnibus (accession no: PRJNA314076).
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Identification of small RNAs in rice AGO1 complexes and their targetsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE18251).
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Endogenous small RNAs of meristematic and a terminally differentiated tissue of ricePublicly available at the NCBI Gene Expression Omnibus (accession no: GSE16350).
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Characterization of AGO1-/AGO4-associated smRNAsPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE28591).
Article and author information
Author details
Funding
European Research Council (322621)
- Jungnam Cho
- Jerzy Paszkowski
Gatsby Charitable Foundation (AT3273/GLE)
- Jerzy Paszkowski
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2017, Cho & Paszkowski
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Regulation of rice root development by a retrotransposon acting as a microRNA sponge
eLife 6:e30038.
https://doi.org/10.7554/eLife.30038
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