Regulation of rice root development by a retrotransposon acting as a microRNA sponge

Abstract
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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

The following previously published data sets were used

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Article and author information

Author details

Jungnam Cho

University of Cambridge, Sainsbury Laboratory, Cambridge, United Kingdom

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4078-7763
Jerzy Paszkowski

University of Cambridge, The Sainsbury Laboratory, Cambridge, United Kingdom

For correspondence
jerzy.paszkowski@slcu.cam.ac.uk

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1378-5666

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

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.