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

  1. Jungnam Cho
  2. Jerzy Paszkowski  Is a corresponding author
  1. Sainsbury Laboratory, United Kingdom
  2. The Sainsbury Laboratory, United Kingdom


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
    1. Wei L
    2. Gu L
    3. Cao X
    (2014) Control of agricultural traits by hc-siRNA associated MITEs in rice
    Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE50778).
    1. Zhai R
    2. Cheng S
    (2013) Transcriptome Analysis of Rice Root Heterosis by RNA-Seq
    Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE41797).

Article and author information

Author details

  1. Jungnam Cho

    University of Cambridge, Sainsbury Laboratory, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4078-7763
  2. Jerzy Paszkowski

    University of Cambridge, The Sainsbury Laboratory, Cambridge, United Kingdom
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1378-5666


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.

Reviewing Editor

  1. Christian S. Hardtke, University of Lausanne, Switzerland

Publication history

  1. Received: June 29, 2017
  2. Accepted: August 21, 2017
  3. Accepted Manuscript published: August 26, 2017 (version 1)
  4. Version of Record published: September 14, 2017 (version 2)


© 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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  1. Jungnam Cho
  2. Jerzy Paszkowski
Regulation of rice root development by a retrotransposon acting as a microRNA sponge
eLife 6:e30038.

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