Translational repression by a miniature inverted-repeat transposable element in the 3\u2032 untranslated region

Jianqiang Shen,Kabin Xie,Fang Xiong,Lizhong Xiong,Juhong Liu,Jinghua Xiao,Xianghua Li,Feng Xing

doi:10.1038/ncomms14651

Jianqiang Shen, Kabin Xie + Show 6 more

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https://doi.org/10.1038/ncomms14651

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Journal: Nature Communications	Publication Date: Mar 3, 2017
Citations: 65	License type: open-access

Affiliation: Huazhong Agricultural University

Abstract

Transposable elements constitute a substantial portion of eukaryotic genomes and contribute to genomic variation, function, and evolution. Miniature inverted-repeat transposable elements (MITEs), as DNA transposons, are widely distributed in plant and animal genomes. Previous studies have suggested that retrotransposons act as translational regulators; however, it remains unknown how host mRNAs are influenced by DNA transposons. Here we report a translational repression mechanism mediated by a stowaway-like MITE (sMITE) embedded in the 3′-untranslated region (3′-UTR) of Ghd2, a member of the CCT (CONSTANS [CO], CO-LIKE and TIMING OF CAB1) gene family in rice. Ghd2 regulates important agronomic traits, including grain number, plant height and heading date. Interestingly, the translational repression of Ghd2 by the sMITE mainly relies on Dicer-like 3a (OsDCL3a). Furthermore, other MITEs in the 3′-UTRs of different rice genes exhibit a similar effect on translational repression, thus suggesting that MITEs may exert a general regulatory function at the translational level.

Highlights

Transposable elements constitute a substantial portion of eukaryotic genomes and contribute to genomic variation, function, and evolution
Neither the Ghd[2] mRNA nor the Ghd[2] protein level showed significant differences between the siRNA overexpression lines and the WT lines (Supplementary Fig. 5). These results suggest that the translational repression may not be related to the abundance of the siRNAs derived from the stowaway-like MITE (sMITE)
In animal and plant genomes, Miniature inverted-repeat transposable elements (MITEs) constitute 0.32–15.8% of the genomic sequences[54]. These MITEs are found in untranslated regions of mRNA including 50-UTRs, introns and 30-UTRs27

Summary

Introduction

Transposable elements constitute a substantial portion of eukaryotic genomes and contribute to genomic variation, function, and evolution. Miniature inverted-repeat transposable elements (MITEs), as DNA transposons, are widely distributed in plant and animal genomes. Previous studies have suggested that retrotransposons act as translational regulators; it remains unknown how host mRNAs are influenced by DNA transposons. TEs are classified as retrotransposons (Class I) intermediated by RNAs, and DNA transposons (Class II) that move directly in a ‘cut and paste’ mode[3]. Other studies support that MITEs could regulate gene transcription on a genome-wide scale[31,32] It remains unknown whether MITEcontained transcripts could regulate the host gene expression at the translational level in plants. We demonstrate that a stowaway-like MITE represses the protein synthesis of an agronomically important gene Ghd[2], which controls grain number, plant height and heading date in rice (Oryza sativa). Our findings reveal an unreported role of DNA transposons in the regulation of gene expression at the translational level

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