The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabid...

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Published in:Nucleic acids research 2017-04, Vol.45 (6), p.3460-3472
Main Authors: Cognat, Valérie, Morelle, Geoffrey, Megel, Cyrille, Lalande, Stéphanie, Molinier, Jean, Vincent, Timothée, Small, Ian, Duchêne, Anne-Marie, Maréchal-Drouard, Laurence
Format: Article
Language:English
Subjects:
Arabidopsis - genetics
Arabidopsis - metabolism
Arabidopsis Proteins - metabolism
Argonaute Proteins - metabolism
Cell Nucleus - genetics
Cell Nucleus - metabolism
Plant Leaves - genetics
Plant Leaves - metabolism
Plant Roots - genetics
Plant Roots - metabolism
Plastids - metabolism
RNA
RNA - metabolism
RNA, Chloroplast - metabolism
RNA, Mitochondrial
RNA, Transfer - chemistry
RNA, Transfer - metabolism
RNA, Untranslated - chemistry
RNA, Untranslated - metabolism
Stress, Physiological
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Summary:In the expanding repertoire of small noncoding RNAs (ncRNAs), tRNA-derived RNA fragments (tRFs) have been identified in all domains of life. Their existence in plants has been already proven but no detailed analysis has been performed. Here, short tRFs of 19-26 nucleotides were retrieved from Arabidopsis thaliana small RNA libraries obtained from various tissues, plants submitted to abiotic stress or fractions immunoprecipitated with ARGONAUTE 1 (AGO1). Large differences in the tRF populations of each extract were observed. Depending on the tRNA, either tRF-5D (due to a cleavage in the D region) or tRF-3T (via a cleavage in the T region) were found and hot spots of tRNA cleavages have been identified. Interestingly, up to 25% of the tRFs originate from plastid tRNAs and we provide evidence that mitochondrial tRNAs can also be a source of tRFs. Very specific tRF-5D deriving not only from nucleus-encoded but also from plastid-encoded tRNAs are strongly enriched in AGO1 immunoprecipitates. We demonstrate that the organellar tRFs are not found within chloroplasts or mitochondria but rather accumulate outside the organelles. These observations suggest that some organellar tRFs could play regulatory functions within the plant cell and may be part of a signaling pathway.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkw1122