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The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic.
Nucleic Acids Res. 2017 04 07; 45(6):3460-3472.NA

Abstract

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.

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Authors+Show Affiliations

Cognat V
Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
Morelle G
Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France. Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA6009, Australia.
Megel C
Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
Lalande S
Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
Molinier J
Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
Vincent T
Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
Small I
Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA6009, Australia.
Duchêne AM
Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
Maréchal-Drouard L
Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.

MeSH

ArabidopsisArabidopsis ProteinsArgonaute ProteinsCell NucleusPlant LeavesPlant RootsPlastidsRNARNA, ChloroplastRNA, MitochondrialRNA, TransferRNA, UntranslatedStress, Physiological

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27899576

Citation

Cognat, Valérie, et al. "The Nuclear and Organellar tRNA-derived RNA Fragment Population in Arabidopsis Thaliana Is Highly Dynamic." Nucleic Acids Research, vol. 45, no. 6, 2017, pp. 3460-3472.
Cognat V, Morelle G, Megel C, et al. The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic. Nucleic Acids Res. 2017;45(6):3460-3472.
Cognat, V., Morelle, G., Megel, C., Lalande, S., Molinier, J., Vincent, T., Small, I., Duchêne, A. M., & Maréchal-Drouard, L. (2017). The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic. Nucleic Acids Research, 45(6), 3460-3472. https://doi.org/10.1093/nar/gkw1122
Cognat V, et al. The Nuclear and Organellar tRNA-derived RNA Fragment Population in Arabidopsis Thaliana Is Highly Dynamic. Nucleic Acids Res. 2017 04 7;45(6):3460-3472. PubMed PMID: 27899576.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic. AU - Cognat,Valérie, AU - Morelle,Geoffrey, AU - Megel,Cyrille, AU - Lalande,Stéphanie, AU - Molinier,Jean, AU - Vincent,Timothée, AU - Small,Ian, AU - Duchêne,Anne-Marie, AU - Maréchal-Drouard,Laurence, PY - 2016/05/06/received PY - 2016/10/27/accepted PY - 2016/12/3/pubmed PY - 2017/8/15/medline PY - 2016/12/1/entrez SP - 3460 EP - 3472 JF - Nucleic acids research JO - Nucleic Acids Res VL - 45 IS - 6 N2 - 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. SN - 1362-4962 UR - https://www.unboundmedicine.com/medline/citation/27899576/The_nuclear_and_organellar_tRNA_derived_RNA_fragment_population_in_Arabidopsis_thaliana_is_highly_dynamic_ L2 - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1122 DB - PRIME DP - Unbound Medicine ER -