title: The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic.
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.
authors.affiliation: Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Cognat
authors.affiliation: 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.
authors.forename: Geoffrey
authors.initials: G
authors.lastname: Morelle
authors.affiliation: Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
authors.forename: Cyrille
authors.initials: C
authors.lastname: Megel
authors.affiliation: Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Lalande
authors.affiliation: Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Molinier
authors.affiliation: Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
authors.forename: Timothée
authors.initials: T
authors.lastname: Vincent
authors.affiliation: Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA6009, Australia.
authors.forename: Ian
authors.initials: I
authors.lastname: Small
authors.affiliation: Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Duchêne
authors.affiliation: Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Maréchal-Drouard
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism; D060565:Argonaute Proteins / Q000378:metabolism; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism*; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D018087:Plastids / Q000378:metabolism; D012313:RNA / Q000378:metabolism; D018747:RNA, Chloroplast / Q000378:metabolism; D000077278:RNA, Mitochondrial; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism*; D022661:RNA, Untranslated / Q000737:chemistry / Q000378:metabolism*; D013312:Stress, Physiological
chemical_list: C117457:AGO1 protein, Arabidopsis; D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D018747:RNA, Chloroplast; D000077278:RNA, Mitochondrial; D022661:RNA, Untranslated; D012313:RNA; D012343:RNA, Transfer