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GENOME ANALYSIS

Characterization of 43 Non-Protein-Coding mRNA Genes in Arabidopsis, Including the MIR162a-Derived Transcripts^1,[W]

Institut des Sciences du Végétal (J.H., A.B., M.C.) and Centre de Génétique Moléculaire (V.L., M.V., A.L., C.T., Y.A.-C.), Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France

Messenger RNAs that do not contain a long open reading frame (ORF) or non-protein-coding RNAs (npcRNAs) are an emerging novel class of transcripts. Their functions may involve the RNA molecule itself and/or short ORF-encoded peptides. npcRNA genes are difficult to identify using standard gene prediction programs that rely on the presence of relatively long ORFs. Here, we used detailed bioinformatic analyses of expressed sequence tag/cDNA databases to detect a restricted set of npcRNAs in the Arabidopsis (Arabidopsis thaliana) genome and further characterized these transcripts using a combination of bioinformatic and molecular approaches. Compositional analyses revealed strong nucleotide strand asymmetries in the npcRNAs, as well as a biased GC content, suggesting the existence of functional constraints on these RNAs. Thirteen of these transcripts display tissue-specific expression patterns, and three are regulated in conditions affecting root architecture. The npcRNA 78 gene contains the miR162 sequence in an alternative intron and corresponds to the MIR162a locus. Although DICER-LIKE 1 (DCL1) mRNA is known to be regulated by miR162-guided cleavage, its level does not change in a mir162a mutant. Alternative splicing of npcRNA 78 leads to several transcript isoforms, which all accumulate in a dcl1 mutant. This suggests that npcRNA 78 is a genuine substrate of DCL1 and that splicing of this microRNA primary transcript and miR162 processing are competitive nuclear events. Our results provide new insights into Arabidopsis npcRNA biology and the potential roles of these genes.

² These authors contributed equally to the paper.

³ Present address: Laboratoire de Biologie du Développement des Plantes, Département d'Ecophysiologie Végétale et de Microbiologie, Commissariat à l'Energie Atomique, Cadarache, 13108 Saint Paul Lez Durance, France.

⁴ Present address: Institut de Biologie et Chimie des Protéines-LBRS, 7 Passage du Vercors, 69367 Lyon cedex 7, France.

⁵ Present address: TAGC ERM206 Case 928, 163 Avenue de Luminy, 13288 Marseille cedex 09, France.

⁶ Present address: Unité de Recherche en Génomique Végétale, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, 2 Rue Gaston Crémieux, CP 5708, 91057 Evry cedex, France.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Martin Crespi (crespi{at}isv.cnrs-gif.fr).

^[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.073817.

^* Corresponding author; e-mail crespi{at}isv.cnrs-gif.fr; fax 33–1–69823695.

Received November 4, 2005; returned for revision February 2, 2006; accepted February 2, 2006.

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