Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

Abstract

Long non-protein coding RNAs (npcRNA) represent an emerging class of riboregulators, which either act directly in this long form or are processed to shorter miRNA and siRNA. Genome-wide bioinformatic analysis of full-length cDNA databases identified 76 Arabidopsis npcRNAs. Fourteen npcRNAs were antisense to protein-coding mRNAs, suggesting cis-regulatory roles. Numerous 24-nt siRNA matched to five different npcRNAs, suggesting that these npcRNAs are precursors of this type of siRNA. Expression analyses of the 76 npcRNAs identified a novel npcRNA that accumulates in a dcl1 mutant but does not appear to produce trans-acting siRNA or miRNA. Additionally, another npcRNA was the precursor of miR869 and shown to be up-regulated in dcl4 but not in dcl1 mutants, indicative of a young miRNA gene. Abiotic stress altered the accumulation of 22 npcRNAs among the 76, a fraction significantly higher than that observed for the RNA binding protein-coding fraction of the transcriptome. Overexpression analyses in Arabidopsis identified two npcRNAs as regulators of root growth during salt stress and leaf morphology, respectively. Hence, together with small RNAs, long npcRNAs encompass a sensitive component of the transcriptome that have diverse roles during growth and differentiation.[Supplemental material is available online at www.genome.org.]Non-protein coding RNAs (npcRNAs) are a class of RNAs that do not encode proteins, but instead their function lies on the RNA molecule. They are a heterogeneous group and have been divided into different classes according to their length and function. With respect to length, npcRNAs can range from 20 to 27 nucleotides (nt) for the families of microRNAs (miRNAs) and small interfering RNAs (siRNAs), 20-300 nt for small RNAs commonly found as transcriptional and translational regulators, or up to and beyond 10,000 nt for medium and large RNAs involved in other processes, including splicing, gene inactivation, and translation (Costa 2007). We use the term non-protein-coding RNAs instead of noncoding RNAs as every sequence has the potential to be coding, and certain large npcRNAs might encode small oligopeptides, which could be translated under specific conditions as shown for a pentapeptide located inside rRNA, a canonical RNA in Escherichia coli (Tenson et al. 1996). In recent years, numerous novel npcRNA candidates have been identified in a variety of organisms from E. coli to Homo sapiens (Argaman et al. 2001;Storz et al. 2004;Washietl et al. 2005).Several strategies have been employed to detect and discover novel npcRNAs, including both experimental and computational screenings (Huttenhofer et al. 2002). Genomic approaches, such as tiling arrays and systematic sequencing of full-length cDNA libraries, in model organisms have recently revealed that much larger portions of eukaryote transcriptomes represent nonprotein-coding transcripts than previously believed (Okazaki et al. 2002;Numata et al. 2003;Rinn et al. 2003;Ota et al. 2004;Chekanova et al. 2007). Diverse npcRNAs, including a surpris...

Genetic, proteomic and metabolic analysis of the regulation of energy storage in rice seedlings in response to drought

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Evolution and Functional Diversification of MIRNA Genes

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Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

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