Description:
<jats:p>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 <jats:italic>Arabidopsis</jats:italic> npcRNAs. Fourteen npcRNAs were antisense to protein-coding mRNAs, suggesting <jats:italic>cis</jats:italic>-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 <jats:italic>dcl1</jats:italic> mutant but does not appear to produce <jats:italic>trans</jats:italic>-acting siRNA or miRNA. Additionally, another npcRNA was the precursor of miR869 and shown to be up-regulated in <jats:italic>dcl4</jats:italic> but not in <jats:italic>dcl1</jats:italic> 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 <jats:italic>Arabidopsis</jats:italic> 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.</jats:p>