ref-type="table"}, [Table S4](#pone.0021330.s008){ref-type="supplementary-material"}), including the locus for the known decoy, IPS1. Although transcripts described as pseudogenes, transposable elements (TE) and "other RNA," as annotated by The Arabidopsis Information Resource (TAIR), are represented, most predicted decoys are within protein-coding transcripts ([Table 1](#pone-0021330-t001){ref-type="table"}). To analyze a distribution of predicted decoys along protein-coding transcripts, we assigned predicted decoy sites from protein-coding genes to 5′ UTR, ORF or 3′ UTR, normalizing the number of decoy sites to the length of the three features. Analysis indicates that decoy sites are predicted as abundantly in UTR regions as ORF regions ([Fig. 7A](#pone-0021330-g007){ref-type="fig"}). Currently, we have not evaluated the impact decoys could have on translation when resident within an ORF. While we identified a significant number of putative decoys, ranging in number of critical mismatches or insertions, the majority belong to a category of decoys with one or two mismatches ([Fig. 7B](#pone-0021330-g007){ref-type="fig"}) which, from our studies, possess a lower miRNA regulatory potential relative to the bulge category of decoys, suggesting that most predicted decoys may function for fine-tuning of miRNA-mediated silencing. One of the limitations of this computational prediction is that the current *Arabidopsis* transcriptome set used in this analysis has only a small number of annotated ncRNAs (detailed in [Methods](#s4){ref-type="sec"}), and so the number of ncRNA transcripts that may function as decoys is very likely underestimated. Validation of predicted endogenous decoys is a next critical step in elucidating the role that miRNA decoys play in genetic regulation in plants.

![Computational prediction of endogenous miRNA decoys in Arabidopsis.\
(**A**) Distribution of predicted decoy sites in 5′ UTR, CDS and 3′ UTR of 286 protein-coding transcripts. If a decoy site spans two regions, i.e., 5′ UTR -