%0 Journal Article
%T Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity
%A H Alexander Ebhardt
%A Amber Fedynak
%A Richard P Fahlman
%J Silence
%D 2010
%I BioMed Central
%R 10.1186/1758-907x-1-12
%X In this paper, we demonstrate that a fifth of annotated A. thaliana miRNAs recorded in miRBase V.14 have stable miRNA isoforms that are one or two nucleotides longer than their respective recorded miRNA. Further, we demonstrate that miRNA isoforms are co-expressed and often show differential argonaute complex association. We postulate that these extensions are caused by differential cleavage of the parent precursor miRNA.Our systematic analysis of A. thaliana miRNAs reveals that miRNA length isoforms are relatively common. This finding not only has implications for miRBase and miRNA annotation, but also extends to miRNA validation experiments and miRNA localization studies. Further, we predict that miRNA isoforms are present in other plant species also.Micro(mi)RNAs are important for gene regulation [1] and for cell fate decisions during development [2]. Aberrant levels of miRNAs are seen in various disease states [3-6]. miRNAs are transcribed from one strand of their genomic loci into a primary miRNA transcript, which folds into a characteristic bulge with stem-loop conformation [7]. In plants, the primary transcript is cleaved by a Dicer-like (DCL) RNase III enzyme, DCL1, into an approximately 19 bp duplex with a two-nucleotide (nt) overhang at either end [8]. Of the two strands forming the duplex, one strand, designated miRNA*, is typically degraded while the other is incorporated into the argonaute (AGO)-containing effector complex [9,10]. Co-immunoprecipitation experiments demonstrate an enrichment of miRNAs in AGO1, whereas AGO2 shows depletion of miRNAs compared with non-immunoprecipitated samples [11].The biological significance of sequence length heterogeneity has been recently identified for a mature miRNA in Arabidopsis thaliana, in which ath-MIR168 is processed as miRNAs of 21 and 22 nucleotides in length from its two genomic loci. Vaucheret demonstrated that reducing the amount of 21 nt miRNA greatly reduces homeostasis and leads to developmental defect
%U http://www.silencejournal.com/content/1/1/12