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Molecular phylogeny of miR390-guided trans-acting siRNA genes.pdf

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Molecular phylogeny of miR390-guided trans-acting siRNA genes

ORIGINAL ARTICLE Molecular phylogeny of miR390-guided trans-acting siRNA genes (TAS3) in the grass family Dan Shen ? Sheng Wang ? Huan Chen ? Qian-Hao Zhu ? Chris Helliwell ? Longjiang Fan Received: 13 January 2009 / Accepted: 3 September 2009 Springer-Verlag 2009 Abstract Trans-acting siRNAs (tasiRNAs) are a plant- specific class of 21-nt endogenous siRNAs that function as miRNA-like posttranscriptional negative regulators. Several tasiRNA loci (known as TAS genes) have been characterized to date in rice and Arabidopsis. The TAS3 family is distinguished from other TAS loci by the dual miR390 complementary sites flanking the tasiRNA region and its dependence on ARGONAUTE7. In this study, 55 putative TAS3 genes were identified by database mining and PCR amplification from the grass family. Phylogenetic analysis indicated that several genome/gene duplication events have been involved in the expansion of TAS3 genes while some TAS3 genes might have been lost during evo- lution of the grass family. The role of miR390 target genes in the origin of TAS3 genes are discussed. Keywords Trans-acting siRNA (tasiRNA) TAS3 Poaceae Evolution miR390 Introduction Most eukaryotes contain RNA-based silencing pathways that direct transcriptional and posttranscriptional activities to negatively regulate genes, repetitive/mobile elements, and viruses (Kasschau et al. 2007). Small RNAs play a major role in these pathways. The small RNA population of plants is composed of 20- to 24-nucleotide (nt) microRNAs (miRNAs) and several classes of small interfering RNAs (siRNA), each derived from distinct modes of biogenesis and genomic loci (Rajagopalan et al. 2006). miRNAs and siRNAs are distinguished by the structure of their precur- sors and by their targets. miRNAs are derived from the short, imperfectly paired stem of a much longer foldback transcript by the activity of Dicer or Dicer-like (DCL) ribonucleases and regulate the expression of transcripts with which they may have limite