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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
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