Reference "Identification and characterization of endogenous small interfering RNAs from rice"

Reference ID

11276

Title

Identification and characterization of endogenous small interfering RNAs from rice

Source

Nucleic acids research, 2005, vol. 33, pp. 4443-4454

Authors (3)

Sunkar-R	Girke-T
Zhu-J-K

Abstract

RNA silencing-mediated small interfering RNAs (siRNAs) and microRNAs (miRNAs)
have diverse natural roles, ranging from regulation of gene expression and
heterochromatin formation to genome defense against transposons and viruses.
Unlike miRNAs, endogenous siRNAs are generally not conserved between species;
consequently, their identification requires experimental approaches. Thus far,
endogenous siRNAs have not been reported from rice, which is a model species for
monocotyledonous plants. We identified a large set of putative endogenous siRNAs
from root, shoot and inflorescence small RNA cDNA libraries of rice. Most of
these siRNAs are from intergenic regions, although a substantial proportion
(22%) originates from the introns and exons of protein-coding genes. Northern
and RT-PCR analysis revealed that the expression of some of the siRNAs is tissue
specific or developmental stage specific. A total of 25 transposons and 21 protein-
coding genes were predicted to be cis-targets of some of the siRNAs. Based on
sequence homology, we also predicted 111 putative trans-targets for 44 of the
siRNAs. Interestingly, approximately 46% of the predicted trans-targets are
transposable elements, which suggests that endogenous siRNAs may play an
important role in the suppression of transposon proliferation. Using RNA ligase-mediated-
5' rapid amplification of cDNA end assays, we validated three of the predicted
targets and provided evidence for both cis- and trans-silencing of target genes
by siRNAs-guided mRNA cleavage.