IntroductionMicroRNAs (miRNAs) are endogenous, small, noncoding RNA molecules playing crucial roles in the regulation of gene expression at the post-transcriptional level in eukaryotes and viruses (Carrington and Ambros 2003;Bartel 2004;Schwab et al. 2005;). These regulatory small RNA molecules achieve their roles through sequence-specific interactions with complementary sites of target mRNA that lead to their degradation (cleavage) or translational repression. Plant miRNAs are approximately 21-24 nucleotides in length, generally having a high degree of complementarity (nearperfect) between miRNAs and their targets, whereas animal miRNAs usually display partial complementarities to their targets; however, that is not the only difference between plant and animal miRNAs (Millar and Waterhouse 2005;Axtell et al. 2011). Although miRNAs share similarities in general, plant pre-miRNAs have larger and more variable stem-loop structures. Mature plant miRNAs often recognize a single target site in the coding region, pair their target sites with near-perfect complementarity, and guide the mRNA to cleavage, suggesting that plant miRNAs may act like siRNAs due to this specificity (Yang et al. 2007). To date, a total of 21,643 mature miRNAs have been identified from 168 species including viruses, a filamentous brown alga (Ectocarpus siliculosus), a diatome (Phaeodactylum tricornutum), a soil-living amoeba (Dictyostelium discoideum), a green alga (Chlamydomonas reinhardtii), plants, and animals. Identified miRNAs have been deposited in the publicly available miRNA database (miRBase v18 release November 2011; http://www. mirbase.org) (Kozomara and Griffiths-Jones 2011). Now, totally 4014 miRNAs belonging to 52 plant species have been loaded since the discovery of miRNAs in plants in (Park et al. 2002Reinhart et al. 2002).
Biogenesis of plant miRNAThe miRNAs are expressed from their own genes located in the intergenic (between protein-coding genes) or intragenic region (within protein-coding genes, in an exonic or intronic manner) on the chromosomes (Lagos-Quintana et al. 2001;Wang and Blelloch 2009). In plants, most miRNA genes are intergenic and transcribed individually from their own region, but a few genes are organized into polycistronic transcription units and cotranscribed from a single promoter at the end of a miRNA gene cluster (Bartel 2004;He and Hannon 2004;Voinnet 2009). It has been also reported that most miRNA genes in plants and animals have TATA box motifs upstream of their transcription start sites (TSSs), which are transcribed, 3´-poly-adenylated, and 5´ capped by RNA Polymerase II (POL II) like most protein-coding genes (Houbaviy et al. 2005;Xie et al. 2005;Megraw et al. 2006). Biogenesis of plant miRNAs requires a multiple biological process Abstract: MicroRNAs (miRNAs) are small, endogenously expressed, and nonprotein coding RNAs that regulate gene expression via post-transcriptional inhibition and cleavage. To date, several plant miRNAs have been identified via direct cloning, high-throughput sequencing, an...