In turn the RISC complex regulates specific target mRNAs, usually by cleavage at the miRNA complementary sequence, ,. Shortly after this, the single-stranded miRNA or miRNA* is incorporated into the RNA-induced silencing complex (RISC). The duplex is then methylated by HEN1 and exported to the cytoplasm by a protein called HASTY, an exportin-5 homologue. This hairpin is further cleaved to excise a double stranded miRNA/miRNA* fragment from the stem of the hairpin. Pri-miRNAs that are generated from miRNA genes in the nucleus are then cleaved by Dicer-like1 nuclease (DCL1) to produce a precursor (pre-miRNA) that folds into a hairpin structure. Mature miRNAs are processed from long primary transcripts (pri-miRNAs) in a multistep manner. They act as post-transcriptional regulators in gene expression via target specific cleavage and translational repression –. Plant miRNAs have been shown to play a critical role in diverse biological processes including growth, development, adaptation to biotic and abiotic stresses, signal transduction and protein degradation as well as their own biogenesis –. MicroRNAs (miRNAs), a class of short (∼21 nt) non-coding, single stranded RNAs, are highly conserved across plant species. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). In total, 14 of the predicted miRNAs were identified in wheat for the first time. In silico and structural analyses revealed a total of 55 miRNAs 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow-sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression.
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