Comparative Analysis of Small RNA

Small RNAs (siRNAs), important players in gene regulation, comprise 21-24 long nucleotide fragments, that have been most thoroughly studied in Arabidopsis. On the basis of their function and maturation, small RNAs have been categorized into short interfering RNAs (siRNAs) and micro-RNAs (miRNAs), both are involved in gene silencing by targeting complementary mRNA (Bartel 2004). The identification of siRNAs has largely been accomplished by comparative methods, which detect only conserved families of siRNAs (Rajagopalan et al. 2006). Deep sequencing of siRNAs permits the discovery of new and small classes of these molecules (Henderson et al. 2006).

There is remarkable variation in the size of miRNA populations across plant genomes, and the number that are species specific. For example, 114, 164 and 182 miRNAs has been discovered in Arabidopsis, grapevine and rice respectively (Griffiths-Jones 2004; Griffiths-Jones et al. 2006; Jaillon et al. 2007). Microevolution and regulation of miRNAs is an attractive subject for further investigation to explore the nature of miRNAs, their role in gene regulation, and rate of evolution in their target sites.

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