ABSTRACT
RNA interference has emerged as a powerful approach to gain knowledge about the role and function of various genes in plants and animals. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are two such small RNAs reported to be involved in silencing of genes involving gene/transcript–target complementarity. Small RNAs were discovered initially based on reverse and forward genetics approached as in Petunia and C. elegans; a number of subsequent discoveries were made based on direct cloning [selective ligation, purification, and sequencing of small RNA generated by dicer (characterized by 5’-mono-Phosphate and 3’-OH)], and now has gathered momentum with the advent of next generation small RNA sequencing technologies coupled with computational/bioinformatics prediction tools (e.g., miRU, miRNATools, findmiRNA), and comparative genomics strategies (e.g., miROrtho). The biogenesis of miRNAs involves single stranded RNA that forms typical hairpin precursors and are derived endogenously from host genome itself. SiRNAs originate from long dsRNAs involving precursors that are derived either from transposons, repeated elements or fromexogenously introduced transgenes or viruses. HEN1, HYL1, dicer/drosha, DCL1, SE, EXP, RdRP (RNA-dependent RNA polymerase), and AGO1, etc. are some of the critical players in biogenesis of miRNA and siRNA and their mutants (dcl1, hen1-1, and hyl1) that affect small RNA biogenesis and accumulation exhibit developmental defects. Small RNAs are reported to be involved in developmental regulation in plants via mRNA degradation, translational repression, and chromatin modification through auto-silencing or hetero-silencing. In plants, some developmental traits regulated by miRNA include seed germination (miR159), leaf development (miR164, miR165), root development (miR160, miR166, miR399), phase change/floral transition (miR156), flower development and timing (miR172), and tuberization (miR172). Small RNAs are also found to be involved in important adaptive roles such as plant responses to different types of biotic and abiotic stress (miR156, miR159, miR167, miR390, miR393, miR398, miR399, and several others). In addition to summarizing the discovery, biogenesis and role of small RNAs in development and adaptation, the chapter also highlights cross-talk between the various pathways involving miRNAs, and siRNA and miRNA.
