Biogenesis of MiRNAs

Plant miRNAs are typically encoded by miRNA genes (or MIRNA locus). In most cases, they exist in inter-regions of protein-coding genes and transcribe independently (Voinnet 2009). Biogenesis of miRNA begins with transcription at a MIRNA locus by RNA Polymerase II (Pol II) and produce 5′-capped and 3′-polyadenylated primary microRNA transcripts (pri-miRNAs) (Aukerman and Sakai 2003; Kurihara and Watanabe 2004; Voinnet 2009).

The pri-miRNAs contain imperfect stem-loop structure from which precursors (pre-miRNAs) are excised through the RNase III enzyme DICER LIKE 1 (DCL1) and several other proteins (Park et al. 2002; Reinhart et al. 2002; Voinnet 2009). The factors involved in the initial processing of pri — miRNAs in model plant Arabidopsis thanlina include subunits of the nuclear cap-binding complex (CBC), CBP20 and CBP80; SERRATE (SE), a C2H2- type zinc finger domain-containing protein; HYPONASTIC LEAVES 1 (HYL1), a member of dsRNA-binding protein family, and other components (Bartel 2009; Chen 2009; Chuck et al. 2009; Poethig 2009; Voinnet 2009; Zhu et al. 2009). A key feature of a pri-miRNA is that it is self-complementary and capable of forming the characteristic fold-back hairpin-like structure recognized by DCL1. Processing of a pri-miRNA by the DCL1 complex releases the precursor miRNAs (pre-miRNAs) which contain the stem-loop structure (Voinnet 2009; Zhu et al. 2009).

The pre-miRNAs are further processed by the DCL1 protein complex to generate a small RNA duplex consisting of a miRNA and its passenger strand (miRNA*). The duplex is exported into the cytoplasm by HASTY and methylated at the 3′ end by HEN1 (Park et al. 2002; Yu et al. 2005). One strand functions as the mature miRNA and is incorporated into the RNA — Induced Silencing Complex (RISC) to target mRNAs. The other strand, miRNA* is usually degraded, although some miRNA*s have been reported to be functional under certain conditions (Zhang et al. 2011).

Plant miRNAs recognize their targets through near-perfect complementarity to direct RISC-mediated cleavage, although in some cases translational inhibition and DNA methylation can be the mode of action of miRNA-mediated gene silencing (Chen 2004; Brodersen et al. 2008; Wu et al. 2010).