Multiple lines of evidence suggest that the mammalian genome is pervasively transcribed. The recent discovery that protein-coding genes comprise only 1% of the genome despite the fact that the majority of the bases are associated with at least one primary transcript led to a new appreciation of the functional significance of noncoding RNAs (Ecker et al. 2012; Sabin et al. 2013). Based mainly on their size, two important classes have been identified: long noncoding and small noncoding RNAs.
MicroRNA Biogenesis and Function
MicroRNAs (miRNAs) are among the best characterised small noncoding RNAs, generated from longer precursors by RNA pol II as primary transcripts with the typical 5' cap structures and poly(A) tails. These primary miRNAs that comprise one or more hairpin structures with the characteristic long stem and a terminal loop are recognised and processed by the microprocessor complex. The RNase III endonuclease Drosha cleaves the double-stranded stem region to generate the precursor miRNA that is then exported to the cytosol. Here, it undergoes a second round of cleavage by another RNase III endonuclease, Dicer, that removes the terminal loop and generates a 20-22 nucleotide double-stranded miRNA complex. Recent evidence suggests that both strands may be stable and function as mature miRNAs (Indolfi and Curcio 2014). Intriguingly, miRNAs biogenesis can be subjected to an autoregulatory feedback loop as is the case for mature let-7 that can induce its own maturation, a critical observation particularly in the diseased heart (Zisoulis et al.
2012). Additionally, using transgenic expression of pre-microRNAs for miR-378 and miR-499 in the heart, it was revealed that these cardiac miRNAs can indirectly regulate several cardiac miRNAs (Matkovich et al. 2013).
MiRNAs exert their function mainly through hybridization to their target mRNAs (Bartel 2009), although binding to DNA in promoter regions has also been reported (Zardo et al. 2012). The mature miRNA strand is loaded to the RNA-induced silencing complex (RISC) by binding to the Argonaute protein (Ago) and directs the complex to its target mRNA. This binding occurs with imperfect complementarity and results in transcript degradation through deadenylation and repression of translation. Although the details of miRNA-mRNA recognition are still elusive, it is thought that the seed region, nucleotides 2-8, shows the strongest affinity and is critical for the interaction.
Most miRNAs display a highly conserved sequence among mammals (Liu and Olson 2010). Their hybridization-based function and the multiplicity of their targets could prevent evolutionary drift and perhaps explain their highly conserved sequence. As far as their function is concerned, miRNAs seem to be an evolutionary tool developed to reinforce system robustness and ensure that gene expression occurs both at desirable levels and with appropriate timing (Inui et al. 2010). MiRNAs are largely considered to be the fine tuners of gene expression that exert mild effects under basal conditions and have more pronounced responses after stress. They form regulatory networks that target multiple effectors of the same signalling pathway and thus elicit system-wide biological responses. Co-targeting miRNA networks that regulate the same transcript are also common (Zampetaki and Mayr 2012). Diverse mechanisms of action have been identified. MiRNAs may facilitate signal mediation and modulation and may participate in both positive and negative feedback loops mediating phenotypic switch or signal resolution (Mendell and Olson 2012).