Growing Diversity of Plant MicroRNAs and MIR-Derived Small RNAs

Abstract

Small, noncoding RNAs are essential regulatory molecules of plant genome. Small RNAs (sRNAs) have been classified on the basis of their biogenesis and mode of action in two major types—microRNAs (miRNAs) and small interfering RNAs (siRNAs). Plant miRNAs are typically 21 nucleotides in length and derive from unique genetic loci (MIR genes). Next-generation sequencing approaches have increased significantly the number of known plant miRNAs and have revealed that MIR genes frequently produce sRNAs, known as miRNA variants, isoforms or isomiRs, which exhibit differences from their corresponding “reference” mature sequences. The main mechanism of action of canonical miRNAs is sequence-specific repression of gene expression on posttranscriptional level. Recent studies have revealed that noncanonical miRNAs and MIR-derived siRNAs (a particular subset of isomiRs) can act as well in sequence-specific transcriptional silencing thus influencing genome function through DNA methylation. Moreover, miRNAs can be regulated by epigenetic alteration such as DNA methylation and histone modifications of MIR genes. Having profound role in genetic and epigenetic control, plant miRNAs, and MIR-derived siRNAs can potentially participate in most developmental processes, plant stress response, and adaptation. In this chapter, we discuss the biogenesis of miRNAs and MIR-derived sRNAs and their regulatory impact on plant gene expression.