Abstract

microRNAs (miRNAs) are a group of ∼22-nucleotide endogenous non-coding RNAs identified in both animal and plant genomes. miRNAs play an important regulatory role in almost all fundamental processes and are involved in cellular alterations and diverse disease progression. miRNA can regulate a target gene at both the transcriptional level and the post-transcriptional level. In miRNA directed transcriptional gene silencing, miRNAs can induce heterochromatin formation via binding to the promoter regions of their target genes. In post-transcriptional gene regulation, miRNAs regulate gene expression via attenuating protein translation or promoting mRNA degradation. Since the discovery of this small regulator, bioinformatics methods have become standard techniques to elucidate hierarchical functions of miRNAs in gene regulatory networks. In this chapter, we briefly compare the characteristics for metazoans and plant miRNAs in terms of genomic features, miRNA biogenesis and miRNA target recognition. We then focus on the chromatin effects raised by nuclear localized miRNAs. We also discuss computational tools used for analyzing the miRNA’s macro role in gene networking. Available web-based resources for miRNAs are summarized.