MicroRNA Identification Based on Bioinformatics Approaches

Abstract

One of the most fascinating aspects of RNA interference (RNAi) is the non-cell-autonomous nature of silencing. Seminal studies on RNAi focused on the ability of transgene silencing to propagate systemically throughout an organism, such as from a single Agrobacterium infiltrated leaf to other parts of the plant, or from a grafted silenced stock into a non-silenced scion[1, 2] The discovery of RNAi was preceded first by observations of transcriptional inhibition by antisense RNA expressed in transgenic plants[3] and more directly by reports of unexpected outcomes in experiments performed by plant scientists in the U.S. and The Netherlands in the early 1990s[4] In an attempt to alter flower colors in petunias, researchers introduced additional copies of a gene encoding chalcone synthase, a key enzyme for flower pigmentation into petunia plants of normally pink or violet flower color. Soon after, a related event termed quelling was noted in the fungus Neurospora crassa [5], although it was not immediately recognized as related. Further investigation of the phenomenon in plants indicated that the downregulation was due to post-transcriptional inhibition of gene expression via an increased rate of mRNA degradation[6]. This phenomenon was called cosuppression of gene expression, but the molecular mechanism remained unknown. Not long after, plant virologists working on improving plant resistance to viral diseases observed a similar unexpected phenomenon. While it was known that plants expressing virus-specific proteins showed enhanced tolerance or resistance to viral infection, it was not expected that plants carrying only short, non-coding regions of viral RNA sequences would show similar levels of protection. Researchers believed that viral RNA produced by transgenes could also inhibit viral replication[7]. The reverse experiment, in which short sequences of plant genes were introduced into viruses, showed that the targeted gene was suppressed in an infected plant. This phenomenon was labeled "virus-induced gene silencing" (VIGS), and the set of such phenomena were collectively called post transcriptional gene silencing [8][15]. The spread of RNA silencing is not limited to plants or viruses: the first reported experiments of RNAi in Caenorhabditis elegans (C. elegans) demonstrated a systemic silencing response induced by locally injected or ingested double-stranded RNA (dsRNA) molecules[9, 10]. In plants, as in C. elegans, the systemic silencing signal acts in a sequencespecific manner, invoking the involvement of an RNA component. Sequence-specific RNA