Over the past decade we have learned a tremendous amount about the role that RNA plays in regulating gene expression. This is particularly true for eukaryotes but there is also a significant role for RNA in prokaryotic regulation. This field is changing rapidly and our understanding of how RNA regulates expressions is certain to change dramatically over the coming years.

We currently recognize several different classes of regulatory RNA molecules in eukaryotes. The main classes are listed below with brief descriptions and links to details on how each class functions. In each case the basic action of a regulatory RNA involves the RNA binding with a target (regulated) sequence. This involves either full or partial complementarity between the regulatory and the target RNA sequences. The specific details of the RNA:RNA binding differ for the different classes but the overall result is the same: an influence on the expression level of the target.

Finally, in addition to affecting target RNA levels, regulation by RNA can in some cases lead to changes in chromatin structure at target genes, leading to transcriptional gene silencing (TGS). There are several mechanisms for this, the best studied of which occurs in the yeast S. pombe and is called RNA-induced transcriptional silencing or RITS.

long non-coding RNA (lncRNA)	lncRNA are RNA transcripts that are greater than 200 nucleotides in length. The designation non-coding refers to the fact that they are not translated into proteins. One sub-category of lncRNA is lincRNA for long intergenic non-coding RNA which are lncRNAs that are transcribed from intergenic regions as opposed to those that are transcribed from sequences that also code for another product. (In the latter cases the coding transcript is distinct from the lncRNA but the regions they are transcribed from overlap.) The Xist transcript that is involved X chromosome inactivation in mammals is an example of an lncRNA.
small interfering RNA (siRNA)	siRNA molecules are involved in down-regulating translation of a target mRNA through RNA interference (also called RNA silencing). siRNAs are usually from an exogenous source, that is they originate outside the cell (e.g. viral RNA), although endogenous siRNAs (encoded within the cell’s genome) have also been described. siRNAs are about 22-24 nucleotides in length and have a 100% complementarity to their target sequences over this range. It is this complementarity that allows recognition of the target RNA. Note: siRNA is also sometimes referred to as short interfering RNA.
micro RNA (miRNA)	Like siRNA, miRNA molecules are about 22-24 nt in length and they are involved in down-regulation of a target via RNA interference. However, they differ from siRNA in that they are generated from precursor RNAs that are transcribed from a different locus than their target and usually do not have a 100% match to their target, particularly in the case of animal miRNAs. Instead, miRNAs usually show a few mismatches across their 24 nt length. Despite the mismatches, sequence complementarity is what allows for the recognition of the target sequence.
piwi-interacting RNA (piRNA)	piRNAs range from 21 to 30 nucleotides in length. They are typically active in germ-line cells and involved in silencing transposon activity through RNA:RNA binding with transposon transcripts. Their name comes from the fact that this process involves interaction with a protein component called Piwi.

Eukaryotic Regulation

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