Repeat associated small interfering RNA (rasiRNA) is a class of small RNA that is involved in the RNA interference (RNAi) pathway. RasiRNA are in fact Piwi-interacting RNAs (piRNAs), which are small RNA molecules that interact with Piwi proteins. Piwi proteins are a clade of the Argonaute family of proteins. In the germline, RasiRNA is involved in establishing and maintaining heterochromatin structure, controlling transcripts that emerge from repeat sequences, and silencing transposons and retrotransposons.
There are at least three Argonaute subfamilies that have been found in eukaryotes. Unlike the Ago subfamily which is present in animals, plants, and fission yeast, the Piwi subfamily has only been found in animals. RasiRNA has been observed in Drosophila and some unicellular eukaryotes but its presence in mammals has not been determined, unlike piRNA which has been observed in many species of invertebrates and vertebrates including mammals; however, since proteins which associate with rasiRNA are found in both vertebrates and invertebrates, it is possible that active rasiRNA exist and have yet to be observed in other animals. RasiRNAs have been observed in Schizosaccharomyces pombe, a species of yeast, as well in some plants, neither of which have been observed to contain the Piwi Argonaute protein subfamily. It has been observed that both rasiRNA and piRNA are maternally linked, but more specifically it is the Piwi protein subfamily that is maternally linked and therefore leads to the observation that rasiRNA and piRNA are maternally linked.
RasiRNA are Distinct from other RNAi pathways
RasiRNA is distinct from other RNAi pathways such as microRNA (miRNA) and small interfering RNA (siRNA) as well as from piRNA. Unlike miRNA and siRNA which function through the Ago Argonaute protein subfamily, RasiRNA function through the Piwi Argonaute protein subfamily. RasiRNA is also distinct in its size. Contrary to miRNAs which are 21-23 nucleotides in length, siRNAs which are 20-25 nucleotides in length, and piRNAs which are 24-31 nucleotides in length, rasiRNAs are 24-29 nucleotides in length depending on the organism of origin. Unlike siRNA which are derived from both the sense and antisense strand, rasiRNA are derived from the antisense. Interestingly, while miRNA requires Dicer-1 for its production, and siRNA requires Dicer-2, rasiRNA does not require either; however, in some plants there are Dicer-like (Dcl) proteins that have been identified where Dcl1 produces 24 nucleotide miRNA and siRNA while Dcl2 produces 24 nucleotide rasiRNA. This research shows that not only is rasiRNA production distinct from miRNA and siRNA, but that rasiRNA may be found in plants while Piwi proteins are not.
It is presumed that the source of rasiRNA is double stranded RNA produced by annealing of sense and antisense related transposable elements. The biogenesis of rasiRNA is independent of Dicer, but does require the Argonaute proteins Argonaute 3 (Ago 3), Piwi and Aubergine which is a Piwi-like protein. The mechanism for rasiRNA biogenesis is a ping-pong mechanism. The Piwi/Aub associated RNA is the rasiRNA. The rasiRNAs match the antisense strand of retrotransposons and repetitive sequence elements (hence the name rasiRNA). The Ago3 associated RNAs are derived from the sense strand. The ping-pong mechanism which is observed in this image is the mechanism for the generation of the 5’ end of rasiRNA while the generation of the 3’ end of rasiRNA is still unknown.
Importance of rasiRNA
While miRNA act in translational repression and mRNA cleavage and siRNA act in mRNA cleavage, rasiRNA act to regulate chromatin structure and transcriptional silencing. In Drosophila, mutations in the Piwi proteins that associate with rasiRNA lead to sterility and loss of germline cells in both males and females. Transposon repression is not affected by the loss of Dicer within the germline cells revealing that this is the target of the rasiRNA pathway. Similar to miRNA and siRNA, the rasiRNA silencing pathway is evolutionarily conserved and homology dependent. When the rasiRNA pathway is not present, germline cells may undergo retrotransposition which are sensed as DNA damage and signal the cell to apoptosis. RasiRNA is key to the regulatory mechanism of many organisms as part of the RNA interference pathway.
History and Discovery
Small RNAs guiding RNA silencing pathways were first discovered in 1993 in Caenorhabditis elegans and since then have been observed in many organisms. RasiRNA were discovered in 2001  in Drosophila melanogaster. Rasi-RNAs are called piRNAs since 2007.
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