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RasiRNA – repeat associated small interfering RNA

As the name itself suggests, rasiRNAs are involved in the RNAi pathway (RNA interference). They are actually a subclass of piRNAs (piwi-interacting RNAs), which means that they too are expressed in the germline cells.

Overall, rasiRNAs differs from other RNAi pathways (from microRNAs and small interfering RNAs) in the proteins they use. MiRNAs and siRNAs are usually produced by Dicer proteins and use the Ago Argonaute protein subfamily, while rasiRNAs do not need Dicer and they use Piwi Argonaute protein subfamily, of course. However, even though they are the subtype of piRNAs, there are still some differences between these two.

The difference is that piRNAs are present in invertebrates and vertebrates, while rasiRNAs have been discovered only in Drosophila, yeast and some other organisms, while they still have not been found in mammals. This does not mean that they are not present there, though, because the proteins with which they form complexes are present in mammals. Moreover, rasiRNA molecules differ in length from piRNAs. Also, another interesting thing is that in some instances, rasiRNA have been found in plants where they were produced by Dicer complex and there were no piwi proteins present.

So far, scientists have identified three major functions that rasiRNAs have. The first one is about heterochromatin, namely establishing and maintaining its structure. The second one is about transcription and control of the transcripts, but only the ones which emerge from repeat sequences. The last function of rasiRNA is about silencing transposons and retrotransposons.

Transposons and Retrotransposons

Transposons are the elements which can change their position in the genome, replicate themselves autonomously, disrupt other genes, etc., while retrotransposons basically fall into different category of “jumping genes”. The main difference between them is in the enzyme they use (transposons use transposase, while retrotransposons use reverse transcriptase and integrase) and the way they “jump” – transposons are cut from one place and moved to the next one while retrotransposons copy themselves while remaining at the old position as well. There are also some other differences between them. For example, the terminal ends in retrotransposons are much longer than in transposons. Also, the moving of retrotransposons requires RNA, while transposons don’t need it.