Y RNA

Y RNAs are small non-coding RNA components of the Ro ribonucleoprotein particle (Ro RNP). The Ro RNP was first identified by Lerner et al. as a target of autoimmune antibodies in patients with systemic lupus erythematosus.

Function
Two functions have been described for Y RNAs in the literature: In one line of evidence, Y RNA appears to function as a repressor of Ro. In its free state, Ro binds to a variety of misfolded RNAs including misfolded 5S rRNAs, and is thought to act as some sort of quality control mechanism. Crystal structures of Ro complexed either with Y RNA or another RNA showed that Ro binds single-stranded 3' ends of RNAs relatively nonspecifically, whereas Y RNA binds specifically at a second site that regulates access of other RNAs. In Deinococcus, free Ro has also been shown to function in 23S rRNA maturation. In Deinococcus, mutants lacking Y RNA are viable, and Y RNA appears to be unstable except when complexed with Ro. Secondly, it has been described recently that human Y RNAs are functionally required for DNA replication. Biochemical fractionation and reconstitution experiments have established a functional requirement of human Y RNAs for chromosomal DNA replication in isolated vertebrate cell nuclei in vitro. Specific degradation of human Y RNAs in vitro, or in intact cells in vivo, have led to an inhibition of chromosomal DNA replication. Interestingly, mutant human Y RNAs lacking the conserved binding site for Ro60 protein still support DNA replication, indicating that binding to Ro protein and promoting DNA replication are two separable functions of Y RNAs.

Structure
These small RNAs are predicted to fold into a conserved secondary structure.

Species distribution
Presumptive Y RNA and Ro protein homologs have been found in eukaryotes and bacteria. Humans appear to have four Y RNAs, named hY1, hY3, hY4 and hY5 and also a large number of pseudogenes. C. elegans has one, named CeY RNA. The radiation-resistant bacterium Deinococcus radiodurans encodes a homolog of Ro called rsr ("Ro sixty related"), and at least four small RNAs accumulate in Deinococcus under conditions where rsr expression is induced (UV irradiation); one of these RNAs appears to be a Y RNA homolog.