Y RNA

Y RNA
Predicted secondary structure and sequence conservation of Y_RNA
Identifiers
Symbol	Y_RNA
Alt. Symbols	Y1; Y2; Y3; Y5
Rfam	RF00019
Other data
RNA type	Gene
Domain(s)	Eukaryota
SO	0000405

Y RNAs are small non-coding RNAs. They are components of the Ro60 ribonucleoprotein particle which is a target of autoimmune antibodies in patients with systemic lupus erythematosus. They are also necessary for DNA replication through interactions with chromatin and initiation proteins.

These small RNAs are predicted to fold into a conserved stem formed by the RNA's 3' and 5' ends and characterized by a single bulged cytosine, which are the known requirements for Ro binding.

Two functions have been described for Y RNAs in the literature: As a repressor of Ro60, and as an initiation factor for DNA replication. 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. Although Y RNA-derived small RNAs are similar in size to microRNAs, it has been shown that these Y RNA fragments are not involved in the microRNA pathway.

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.

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 and specific degradation of human Y RNAs inhibits DNA replication in vitro, and in intact cells in vivo. Y RNA function is thought to be mediated via interactions with chromatin and initiation proteins (including the origin recognition complex)