Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis

Y RNAs are small 'cytoplasmic' RNAs which are components of the Ro ribonucl eoprotein (RNP) complex. The core of this complex, which is found in the ce ll nuclei of higher eukaryotes as well as the cytoplasm, is composed of a c omplex between the 60 kDa Ro protein and Y RNAs, Human cells contain four d istinct Y RNAs (Y1, Y3, Y4 and Y5), while other eukaryotes contain a variab le number of Y RNA homologues, When detected in a particular species, the R o RNP has been present in every cell type within that particular organism. This characteristic, along with its high conservation among vertebrates, su ggests an important function for Ro RNP in cellular metabolism; however, th is function has not yet been definitively elucidated. In order to identify conserved features of Y RNA sequences and structures which may be directly involved in Ro RNP function, a phylogenetic comparative analysis of Y RNAs has been performed. Sequences of Y RNA homologues from five vertebrate spec ies have been obtained and, together with previously published Y RNA sequen ces, used to predict Y RNA secondary structures. A novel RNA secondary stru cture comparison algorithm, the suboptimal RNA analysis program, has been d eveloped and used in conjunction with available algorithms to find phylogen etically conserved secondary structure models for Y1, Y3 and Y4 RNAs, Short , conserved sequences within the Y RNAs have been identified and are invari ant among vertebrates, consistent with a direct role for Y RNAs in Ro funct ion, A subset of these are located wholly or partially in looped regions in the Y3 and Y4 RNA predicted model structures, in accord with the possibili ty that these Y RNAs base pair with other cellular nucleic acids or are sit es of interaction between the Ro RNP and other macromolecules.