THE FAMILY OF BOX ACA SMALL NUCLEOLAR RNAS IS DEFINED BY AN EVOLUTIONARILY CONSERVED SECONDARY STRUCTURE AND UBIQUITOUS SEQUENCE ELEMENTS ESSENTIAL FOR RNA ACCUMULATION

Eukaryotic cells contain a large number of small nucleolar RNAs (snoRN As). A. major family of snoRNAs features a consensus ACA motif positio ned 3 nucleotides from the 3' end of the RNA. In this study we have ch aracterized nine novel human ACA snoRNAs (U64-U72). Structural probing of U64 RNA followed by systematic computer modeling of all known box ACA snoRNAs revealed that this class of snoRNAs is defined by a phylog enetically conserved secondary structure. The ACA snoRNAs fold into tw o hairpin structures connected by a single-stranded hinge region and f ollowed by a short 3' tail. The hinge region carries an evolutionarily conserved sequence motif, called box H (consensus, AnAnnA). The H box , probably in concert with the flanking helix structures and the ACA b ox characterized previously, plays an essential role in the accumulati on of human U64 intronic snoRNA. The correct processing of a yeast ACA snoRNA, snR36, in mammalian cells demonstrated that the cis- and tran s-acting elements required for processing and accumulation of ACA snoR NAs are evolutionarily conserved. The notion that ACA snoRNAs share a common secondary structure and conserved box elements that likely func tion as binding sites for common proteins (e.g., GAR1) suggests that t hese RNAs possess closely related nucleolar functions.