The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation.

Open Access
Publisher Website
Google Scholar
Abstract
Eukaryotic cells contain a large number of small nucleolar RNAs (snoRNAs). A major family of snoRNAs features a consensus ACA motif positioned 3 nucleotides from the 3' end of the RNA. In this study we have characterized 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 phylogenetically conserved secondary structure. The ACA snoRNAs fold into two hairpin structures connected by a single-stranded hinge region and followed 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 box characterized previously, plays an essential role in the accumulation of human U64 intronic snoRNA. The correct processing of a yeast ACA snoRNA, snR36, in mammalian cells demonstrated that the cis- and trans-acting elements required for processing and accumulation of ACA snoRNAs are evolutionarily conserved. The notion that ACA snoRNAs share a common secondary structure and conserved box elements that likely function as binding sites for common proteins (e.g., GAR1) suggests that these RNAs possess closely related nucleolar functions.