Identification and analysis of U5 snRNA variants in Drosophila

Distinct isoforms of spliceosomal RNAs may be involved in regulating pre-messenger RNA splicing in eukaryotic cells. During a large-scale effort to identify small noncoding RNAs in Drosophila, we isolated a US snRNA-like molecule containing a 5' segment identical to that of the canonical (major) US snRNA but with a variant Sm binding site and a distinct 3' hairpin sequence. Based on this finding, another six similar US snRNA-like sequences were identified within the Drosophila genome by sequence similarity to the invariant loop in the 5' half of US. Interestingly, although all of these variants are expressed in vivo, each shows a distinct temporal expression profile during Drosophila development, and one is expressed primarily in fly heads. The presence of these US snRNA variants within RNP particles suggests their role in splicing and implies a possible connection to regulation of developmental and tissue-specific gene expression.