Characterization of snRNA and snRNA-type genes in the pufferfish Fugu rubripes.

Vertebrate snRNA and snRNA-type genes occur in independent transcription units with external promoters. The transcription level from the basal promoter is enhanced by the distal sequence element DSE. This element contains almost invariably two activator submotifs, the Staf binding site and the octamer motif, recruiting the Staf and Oct-1 transcriptional activators. In the present work, database search identified 35 snRNA and snRNA-type genes in the genome sequence of the pufferfish Fugu rubripes. Sequence comparisons of promoter elements, determination of template activities by microinjection into Xenopus oocytes and DNA binding assays of the transcriptional activators led to the surprising finding that only two Fugu genes conform to the general scheme with the expected two submotifs in the DSE. Distinctively, all the other DSEs harbor a unique Staf binding site. Also striking was the observation that the tRNA(Sec), and the snRNA genes that are tandemly repeated, are transcribed from promoter-less DSEs. Evolutionary implications of these results are discussed.