Structure and organization of mouse U3B RNA functional genes

We report the isolation and primary structure of three genes encoding mouse U3B RNA which are expressed after injection into Xenopus laevis oocytes. Over the U3B RNA coding region, their sequences are perfectly identical, showing nine point differences with rat U3B, which do not alter the RNA secondary structure. A comparison of the three mouse sequences for the gene flanks reveals the extensive divergence of the downstream regions, except for a few nucleotides adjacent to the U3 RNA coding region, which contain a motif matching the consensus sequence for the U small nuclear RNA 3' end formation signal. By contrast, the upstream flanking regions are strongly homologous up to position -500, but they completely diverge thereafter. Within the homologous portion of 5' flanks, several motifs can be recognized which are unambiguously related to sequence elements involved in the transcriptional control of other U small nuclear RNA genes: two of these motifs precisely map at the locations (relative to the transcription start site) expected for the proximal and distal (enhancer-like) sequence elements of U small nuclear RNA genes, and "Sp1"-GC boxes and a CCAAT box are also present in their vicinity. The comparison with the rat U3B gene confirms that the preferential preservation of the 5'-flanking sequences extends up to position -500, suggesting the functional importance of sequences well upstream from the distal sequence element of the promoter. Two of the mouse genes are closely linked in genomic DNA (5 kilobase pairs apart, same orientation) and seem to have been homogenized through a recent conversion event. More generally, this small multigene family (at most six to seven copies of functional U3B genes per mouse haploid genome) appears to have undergone a concerted evolution in rodents.