Chicken U2 and U1 RNA genes are found in very different genomic environments but have similar promoter structures.

We have cloned and analyzed a gene that codes for chicken U2 small nuclear RNA (snRNA). In the haploid chicken genome, there are approximately 35-40 copies of the U2 RNA gene arranged in tandemly repeated units 5.35 kilobase pairs in length. This U2 gene organization contrasts with that of chicken U1 RNA genes, which are found in heterogeneous genomic environments. Although U snRNA genes are transcribed by RNA polymerase II, they lack the usual TATA and CAAT homologies found in the 5' control regions of most RNA polymerase II transcription units. Nevertheless, a comparison of chicken U2 and U1 RNA gene 5'-flanking DNA sequences reveals two upstream blocks of homology which are also evolutionarily conserved in U2 and U1 RNA genes of other vertebrate species. The first block of conserved sequence is centered around position -55 relative to the RNA cap site, and the other is located near position -200. Interestingly, stretches of sequence with the potential to form Z DNA are located either within or immediately adjacent to both of these two conserved upstream sequence elements, suggesting a possible role for Z DNA in U1/U2 gene expression. Moreover, the chicken U2 and U1 gene promoter regions also contain specific short sequences (i.e., the hexamer GGGCGG and the octamer ATGCAAAT) that have been shown to be required for the expression of a number of mRNA-encoding genes. These findings suggest that the transcription of snRNA genes is controlled by a complex set of factors, some shared with other RNA polymerase II transcription units and others which may be unique to the snRNA genes.