Structure of the gene for rat nucleolar protein B23

Protein B23 is an abundant RNA-associated nucleolar phosphoprotein involved in the ribosome assembly process. Previous studies showed that two forms of the protein (B23.1 and B23.2) are generated from a single gene via alternative splicing of 3' exons at the mRNA level (Chang, J. H., and Olson, M. O. J. (1989) J. Biol. Chem. 264, 11732-11737). We now report the structure of the complete B23 gene which spans 11-kilobases of DNA and contains 12 exons coding for the 294 amino acid residues. B23.1 mRNA is encoded by exons 1-9, 11, and 12, whereas exons 1-10 code for the B23.2 mRNA. Each exon codes for a relatively short segment of the protein (2-40 amino acid residues). The exons, which are distributed unevenly over the length of the gene, are separated by introns varying in size between 122 base pairs and 2.2 kilobases. Southern blot analyses using a probe derived from the untranslated segment of exon 10 suggests that a single expressed gene is present in the rat genome. Additional genomic clones contained apparent processed pseudogenes for protein B23. Primer extension studies and comparison with a processed pseudogene reveal a probable transcription initiation site at position -96 from the first ATG. The 5' region of the gene contains several possible regulatory elements. Three GC boxes which are potential binding sites for transcription factor Sp1 were found, including one within the first intron. A segment of about 1500 base pairs in the 5' region is unusually rich in the dinucleotide CpG. Although no CCAAT box was found a well-defined TATA box is present at position -126. The latter feature suggests that the B23 gene has some properties of tissue-specific genes in addition to the predominant characteristics of housekeeping genes.