Large-Scale Comparative Sequence Analysis of the Human and Murine Bruton’s Tyrosine Kinase Loci Reveals Conserved Regulatory Domains

Large-scale genomic DNA sequencing of orthologous and paralogous loci in different species should contribute to a basic understanding of the evolution of both the protein-coding regions and noncoding regulatory elements. We compared 93 kb of human sequence to 89 kb of mouse sequence in the Bruton’s tyrosine kinase (BTK) region. In addition to showing the conservation of both position and orientation of the five functionally unrelated genes in the region (BTK, a-D-galactosidase A, L44L, FTP-3, and FCI-12), the comparison revealed conservation of clusters of noncoding sequence flanking the first exon of each gene. Furthermore, in the sequence comparison at the BTK locus, the conservation of clusters of noncoding sequence extends throughout the locus; the noncoding sequence is more highly conserved in the BTK locus in comparison to the flanking loci. This suggests a correlation with the complex developmental regulation of expression of btk. To determine whether a highly conserved 3.5-kb segment flanking the first exon of BTK contains transcriptional regulatory signals, we tested various portions of the segment for promoter and expression activity in several appropriate cell lines. The results demonstrate the contribution of the conserved region flanking the first exon to the cell lineage-specific expression pattern of btk. These data show the usefulness of large scale sequence comparisons to focus investigation on regions of noncoding sequence that play essential roles in complex gene regulation. [The sequence data described in this paper have been submitted to GenBank under accession nos. U78027 and U58105.] One analytical approach to functional characterization of both coding and noncoding DNA sequences is through comparison of sequence of syntenic regions in multiple species. Conserved noncoding sequence has been hypothesized to be important in regulating gene expression, maintaining the structural organization of the genome, and contributing to yet unknown functions of the chromosome (Koop and Hood 1994). Sequence data from murine and human 58