Campomelic dysplasia translocation breakpoints are scattered over 1 Mb proximal to SOX9: Evidence for an extended control region

Campomelic dysplasia (CD), a skeletal malformation syndrome with or without XY sex reversal, is usually caused by mutations within the SOX9 gene on di stal 17q. Several CD translocation and inversion cases have been described with breakpoints outside the coding region, mapping to locations >130 kb pr oximal to SOX9. Such cases are generally less severely affected than cases with SOX9 coding-region mutations, as is borne out by three new translocati on cases that we present. We have cloned the region extending 1.2 Mb upstre am of the SOX9 gene in overlapping bacterial-artificial-chromosome and P1-a rtificial-chromosome clones and have established a restriction map with rar e-cutter enzymes. With sequence-tagged-site-content mapping in somatic-cell hybrids, as well as with FISH, we have precisely mapped the breakpoints of the three new and of three previously described CD cases. The six CD break points map to an interval that is 140-950 kb proximal to the SOX9 gene. Wit h exon trapping, we could isolate five potential exons from the YAC 946B12 that spans the region, four of which could be placed in the contig in the v icinity of the breakpoints. They show the same transcriptional orientation, but only two have an open reading frame (ORF). We failed to detect express ion of these fragments in several human and mouse cDNA libraries, as well a s on northern blots. Genomic sequence totaling 1,063 kb from the SOX9 5'-fl anking region was determined and was analyzed by the gene-prediction progra m GENSCAN and by a search of dbEST and other databases. No genes or transcr ipts could be identified. Together, these data suggest that the chromosomal rearrangements most likely remove one or more cis-regulatory elements from an extended SOX9 control region.