The promoter of a lysosomal membrane transporter gene, CTNS, binds Sp-1, shares sequences with the promoter of an adjacent gene, carkl, and causes cystinosis if mutated in a critical region

Although >55 CTNS mutations occur in patients with the lysosomal storage di sorder cystinosis, no regulatory mutations have been reported, because the promoter has not been defined. Using CAT reporter constructs of sequences 5 ' to the CTNS coding sequence, we identified the CTNS promoter as the regio n encompassing nucleotides -316 to +1 with respect to the transcription sta rt site. This region contains an Sp-1 regulatory element (GGCGGCG) at posit ions -299 to -293, which binds authentic Sp-1, as shown by electrophoretic- mobility-shift assays. Three patients exhibited mutations in the CTNS promo ter. One patient with nephropathic cystinosis carried a -295 G -->C substit ution disrupting the Sp-1 motif, whereas two patients with ocular cystinosi s displayed a -303 G -->T substitution in one case and a -303 T insertion i n the other case. Each mutation drastically reduced CAT activity when inser ted into a reporter construct. Moreover, each failed either to cause a mobi lity shift when exposed to nuclear extract or to compete with the normal ol igonucleotide's mobility shift. The CTNS promoter region shares 41 nucleoti des with the promoter region of an adjacent gene of unknown function, CARKL , whose start site is 501 bp from the CTNS start site. However, the patient s' CTNS promoter mutations have no effect on CARKL promoter activity. These findings suggest that the CTNS promoter region should be examined in patie nts with cystinosis who have fewer than two coding-sequence mutations.