Molecular Characterization of Choroideremia-Associated Deletions Reveals an Unexpected Regulation of Gene Transcription.

Choroideremia (CHM) is a X-linked recessive chorioretinal dystrophy due to deficiency of the gene product, i.e., Rab escort protein isoform 1 (REP1). To date, gene therapy for CHM has shown variable effectiveness, likely because the underlying pathogenic mechanisms as well as genotype-phenotype correlation are not yet fully known. Small nucleotide variants leading to premature termination codons (PTCs) are a major cause of CHM, but about 20% of patients has gene deletions. To improve understanding of the disease mechanisms, we analyzed molecular features of seven deletions involving the gene sequence. We mapped the deletion breakpoints by using polymerase chain reaction, sequencing and array comparative genomic hybridization; to identify rearrangement-promoting DNA sequences, we analyzed genomic architecture surrounding the breakpoint regions. Moreover, in some CHM patients with different mutation types, we measured transcript level of and of , encoding the REP2 isoform. Scattered along the whole gene and in close proximity to the deletion breakpoints we found numerous repeat elements that generate a locus-specific rearrangement hot spot. Unexpectedly, patients with non-PTC variants had increased expression of the aberrant mRNA; expression was higher than normal in a patient lacking and its putative regulatory sequences. This latest evidence suggests that mechanisms regulating and gene expression are worthy of further study, because their full knowledge could be also useful for developing effective therapies for this hitherto untreatable inherited retinal degeneration.