The human XPC DNA repair gene: arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function

Abstract

XPC DNA repair gene mutations result in the cancer-prone disorder xeroderma pigmentosum. The XPC gene spans 33 kb and has 16 exons (82-882 bp) and 15 introns (0.08-5.4 kb). A 1.6 kb intron was found within exon 5. Sensitive real- time quantitative reverse transcription-polymerase chain reaction methods were developed to measure full-length XPC mRNA (the predominant form) and isoforms that skipped exons 4, 7 or 12. Exon 7 was skipped in approximately 0.07% of XPC mRNAs, consistent with the high information content of the exon 7 splice acceptor and donor sites (12.3 and 10.4 bits). In contrast, exon 4 was skipped in approximately 0.7% of the XPC mRNAs, consistent with the low information content of the exon 4 splice acceptor (-0.1 bits). A new common C/A single nucleotide polymorphism in the XPC intron 11 splice acceptor site (58% C in 97 normals) decreased its information content from 7.5 to 5.1 bits. Fibroblasts homozygous for A/A had significantly higher levels (approximately 2.6-fold) of the XPC mRNA isoform that skipped exon 12 than those homozygous for C/C. This abnormally spliced XPC mRNA isoform has diminished DNA repair function and may contribute to cancer susceptibility.

XPC polymorphisms and lung cancer risk

“…Frequencies of the 499Val and IVS11-5A alleles among healthy Koreans were 0.712 and 0.391, respectively, which were similar to those (0.768 and 0.423, respectively) of NIH donors in the United States. 19,20 Frequencies of the PATþ and 939Gln alleles among healthy Koreans were 0.373 and 0.394, respectively, which were also similar to those of Caucasians (0.333 and 0.335, respectively). 21,25 In agreement with previous studies, 19,20,26 we found that the Val499Arg, PAT-/þ, IVS11-5C?A and Lys939Gln polymorphisms were in LD.…”

“…In addition, -449G?C and -371G?A polymorphisms were linked with these 4 polymorphisms. Khan et al 20 reported that haplotypes PAT-/ IVS11-5C/939Lys and PATþ/IVS11-5A/939Gln accounted for approximately 60% and 40%, respectively, of the chromosome among NIH donors. Frequencies of the haplotypes of these 3 polymorphisms among controls in the current study were comparable with their report.…”

“…Frequencies of the haplotypes of these 3 polymorphisms among controls in the current study were comparable with their report. 20 DNA sequences upstream of the XPC transcription initiation site possess multiple putative transcription factor binding sites. The -449G?C, -371G?A and -27G?C polymorphisms lead to changes in the putative transcription factor binding sites by computer prediction using the Alibaba2 program (http://www.alibaba2.…”

“…14,15 Mice defective in the XPC gene are highly prone to skin cancer following exposure to UV radiation and highly vulnerable to cancers of the internal organs, such as liver and lung, when exposed to chemical carcinogens, 16,17 suggesting that XPC is important for preventing carcinogenesis. Several polymorphisms in the XPC gene have been reported [18][19][20][21] and listed in public databases (e.g., http://www.ncbi.nlm.nih.gov/ SNP). While the functional effects of these polymorphisms have not been elucidated, we hypothesized that some of these variants, particularly their haplotypes, may have an effect on NER capacity, thereby modulating the susceptibility to lung cancer.…”

“…Among the intronic variants, the IVS11-5C?A polymorphism (30724C?A, Genbank accession AY131066) in the XPC intron 11 splice acceptor site was evaluated since it exerts influence on the alternative splicing and function of XPC. 20 The PAT-/þ polymorphism [24660_24664delGTAAC inspoly(AT), GenBank accession AY131066] in intron 9 was also evaluated since it has been associated with increased risk for SCC of the head and neck. 21 …”