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Nucleic Acids Research, 2002, Vol. 30, No. 16 3624-3631
© 2002 Oxford University Press

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

Sikandar G. Khan, Vanessa Muniz-Medina, Tala Shahlavi, Carl C. Baker, Hiroki Inui, Takahiro Ueda, Steffen Emmert, Thomas D. Schneider1 and Kenneth H. Kraemer*

Basic Research Laboratory, National Cancer Institute, Building 37 Room 3E24, Bethesda, MD 20892, USA and 1 Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick, MD, USA

*To whom correspondence should be addressed. Tel: +1 301 496 9033; Fax: +1 301 496 8419; Email: kraemerk{at}nih.gov

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 ~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 ~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 (~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.


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