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Human Molecular Genetics Advance Access originally published online on December 8, 2003
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Human Molecular Genetics, 2004, Vol. 13, No. 3 343-352
DOI: 10.1093/hmg/ddh026

Two essential splice lariat branchpoint sequences in one intron in a xeroderma pigmentosum DNA repair gene: mutations result in reduced XPC mRNA levels that correlate with cancer risk

Sikandar G. Khan1, Ahmet Metin2, Engin Gozukara3, Hiroki Inui1, Tala Shahlavi1, Vanessa Muniz-Medina4, Carl C. Baker4, Takahiro Ueda1, Juliet R. Aiken5, Thomas D. Schneider5 and Kenneth H. Kraemer1,*

1Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA, 2Department of Dermatology, Yüzüncü Yil University Medical School, Van, Turkey, 3Department of Biochemistry, Inönü University Medical School, Malatya, Turkey, 4Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA and 5Laboratory of Experimental and Computational Biology, National Cancer Institute, Frederick, MD, USA

Received September 24, 2003; Revised November 15, 2003; Accepted November 23, 2003

The lariat branch point sequence (BPS) is crucial for splicing of human nuclear pre-mRNA yet BPS mutations have infrequently been reported to cause human disease. Using an inverse RT–PCR technique we mapped two BPS to the adenosine residues at positions –4 and –24 in intron 3 of the human XPC DNA repair gene. We identified homozygous mutations in each of these BPS in two newly diagnosed Turkish families with the autosomal recessive disorder xeroderma pigmentosum (XP). Cells from two severely affected children in family A harbor a homozygous point mutation in XPC intron 3 (–9 T to A), located within the downstream BPS. Using a real-time quantitative reverse transcriptase–polymerase chain reaction (QRT–PCR) assay, these cells expressed no detectable (<0.1%) normal XPC message. Instead they expressed an XPC mRNA isoform with deletion of exon 4 that has no DNA repair activity in a host cell reactivation (HCR) assay. In contrast, in cells from three mildly affected siblings in family B, the BPS adenosine located at the –24 position in XPC intron 3 is mutated to a G. Real-time QRT–PCR revealed 3–5% of normal XPC message. These cells from family B had a higher level of HCR than cells from the severely affected siblings in family A, who had multiple skin cancers. Mutations identified in two BPS of the XPC intron 3 resulted in alternative splicing that impaired DNA repair function, thus implicating both of these BPS as essential for normal pre-mRNA splicing. However, a small amount of normal XPC mRNA can provide partial protection against skin cancers.

* To whom correspondence should be addressed at: DNA Repair Section, Basic Research Laboratory, National Cancer Institute, Building 37 Room 4002 MSC 4258, Bethesda, MD 20892-4258, USA. Tel: +13014969033; Fax: +3015943409; Email: kraemerk{at}nih.gov


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