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Human Molecular Genetics Advance Access originally published online on March 17, 2004
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Human Molecular Genetics, 2004, Vol. 13, No. 9 967-974
DOI: 10.1093/hmg/ddh113
Human Molecular Genetics, Vol. 13, No. 9 © Oxford University Press 2004; all rights reserved

Polymorphisms at positions -22 and -348 in the promoter of the BAT1 gene affect transcription and the binding of nuclear factors

Patricia Price1,2,*, Agnes M.-L. Wong1,2, David Williamson1,2, Dominic Voon3, Svetlana Baltic3, Richard J.N. Allcock1,2, Alvin Boodhoo2,4 and Frank T. Christiansen1,2

1School of Surgery and Pathology, University of Western Australia, Nedlands 6009, Australia, 2Department of Clinical Immunology and Biochemical Genetics, Royal Perth Hospital, Perth 6001, Australia, 3GeneStream Pty Ltd, Western Australia and 4University of Mauritius, Reduit, Mauritius

Received January 19, 2004; Accepted March 9, 2004

BAT1 (D6S81E, UAP56) lies in the central MHC between TNF and HLA-B, a region containing genes that affect susceptibility to immunopathologic disorders. BAT1 protein may be directly responsible for the genetic association, as antisense studies show it can down-regulate inflammatory cytokines. Here we investigate polymorphisms at positions -22 and -348 relative to the BAT1 transcription start site. DNA samples from healthy donors were used to confirm haplotypic associations with the type 1 diabetes-susceptible 8.1 ancestral haplotype (AH; HLA-A1,B8,BAT1-22*C,BAT1-348*C,DR3 ) and the diabetes-resistant 7.1 AH (HLA-A3,B7,BAT1-22*G,BAT1-348*T,DR15). Alleles carried at BAT1-22 and -348 were in linkage disequilibrium. Electrophoretic mobility shift assays using nuclear proteins from T-cells (Jurkat and HT2), monocytes (THP1, U937) and epithelial cells (HeLa and MDA468) demonstrated DNA : protein complexes binding oligonucleotides spanning positions -22 and -348 on the 7.1 AH only. Competition assays, supershifts and molecular weight determinations suggest the complexes include the transcription factors YY1 (at -348) and Oct1 (at -22). Promoter activity was demonstrated using 520 bp and 336 bp fragments cloned from immediately upstream of the transcription start site and carrying all combinations of -22 and -348 alleles, suggesting an unidentified non-polymorphic sequence within 336 bp of the start site drives transcription. The 520 bp fragment of the BAT1 promoter cloned from the 8.1 AH was slightly less efficient than the equivalent from the 7.1 AH, whilst the reverse was observed with 336 bp fragments. This suggests BAT1 transcription on the 7.1 AH is modified by interactions involving DNA flanking positions -22 and -348.

* To whom correspondence should be addressed at: Department of Clinical Immunology and Biochemical Genetics, Royal Perth Hospital, Wellington Street, Perth, WA 6001, Australia. Tel: +61 892240378; Fax: +61 892240204; Email: pprice{at}cyllene.uwa.edu.au


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