A physical map of the human APP gene in YACs

Characterization of two APP gene promoter polymorphisms that appear to influence risk of late-onset Alzheimer's disease

Alzheimer's disease (AD) is characterized by formation of plaques of amyloid beta peptide (Abeta). Autosomally-inherited or "familial" AD had been demonstrated only in connection with coding sequence mutations. We characterized DNA-protein interaction and expression influence of two polymorphisms that occur in the promoter (C<-->T at -3829 and T<-->C at -1023, +1 transcription start site) of the Abeta precursor protein (APP) gene. We report distinct functional differences in reporter expression and in DNA-protein interaction for variant sequences in both -3829 and -1023 polymorphic regions. The -3829T variant has reduced DNA-protein interaction and reporter expression compared to -3829C, while -1023C has greater DNA-protein interaction and reporter expression than -1023T. Our predictions for likely transcription factors for loss of function (-3829T) are ADR1, MIG1, and PuF, and for gain of function (-1023C) are E12/E47, ITF-2, and RFX2. Characterization of the activity of a regulatory polymorphism of the APP gene points towards understanding mechanisms that likely underlie the majority of AD cases and may contribute to promoter-based drug design.

High-resolution physical mapping of a 6.7-Mb YAC contig spanning a region critical for the monosomy 21 phenotype in 21q21.3-q22.1

Deletion of genes from the chromosome 21 region between APP and SOD1 is a potential cause of some of the major phenotypic features of monosomy 21 patients. Fine physical mapping helps identify potential candidate genes. After selecting nonchimeric YACs by FISH analysis, we determined their marker contents by PCR and hybridization studies. Fifteen YACs were chosen and mapped by restriction enzyme analysis and labeling of end fragments. We localized 55 markers, including 31 STSs, 10 YAC ends, and 4 NotI linking clones, along a 6.7-Mb contig. This map facilitates transcriptional analysis of this region and construction of ready-to-sequence contigs. Furthermore, FISH mapping of two patients with partial monosomy 21 using YAC and cosmid clones allowed us to define more accurately the telomeric border of the critical region between markers S226 and S213.