GENERATION OF AN INTEGRATED TRANSCRIPTION MAP OF THE BRCA2 REGION ON CHROMOSOME 13Q12-Q13

An integrated approach involving physical mapping, identification of t ranscribed sequences, and computational analysis of genomic sequence w as used to generate a detailed transcription map of the 1.0-Mb region containing the breast cancer susceptibility locus BRCA2 on chromosome 13q12-q13. This region is included in the genetic interval bounded by D13S1444 and D13S310. Retrieved sequences from exon amplification or h ybrid selection procedures were grouped into physical intervals and su bsequently grouped into transcription units by clone overlap. Overlap was established by direct hybridization, cDNA library screening, PCR c DNA linking (island hopping), and/or sequence alignment. Extensive gen omic sequencing was performed in an effort to understand transcription unit organization. In total, approximately 500 kb of genomic sequence was completed. The transcription units were further characterized by hybridization to RNA from a series of human tissues. Evidence for seve n genes, two putative pseudogenes, and nine additional putative transc ription units was obtained. One of the transcription units was recentl y identified as BRCA2 but all others are novel genes of unknown functi on as only limited alignment to sequences in public databases was obse rved. One large gene with a transcript size of 10.7 kb showed signific ant similarity to a gene predicted by the Caenorhabditis elegans genom e and the Saccharomyces cerevisiae genome sequencing efforts, while an other contained a motif sequence similar to the human 2', 3' cyclic nu cleotide 3' phosphodiesterase gene. Several retrieved transcribed sequ ences were not aligned into transcription units because no correspondi ng cDNAs were obtained when screening libraries or because of a lack o f definitive evidence for splicing signals or putative coding sequence based on computational analysis. However, the presence of additional genes in the BRCA2 interval is suggested as groups of putative exons a nd hybrid selected clones that were transcribed in consistent orientat ions could be localized to common physical intervals. (C) 1996 Academi c Press, Inc.