Nucleic Acids Research, 1995, Vol. 23, No. 1 117-122
© 1995
GENOME STRUCTURE AND MAPPING |
Construction of a genomic DNA ‘feature map’ by sequencing from nested deletions: application to the HLA class I region
1Division of Allergy and Immunology, Department of Internal Medicine St Louis, MO 63110, USA 2Howard Hughes Medical Institute St Louis, MO 63110, USA 3Department of Molecular Microbiology, Washington University School of Medicine St Louis, MO 63110, USA 4Department of Molecular and Cell Biology, University of Connecticut Storrs, CT 06269, USA
*To whom correspondence should be addressed at: Division of Allergy and Immunology, Department of Internal Medicine, Washington University School of Medicine, Box 8122, 660 South Euclid Avenue, St Louis, MO 63110, USA
Received September 22, 1994. Revised November 28, 1994. Accepted November 28, 1994.
We are applying a transposon-based approach for detecting and mapping features of special interest to construct ‘feature maps’ of currently uncharacterized portions of the human leukocyte antigen (HLA) complex on chromosome 6. Such feature maps should facilitate identifying regions for high resolution analysis. Here we describe the feature mapping of a 35 kb DNA fragment located between the HLA-C and HLA-E loci. This fragment was cloned into a transposon 
-based cosmid vector designed for generating nested deletions in vivo. Seventy informative nested deletions extending into the cloned fragment were isolated, and DNA adjacent to the deletion endpoints was sequenced by fluorescent automated technology. These islands of DNA sequences constituted the foundation of the feature map, and (i) identified putative exons, (ii) determined the positions of Alu elements, (iii) determined the span of the keratinocytespecific S gene, and (iv) localized evolutionarily conserved sequences. The construction of feature maps using this in vivo nested deletion-sequencing approach provides a rapid and efficient means to identify DNA regions that merit more detailed analysis.