Construction of a genomic DNA ‘feature map’ by sequencing from nested deletions: application to the HLA class I region

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 resoluti...

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Bibliographic Details
Published in:Nucleic acids research 1995-01, Vol.23 (1), p.117-122
Main Authors: Krishnan, B. Rajendra, Jamry, Isabela, Berg, Douglas E., Berg, Claire M., Chaplin, David D.
Format: Article
Language:English
Subjects:
Base Sequence
Biological Evolution
chromosome 6
Chromosome Mapping
Chromosomes, Human, Pair 6
class I loci
Cloning, Molecular
Conserved Sequence
Cosmids
DNA
DNA - genetics
DNA Primers - genetics
DNA Transposable Elements
Exons
feature mapping
gene mapping
Genetic Vectors
Genome, Human
histocompatibility locus HLA
HLA Antigens - genetics
Humans
man
Molecular Sequence Data
Multigene Family
Repetitive Sequences, Nucleic Acid
S gene
Sequence Deletion
transposon gamma delta
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Summary: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 γδ-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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/23.1.117