Construction and validation of yeast artificial chromosome contig maps by RecA-assisted restriction endonuclease cleavage.
RecA-assisted restriction endonuclease (RARE) cleavage is an "Achilles' heel" approach to restriction mapping whereby a RecA-protein-oligodeoxynucleotide complex protects an individual restriction site from methylation, thus limiting subsequent digestion to a single, predetermined site. We have used RARE cleavage to cut yeast artificial chromosomes (YACs) at specific EcoRI sites located within or adjacent to sequence-tagged sites (STSs). Each cleavage reaction produces two YAC fragments whose sizes are a direct measure of the position of the STS in the YAC. In this fashion, we have positioned 45 STSs within a contig of 19 independent YACs and constructed a detailed RARE-cleavage map that represents 8.4 Mbp of human chromosome 6p21.3-22. By comparing maps of overlapping YACs, we were able to detect seven internal deletions that ranged from approximately 75 kbp to approximately 1 Mbp in size. Thirteen pairs of EcoRI sites were targeted for double RARE cleavage in uncloned total human DNA. The excised fragments, up to 2 Mbp in size, were resolved by pulsed-field gel electrophoresis and were detected by hybridization. In general, the genomic RARE-cleavage results support the YAC-based map. In one case, the distance in uncloned DNA between the two terminal EcoRI sites of a YAC insert was approximately 1 Mbp larger than the YAC itself, indicating a major deletion. The general concept of RARE-cleavage mapping as well as its applications and limitations are discussed.
Lauer
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Progenitor, Inc., 4040 Campbell Avenue, Menlo Park, CA 94025, USA.
Schneider
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SS
Gnirke
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A
D002874:Chromosome Mapping; D018244:Chromosomes, Artificial, Yeast / Q000235:genetics*; D002896:Chromosomes, Human, Pair 6 / Q000235:genetics; D003001:Cloning, Molecular; D015246:Deoxyribonuclease EcoRI / Q000378:metabolism*; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D006801:Humans; D011938:Rec A Recombinases / Q000494:pharmacology*; D015183:Restriction Mapping / Q000379:methods*; D017384:Sequence Deletion / Q000235:genetics; D016324:Sequence Tagged Sites
D011938:Rec A Recombinases; D015246:Deoxyribonuclease EcoRI; C024669:endodeoxyribonuclease AluI; D015252:Deoxyribonucleases, Type II Site-Specific