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Molecular and Cellular Biology, June 2000, p. 4028-4035, Vol. 20, No. 11
Department of Radiation Oncology,
Massachusetts General Hospital, Boston, Massachusetts 02114
Received 29 June 1999/Returned for modification 10 August
1999/Accepted 24 January 2000
Repetitive DNA elements frequently are precursors to chromosomal
deletions in prokaryotes and lower eukaryotes. However, little is known
about the relationship between repeated sequences and deletion
formation in mammalian cells. We have created a novel integrated
plasmid-based recombination assay to investigate repeated sequence
instability in human cells. In a control cell line, the presence of
direct or inverted repeats did not appreciably influence the very low
deletion frequencies (2 × 10
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Homologous and Nonhomologous Recombination Resulting in
Deletion: Effects of p53 Status, Microhomology, and Repetitive DNA
Length and Orientation

7 to 9 × 10
7) in the region containing the repeat. Similar to what
has been observed in lower eukaryotes, the majority of deletions
resulted from the loss of the largest direct repeat present in the
system along with the intervening sequence. Interestingly, in closely related cell lines that possess a mutant p53 gene, deletion frequencies in the control and direct-repeat plasmids were 40 to 300 times higher
than in their wild-type counterparts. However, mutant p53 cells did not
preferentially utilize the largest available homology in the formation
of the deletion. Surprisingly, inverted repeats were approximately
10,000 times more unstable in all mutant p53 cells than in wild-type
cells. Finally, several deletion junctions were marked by the addition
of novel bases that were homologous to one of the preexisting DNA ends.
Contrary to our expectations, only 6% of deletions in all cell lines
could be classified as arising from nonhomologous recombination.
*
Corresponding author. Mailing address: Department of
Radiation Oncology, Massachusetts General Hospital, 100 Blossom St., Cox 302, Boston, MA 02114. Phone: (617) 726-4143. Fax: (617)
724-8320. E-mail: hliber{at}partners.org.
Present address: Department of Molecular, Cellular and
Developmental Biology, University of California, Santa Barbara, CA 93015.
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