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Nucleic Acids Research, 1990, Vol. 18, No. 3 561-567
© 1990

MOLECULAR BIOLOGY

Recombination via flanking direct repeats is a major cause of large-scale deletions of human mitochondrial DNA

Shuji Mita1, Rosario Rizzuto1, Carlos T. Moraes2, Sara Shanske1, Enrica Arnaudo1, Gian Maria Fabrizi1, Yasutoshi Koga1, Salvatore DiMauro1 and Eric A. Schon1,*

1Departments of Neurology, Columbia University College of Physicians and Surgeons 630 West 168th Street, New York, NY 10032, USA 2Departments of Genetics and Development, Columbia University College of Physicians and Surgeons 630 West 168th Street, New York, NY 10032, USA

* To whom correspondence should be addressed at Istituto di Patologia Generate, Via Loredan 16, 35100 Padova, Italy

Received October 4, 1989. Revised December 18, 1989. Accepted December 18, 1989.

Large-scale deletions of mitochondrial DNA (mtDNA) have been described in patients with progressive external ophthalmoplegia (PEO) and ragged red fibers. We have determined the exact deletion breakpoint in 28 cases with PEO, including 12 patients already shown to harbor an identical deletion; the other patients had 16 different deletions. The deletions fell into two classes. In Class I (9 deletions; 71% of the patients), the deletion was flanked by perfect direct repeats, located (in normal mtDNA) at the edges of the deletion. In Class II (8 deletions; 29% of patients), the deletions were not flanked by any obviously unique repeat element, or they were flanked by repeat elements which were located imprecisely relative to the breakpoints. Computer analysis showed a correlation between the location of the deletion breakpoints and sequences in human mtDNA similar to the target sequence for Drosophila topoisomerase II. It is not known how these deletions originate, but both slipped mispairing and legitimate recombination could be mechanisms playing a major role in the generation of the large mtDNA deletions found in PEO.


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