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Nucleic Acids Research Advance Access published online on January 30, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm036
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© 2007 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Cruciform extrusion propensity of human translocation-mediating palindromic AT-rich repeats

Hiroshi Kogo1, Hidehito Inagaki1, Tamae Ohye1, Takema Kato1,2, Beverly S. Emanuel3,4 and Hiroki Kurahashi1,2,*

1Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan, 221st Century COE Program, Development Center for Targeted and Minimally Invasive Diagnosis and Treatment, Fujita Health University, Toyoake, Aichi 470-1192, Japan, 3Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA and 4Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA

*To whom correspondence should be addressed. Tel: +81 562 939391; Fax: +81 562 938831; Email: kura{at}fujita-hu.ac.jp

Received August 27, 2006. Revised November 28, 2006. Accepted January 8, 2007.

There is an emerging consensus that secondary structures of DNA have the potential for genomic instability. Palindromic AT-rich repeats (PATRRs) are a characteristic sequence identified at each breakpoint of the recurrent constitutional t(11;22) and t(17;22) translocations in humans, named PATRR22 (~600 bp), PATRR11 (~450 bp) and PATRR17 (~190 bp). The secondary structure-forming propensity in vitro and the instability in vivo have been experimentally evaluated for various PATRRs that differ regarding their size and symmetry. At physiological ionic strength, a cruciform structure is most frequently observed for the symmetric PATRR22, less often for the symmetric PATRR11, but not for the other PATRRs. In wild-type E. coli, only these two PATRRs undergo extensive instability, consistent with the relatively high incidence of the t(11;22) in humans. The resultant deletions are putatively mediated by central cleavage by the structure-specific endonuclease SbcCD, indicating the possibility of a cruciform conformation in vivo. Insertion of a short spacer at the centre of the PATRR22 greatly reduces both its cruciform extrusion in vitro and instability in vivo. Taken together, cruciform extrusion propensity depends on the length and central symmetry of the PATRR, and is likely to determine the instability that leads to recurrent translocations in humans.


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T. Kato, H. Inagaki, H. Kogo, T. Ohye, K. Yamada, B. S. Emanuel, and H. Kurahashi
Two different forms of palindrome resolution in the human genome: deletion or translocation
Hum. Mol. Genet., April 15, 2008; 17(8): 1184 - 1191.
[Abstract] [Full Text] [PDF]


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