Cruciform-forming inverted repeats appear to have mediated many of the microinversions that distinguish the human and chimpanzee genomes Jessica Kolb & Nadia A. Chuzhanova & Josef Högel & Karen M. Vasquez & David N. Cooper & Albino Bacolla & Hildegard Kehrer-Sawatzki Received: 15 January 2009 / Revised and Accepted: 8 April 2009 / Published online: 28 May 2009 # Springer Science + Business Media B.V. 2009 Abstract Submicroscopic inversions have contributed significantly to the genomic divergence between humans and chimpanzees over evolutionary time. Those microinversions which are flanked by segmental duplications (SDs) are presumed to have originated via non-allelic homologous recombination between SDs arranged in inverted orientation. However, the nature of the mechanisms underlying those inversions which are not flanked by SDs remains unclear. We have investigated 35 such inversions, ranging in size from 51-nt to 22056-nt, with the goal of characterizing the DNA sequences in the breakpoint-flanking regions. Using the macaque genome as an outgroup, we determined the lineage specificity of these inversions and noted that the majority (N=31; 89%) were associated with deletions (of length beween 1-nt and 6754-nt) immediately adjacent to one or both inversion breakpoints. Overrepresentations of both direct and inverted repeats, ≥ 6-nt in length and capable of non-B DNA structure formation, were noted in the vicinity of breakpoint junctions suggesting that these repeats could have contributed to double strand breakage. Inverted repeats capable of cruciform structure forma- tion were also found to be a common feature of the inversion breakpoint-flanking regions, consistent with these inversions having originated through the resolution of Holliday junction-like cruciforms. Sequences capable of non-B DNA structure formation have previously been implicated in promoting gross deletions and translocations causing human genetic disease. We conclude that non-B DNA forming sequences may also have promoted the occurrence of mutations in an evolutionary context, giving rise to at least some of the inversion/deletions which now serve to distinguish the human and chimpanzee genomes. Keywords inversions . cruciform structures . non-B DNA . human and chimpanzee genomes Chromosome Research (2009) 17:469–483 DOI 10.1007/s10577-009-9039-9 Responsible Editor: Fengtang Yang. Electronic supplementary material The online version of this article (doi:10.1007/s10577-009-9039-9) contains supplementary material, which is available to authorized users. J. Kolb : J. Högel : H. Kehrer-Sawatzki (*) Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany e-mail: hildegard.kehrer-sawatzki@uni-ulm.de N. A. Chuzhanova School of Computing, Engineering and Physical Sciences, University of Central Lancashire, Preston PR1 2HE, UK K. M. Vasquez : A. Bacolla Science Park-Research Division, Department of Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA D. N. Cooper Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK