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Evolutionary-new centromeres preferentially emerge within gene deserts

Mariana Lomiento1, Zhaoshi Jiang2, Pietro D'Addabbo1, Evan E Eichler23 and Mariano Rocchi1*

Author Affiliations

1 Department of Genetics and Microbiology, University of Bari, Via Amendola 165/A, Bari 70126, Italy

2 Department of Genome Sciences, University of Washington School of Medicine Seattle, 1705 NE Pacific St, Seattle, WA 98195, USA

3 Howard Hughes Medical Institute, 1705 NE Pacific St, Seattle, WA 98195, USA

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Genome Biology 2008, 9:R173  doi:10.1186/gb-2008-9-12-r173

Published: 16 December 2008



Evolutionary-new centromeres (ENCs) result from the seeding of a centromere at an ectopic location along the chromosome during evolution. The novel centromere rapidly acquires the complex structure typical of eukaryote centromeres. This phenomenon has played an important role in shaping primate karyotypes. A recent study on the evolutionary-new centromere of macaque chromosome 4 (human 6) showed that the evolutionary-new centromere domain was deeply restructured, following the seeding, with respect to the corresponding human region assumed as ancestral. It was also demonstrated that the region was devoid of genes. We hypothesized that these two observations were not merely coincidental and that the absence of genes in the seeding area constituted a crucial condition for the evolutionary-new centromere fixation in the population.


To test our hypothesis, we characterized 14 evolutionary-new centromeres selected according to conservative criteria. Using different experimental approaches, we assessed the extent of genomic restructuring. We then determined the gene density in the ancestral domain where each evolutionary-new centromere was seeded.


Our study suggests that restructuring of the seeding regions is an intrinsic property of novel evolutionary centromeres that could be regarded as potentially detrimental to the normal functioning of genes embedded in the region. The absence of genes, which was found to be of high statistical significance, appeared as a unique favorable scenario permissive of evolutionary-new centromere fixation in the population.