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Mol. Biol. Evol. 20(9):1463-1479. 2003
DOI: 10.1093/molbev/msg158
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Using a Pericentromeric Interspersed Repeat to Recapitulate the Phylogeny and Expansion of Human Centromeric Segmental Duplications

J. E. Horvath*, C. L. Gulden*, J. A. Bailey*, C. Yohn*, J. D. Mcpherson{dagger}, A. Prescott{ddagger}, B. A. Roe{ddagger}, P. J de Jong§, M. Ventura||, D. Misceo||, N. Archidiacono||, S. Zhao, S. Schwartz*, M. Rocchi|| and E. E. Eichler*,

* Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland
{dagger} Washington University School of Medicine Genome Sequencing Center, St. Louis
{ddagger} Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center
§ Children's Hospital Oakland Research Institute, Oakland, California
|| Sezione di Genetica, DAPEG, University of Bari, Bari, Italy
The Institute for Genomic Research, Rockville, Maryland

E-mail: eee{at}po.cwru.edu.

Despite considerable advances in sequencing of the human genome over the past few years, the organization and evolution of human pericentromeric regions have been difficult to resolve. This is due, in part, to the presence of large, complex blocks of duplicated genomic sequence at the boundary between centromeric satellite and unique euchromatic DNA. Here, we report the identification and characterization of an approximately 49-kb repeat sequence that exists in more than 40 copies within the human genome. This repeat is specific to highly duplicated pericentromeric regions with multiple copies distributed in an interspersed fashion among a subset of human chromosomes. Using this interspersed repeat (termed PIR4) as a marker of pericentromeric DNA, we recovered and sequence-tagged 3 Mb of pericentromeric DNA from a variety of human chromosomes as well as nonhuman primate genomes. A global evolutionary reconstruction of the dispersal of PIR4 sequence and analysis of flanking sequence supports a model in which pericentromeric duplications initiated before the separation of the great ape species (>12 MYA). Further, analyses of this duplication and associated flanking duplications narrow the major burst of pericentromeric duplication activity to a time just before the divergence of the African great ape and human species (5 to 7 MYA). These recent duplication exchange events substantially restructured the pericentromeric regions of hominoid chromosomes and created an architecture where large blocks of sequence are shared among nonhomologous chromosomes. This report provides the first global view of the series of historical events that have reshaped human pericentromeric regions over recent evolutionary time.

Key Words: pericentromeric DNA • segmental duplications • genome architecture • nonhuman primates • genome evolution


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