1. Department of Genetics, Center for Computational Genomics and the Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
2. Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific St, Seattle, Washington 98195, USA
3. UCSC Genome Bioinformatics Group, Center for Biomolecular Science & Engineering, University of California, Santa Cruz, 1156 High St, Santa Cruz, California 95064, USA
4. Washington University School of Medicine, Genome Sequencing Center, 4444 Forest Park Boulevard, St Louis, Missouri 63108, USA
5. School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
6. Sezione di Genetica, DAPEG, University of Bari, Via Amendola 165/A 70126 Bari, Italy
7. Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
8. These authors contributed equally to this work

Correspondence to: Evan E. Eichler^1,2 Correspondence and requests for materials should be addressed to E.E.E. (Email: eee@gs.washington.edu).

Abstract

An understanding of how centromeric transition regions are organized is a critical aspect of chromosome structure and function; however, the sequence context of these regions has been difficult to resolve on the basis of the draft genome sequence. We present a detailed analysis of the structure and assembly of all human pericentromeric regions (5 megabases). Most chromosome arms (35 out of 43) show a gradient of dwindling transcriptional diversity accompanied by an increasing number of interchromosomal duplications in proximity to the centromere. At least 30% of the centromeric transition region structure originates from euchromatic gene-containing segments of DNA that were duplicatively transposed towards pericentromeric regions at a rate of six–seven events per million years during primate evolution. This process has led to the formation of a minimum of 28 new transcripts by exon exaptation and exon shuffling, many of which are primarily expressed in the testis. The distribution of these duplicated segments is nonrandom among pericentromeric regions, suggesting that some regions have served as preferential acceptors of euchromatic DNA.

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