The structure and evolution of centromeric transition regions within the human genome

Xinwei She, Julie E. Horvath, Zhaoshi Jiang, Ge Liu, Terrence S. Furey, Laurie Christ, Royden Clark, Tina Graves, Cassy L. Gulden, Can Alkan, Jeff A. Bailey, Cenk Sahinalp, Mariano Rocchi, David Haussler, Richard K. Wilson, Webb Miller, Stuart Schwartz and Evan E. Eichler ()
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Xinwei She: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Julie E. Horvath: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Zhaoshi Jiang: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Ge Liu: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Terrence S. Furey: University of California, Santa Cruz
Laurie Christ: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Royden Clark: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Tina Graves: Washington University School of Medicine, Genome Sequencing Center
Cassy L. Gulden: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Can Alkan: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Jeff A. Bailey: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Cenk Sahinalp: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Mariano Rocchi: University of Bari
David Haussler: University of California, Santa Cruz
Richard K. Wilson: Washington University School of Medicine, Genome Sequencing Center
Webb Miller: Pennsylvania State University
Stuart Schwartz: Case Western Reserve University School of Medicine and University Hospitals of Cleveland
Evan E. Eichler: Case Western Reserve University School of Medicine and University Hospitals of Cleveland

Nature, 2004, vol. 430, issue 7002, 857-864

Abstract: 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.

Date: 2004
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DOI: 10.1038/nature02806

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