Organization and evolution of primate centromeric DNA from whole genome shotgun sequence data


Can Alkan
Department of Genome Sciences at the University of Washington

The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2-5% of sequence generated as part of primate genome sequencing projects consists of this material, which is neither analyzed nor assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized WGS sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using WGS data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old-World Monkey and ape lineages of evolution.

Bio:Can Alkan is currently a postdoctoral fellow in Professor Evan E. Eichler's group in the Department of Genome Sciences at the University of Washington. He works on evolution and classification of tandemly repeated DNA, and computational prediction of human structural variation. He graduated from Bilkent University Dept. of Computer Engineering in 2000, and received his Ph.D. from Case Western Reserve University in 2005 under the supervision of Prof. Cenk Sahinalp. During his Ph.D. he worked on the evolution of centromeric DNA, RNA-RNA interaction prediction and RNA folding problems.


DATE: 20 July, 2007, Friday@ 13:40