The human genome contains an abundance of interspersed segmental duplications separated by many megabasepairs of unique DNA. Despite the association of these regions with recurrent genetic disease, the underlying mechanism by which this peculiar architecture has evolved and become so prevalent in the human genome is unknown. Using computational genomic methods and large-scale comparative primate genomic sequence data, this proposal will reconstruct the evolutionary history of all segmental duplications. We will test the hypothesis that certain unstable segments have recurrently duplicated during primate evolution and that these have catalyzed the formation of larger more complex patterns of duplication that have emerged in distinct regions of the genome. Further, we hypothesize that these critical segments are associated more frequently with gene innovations that have experienced positive selection. This proposal will correlate structural and functional aspects of segmental duplications. If successful, it will provide a new model to explain the non-random spatial-temporal distribution of segmental duplications in human and great ape euchromatin and will provide fundamental information regarding the birth-death process of genes and gene families. ? ? ?
| Giannuzzi, Giuliana; Siswara, Priscillia; Malig, Maika et al. (2013) Evolutionary dynamism of the primate LRRC37 gene family. Genome Res 23:46-59 |
| Ventura, Mario; Catacchio, Claudia R; Sajjadian, Saba et al. (2012) The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. Genome Res 22:1036-49 |
| Bickhart, Derek M; Hou, Yali; Schroeder, Steven G et al. (2012) Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res 22:778-90 |
| Bekpen, Cemalettin; Tastekin, Ibrahim; Siswara, Priscillia et al. (2012) Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region. Genome Res 22:1050-8 |
| Dennis, Megan Y; Nuttle, Xander; Sudmant, Peter H et al. (2012) Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell 149:912-22 |
| Smith, Jeramiah J; Baker, Carl; Eichler, Evan E et al. (2012) Genetic consequences of programmed genome rearrangement. Curr Biol 22:1524-9 |
| Hurle, Belen; Marques-Bonet, Tomas; Antonacci, Francesca et al. (2011) Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses. BMC Evol Biol 11:23 |
| Liu, George E; Hou, Yali; Zhu, Bin et al. (2010) Analysis of copy number variations among diverse cattle breeds. Genome Res 20:693-703 |
| Liu, George E; Alkan, Can; Jiang, Lu et al. (2009) Comparative analysis of Alu repeats in primate genomes. Genome Res 19:876-85 |
| Marques-Bonet, Tomas; Girirajan, Santhosh; Eichler, Evan E (2009) The origins and impact of primate segmental duplications. Trends Genet 25:443-54 |
Showing the most recent 10 out of 50 publications
