Area of Interest

My laboratory is interested in the study of mobile element related genetic variation. The Alu family of mobile elements comprise approximately 10% of primate genomes and are responsible for a number of different genetic disorders (see our reviews on mobile elements Callinan and Batzer 2006; Cordaux and Batzer, 2009: Konkel and Batzer, 2010, Konkel et al., 2010). These elements are one type of L1 element dependent retrotransposon that is specific to the Primate order. A third composite retrotransposon termed SVA is restricted to hominids and also dependent on L1 elements for mobilization (Wang et al., 2005). Collectively these retrotransposons make up a significant proportion of primate genomes both in terms of copy number and overall mass. Mobile elements play a significant role in the generation of genomic diversity through a variety of processes such as insertional mutagenesis (reviewed in Deininger and Batzer 1999; Batzer and Deininger 2002; Cordaux and Batzer 2009; Konkel and Batzer 2010), transduction (Xing et al., 2006), recombination (Sen et al., 2006) and double strand break repair (Sen et al., 2007).

Initial research on retrotransposable elements demonstrated that, although these elements exist at a very high copy number, individual subfamilies of the elements of different genetic ages exist within the genome. Members of the recently integrated Alu, L1 and SVA subfamilies are restricted to specific parts of the primate lineage including human lineage specific elements (reviewed in Cordaux and Batzer 2009). Many of these "young" mobile elements have inserted so recently within the primate lineage that individuals can be polymorphic for the presence or absence of a mobile element at a particular chromosomal location. Mobile element insertion polymorphisms offer two important advantages over other nuclear based genetic systems for population genetics and phylogenetic studies (reviewed in Ray et al., 2006). First, the presence of a mobile element insertion represents identity by descent, since the probability that two different young mobile elements would integrate independently in the same chromosomal location is negligible. Second, the ancestral state of each mobile element insertion polymorphism is known to be the absence of the mobile element, which can be used to unambiguously root trees. The insertion of mobile elements into the genome represents a novel class of nuclear markers for the study of population genetics and phylogenetic relationships (Batzer and Deininger 1991; Batzer et al., 1994; Li et al., 2009; Minghetti and

Dugaiczyk 1993; McLain et al., 2012; Meyer et al., 2012; Murata et al., 1993; 1996; 1998; Nikaido et al., 1999; Perna et al., 1992; Ray et al., 2005, 2006; Roos et al., 2011; Ryan and Dugaiczyk, 1993; Salem et al., 2003; Schmitz et al., 2001; 2005; Schmitz and Zischler 2003; Shimamura et al., 1997; Watkins et al., 2003; Witherspoon et al., 2006; Xing et al., 2005, 2007).

The research within our laboratory is focused around the characterization of mobile element based genetic variation. For more information visit the laboratory website.

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Selected Publications

Cordaux, R. and M. A. Batzer (2009) The impact of retrotransponsons on human genome evolution. Nature Reviews Genetics 10: 691-703

Konkel, M. K., J. A. Walker and M. A. Batzer (2010) LINEs and SINEs of primate evolution. Evolutionary Anthropology 19: 236-249

de Koning, A. P. J., W. Gu, T. A. Castoe, M. A. Batzer and D. D. Pollock (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genetics 12: e1002384

Locke, D. P., L. W. Hillier, W. C. Warren, K. C. Worley, L. V. Nazareth, D. M. Muzny, S.-P. Yang, Z. Wang, A. T. Chinwalla, P. Minx, M. Mitreva, L. Cook, K. D. Delehaunty, C. Fronick, H. Schmidt, L. A. Fulton, R. S. Fulton, J. O. Nelson, V. Magrini, C. Pohl, T. A. Graves, C. Markovic, A. Cree, H. H. Dinh, J. Hume, C. L. Kovar, G. R. Fowler, G. Lunter, S. Meader, A. Heger, C. P. Ponting, T. Marques-Bonet, C. Alkan, L. Chen, Z. Cheng, J. M. Kidd, E. E. Eichler, S. White, S. Searle, A. J. Vilella, Y. Chen, P. Flicek, J. Ma., B. Raney, B. Suh, R. Burhans, J. Herrero, D. Haussler, R. Faria, O. Fernando, F. Darré, D. Farré, E. Gazave, M. Oliva, A. Navarro, R. Roberto, O. Capozzi, N. Archidiacono, G. Della Valle, S. Purgato, M. Rocchi, M. K. Konkel, J. A. Walker, B. Ullmer, M. A. Batzer, A. F. A. Smit, R. Hubley, C. Casola, D. R. Schrider, M. W. Hahn, V. Quesada, X. S. Puente, G. R. Ordoñez, C. López-Otín, T. Vinar, B. Brejova, A. Ratan, R. S. Harris, W. Miller, C. Kosiol, H. A. Lawson, V. Taliwal, A. L. Martins, A. Siepel, A. RoyChoudhury, X. Ma, J. Degenhardt, C. D. Bustamante, R. N. Gutenkunst, T. Mailund, J. Y. Dutheil, A. Hobolth, M. H. Schierup, O. A. Ryder, Y. Yoshinaga, P. J. de Jong, G. M. Weinstock, J. Rogers, E. R. Mardis, R. A. Gibbs and R. K. Wilson (2011) Comparative and demographic analysis of orang-utan genomes. Nature 469: 529-533 [cover article]

* These authors contributed equally to this work.

The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65

Hormozdiari, F., M. K. Konkel, J. Prado-Martinez, G. Chiatante, I. H. Herraez, J. A. Walker, B. Nelson, C. Alkan, P. H. Sudmant, J. Huddleston, C. R. Catacchio, A. Ko, M. Malig, C. Baker, the Great Ape Genome Project, T. Marques-Bonet, M. Ventura, M. A. Batzer and E. E. Eichler (2013) Rates and patterns of great ape retrotransposition. Proceedings of the National Academy of Sciences, USA 110:13457-13462

Witherspoon, D. J., Y. Zhang, W. S. Watkins, H. Ha, J. Xing, M. A. Batzer and L. B. Jorde (2013) Mobile Element Scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Research 23: 1170-1181

The Marmoset Genome Sequencing and Analysis Consortium (2014) The common marmoset genome provides insight into primate biology and evolution. Nature Genetics 46: 850-857

Carbone, L., R. A. Harris, S. Gnerre, K. R. Veeramah, B. Lorente-Galdos, J. Huddleston, T. J. Meyer, J. Herrero, C. Roos, B. Aken, F. Anaclerio, N. Archidiacono, C. Baker, D. Barrell, M. A. Batzer, K. Beal, A. Blancher, C. L. Bohrson, M. Brameier, M. S. Campbell, O. Capozzi, C. Casola, G. Chiatante, A. Cree, A. Damert, P. J. de Jong, L. Dumas, M. Fernandez-Callejo, P. Flicek, N. V. Fuchs, I. Gut, M. Gut, M. W. Hahn, J. Hernández-Rodríguez, L. W. Hillier, R. Hubley, B. Ianc, Z. Izsvák, N. G. Jablonski, L. M. Johnstone, A. Karimpour-Fard, M. K. Konkel, D. Kostka, N. H. Lazar, S. L. Lee, L. R. Lewis, Y. Liu, D. P. Locke, S. Mallick, F. L. Mendez, M. Muffato, L. V. Nazareth, K. A. Nevonen, M. O'Bleness, C. Ochis, D. T. Odom, K. S. Pollard, J. Quilez, D. Reich, M. Rocchi, G. G. Schumann, S. Searle, J. M. Sikela, G. Skollar, A. Smit, K. Sonmez, B. ten Hallers, E. Terhune, G. W. C. Thomas, B. Ullmer, M. Ventura, J. A. Walker, J. D. Wall, L. Walter, M. C. Ward, S. J. Wheelan, C. W. Whelan, S. White, L. J. Wilhelm, A. E. Woerner, M. Yandell, B. Zhu, M. F. Hammer, T. Marques-Bonet, E. E. Eichler, L. Fulton, C. Fronick, D. M. Muzny, W. C. Warren, K. C. Worley, J. Rogers, R. K. Wilson and R. A. Gibbs (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature 513: 195-201 [cover article]