Mark A. Batzer
Mark A. Batzer 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 recent reviews on mobile elements see Batzer and Deininger, 2002; Callinan and Batzer 2006; Deininger and Batzer, 2002: Deininger et al., 2003). 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), 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 Batzer and Deininger 2002). 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 polymorphisms 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.
The research within our laboratory is focoused around the characterization of mobile element based genetic variation. There are currently four major research foci within the laboratory. For more information
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Selected Recent Publications
Han, K.*, J. Xing*, H. Wang, D. J. Hedges, R. K. Garber, R. Cordaux and M. A. Batzer (2005) Under the genomic radar: the stealth model of Alu amplification. Genome Research 15: 655-664 [cover article]
Wang, H.*, J. Xing*, D. Grover*, D. J. Hedges, K. Han, J. A. Walker and M. A. Batzer (2005) SVA elements: a hominid specific retroposon family. Journal of Molecular Biology 354: 994-1007 [cover article]
Xing, J.*, H. Wang*, V. P. Belancio, R. Cordaux, P. L. Deininger and M. A. Batzer (2006) Emergence of primate genes by retrotransposon-mediated sequence transduction. Proceedings of the National Academy of Sciences, USA 103: 17608-17613 [cover article]
Sen, S. K.*, K. Han*, J. Wang, J. Lee, H. Wang, P. A. Callinan, M. Dyer, R. Cordaux, P. Liang and M. A. Batzer (2006) Human genomic deletions mediated by recombination between Alu elements. American Journal of Human Genetics 79: 41-53
Han, K.*, M. K. Konkel*, J. Xing*, H. Wang*, J. Lee, T. J. Meyer, C. T. Huang, E. Sandifer, K. Hebert, E. W. Barnes, R. Hubley, W. Miller, A. F. A. Smit, B. Ullmer and M. A. Batzer (2007) Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome. Science 316: 238-240 [cover article]
Gibbs, R. A., J. Rogers, M. G. Katze, R. Bumgarner, G. M. Weinstock, E. R. Mardis, K. A. Remington, R. L. Strausberg, J. C. Venter, R. K. Wilson, M. A. Batzer, C. D. Bustamante, E. E. Eichler, M. W. Hahn, R. C. Hardison, K. D. Makova, W. Miller, A. Milosavljevic, R. E. Palermo, A. Siepel, J. M. Sikela, T. Attaway, S. Bells, K. E. Bernard, C. J. Buhay, M. N. Chandrabose, M. Dao, C. Davis, K. D. Delehaunty, Y. Ding, H. H. Dinh, S. Dugan-Rocha, L. A. Fulton, R. A. Gabisi, T. T. Garner, J. Godfrey, A. C. Hawes, J. Hernandez, S. Hines, M. Holder, J. Hume, S. N. Jhangiani, V. Joshi, Z. M. Khan, E. F. Kirkness, A. Cree, R. G. Fowler, S. Lee, L. R. Lewis, Z. Li, Y. S. Liu, S. M. Moore, D. Muzny, L. V. Nazareth, D. N. Ngo, G. O. Okwuonu, G. Pai, D. Parker, H. A. Paul, C. Pfannkoch, C. S. Pohl, Y. H. Rogers, S. J. Ruiz, A. Sabo, J. Santibanez, B. W. Schneider, S. M. Smith, E. Sodergren, A. F. Svatek, T. R. Utterback, S. Vattathil, W. Warren, C. S. White, A. T. Chinwalla, Y. Feng, A. L. Halpern, L. W. Hillier, X. Huang, P. Minx, J. O. Nelson, K. H. Pepin, X. Qin, G. G. Sutton, E. Venter, B. P. Walenz, J. W. Wallis, K. C. Worley, S. P. Yang, S. M. Jones, M. A. Marra, M. Rocchi, J. E. Schein, R. Baertsch, L. Clarke, M. Csürös, J. Glasscock, R. A. Harris, P. Havlak, A. R. Jackson, H. Jiang, Y. Liu, D. N. Messina, Y. Shen, H. X. Song, T. Wylie, L. Zhang, E. Birney, K. Han, M. K. Konkel, J. Lee, A. F. Smit, B. Ullmer, H. Wang, J. Xing, R. Burhans, Z. Cheng, J. E. Karro, J. Ma, B. Raney, X. She, M. J. Cox, J. P. Demuth, L. J. Dumas, S. G. Han, J. Hopkins, A. Karimpour-Fard, Y. H. Kim, J. R. Pollack, T. Vinar, C. Addo-Quaye, J. Degenhardt, A. Denby, M. J. Hubisz, A. Indap, C. Kosiol, B. T. Lahn, H. A. Lawson, A. Marklein, R. Nielsen, E. J. Vallender, A. G. Clark, B. Ferguson, R. D. Hernandez, K. Hirani, H. Kehrer-Sawatzki, J. Kolb, S. Patil, L. L. Pu, Y. Ren, D. G. Smith, D. A. Wheeler, I. Schenck, E. V. Ball, R. Chen, D. N. Cooper, B. Giardine, F. Hsu, W. J. Kent, A. Lesk, D. L. Nelson, W. E. O'brien, K. Prüfer, P. D. Stenson, J. C. Wallace, H. Ke, X. M. Liu, P. Wang, A. P. Xiang, F. Yang, G. P. Barber, D. Haussler, D. Karolchik, A. D. Kern, R. M. Kuhn, K. E. Smith, A. S. Zwieg (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316: 222-234 [cover article]
Mikkelsen, T.S., M. J. Wakefield, B. Aken, C. T. Amemiya, J. L. Chang, S. Duke, M. Garber, A. J. Gentles, L. Goodstadt, A. Heger, J. Jurka, M. Kamal, E. Mauceli, S. M. J. Searle, T. Sharpe, M. L. Baker, M. A. Batzer, P. V. Benos, K. Belov, M. Clamp, A. Cook, J. Cuff, R. Das, L. Davidow, J. E. Deakin, M. J. Fazzari, J. L. Glass, M. Grabherr, J. M. Greally, W. Gu, T. A. Hore, G. A. Huttley, R. L. Jirtle, E. Koina, J. T. Lee, S. Mahony, M. A. Marra, R. D. Miller, R. D. Nicholls, M. Oda, A. T. Papenfuss, Z. E. Parra, D. D. Pollock, D. A. Ray, J. E. Schein, T. P. Speed, K. Thompson, J. L. VandeBerg, C. M. Wade1, J. A. Walker, P. D. Waters, C. Webber, J. R. Weidman, X. Xie, M. C. Zody, Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, J. A. Marshall Graves, C. P. Ponting, M. Breen, P. B. Samollow, E. S. Lander and K. Lindblad-Toh (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447: 167-178 [cover article]
Warren W. C., L. W. Hillier, J. A. Marshall Graves, E. Birney, C. P. Ponting, F. Grützner, K. Belov, W. Miller, L. Clarke, A. T. Chinwalla, S.-P. Yang, A. Heger, D. P. Locke, P. Miethke, P. D. Waters, F. Veyrunes, L. Fulton, B. Fulton, T. Graves, J. Wallis, X. S. Puente, C. López-Otín, G. R. Ordóńez, E. E. Eichler, L. Chen, Z. Cheng, J. E. Deakin, A. Alsop, K. Thompson, P. Kirby, A. T. Papenfuss, M. J. Wakefield, T. Olender, D. Lancet, G. A. Huttley, A. F. A. Smit, A. Pask, P. Temple-Smith, M. A. Batzer, J. A. Walker, M. K. Konkel, R. S. Harris, C. M. Whittington, E. S. W. Wong, N. J. Gemmell, E. Buschiazzo, I. M. Vargas Jentzsch, A. Merkel, J. Schmitz, A. Zemann, G. Churakov, J. O. Kriegs, J. Brosius, E. P. Murchison, R. Sachidanandam, C. Smith, G. J. Hannon, E. Tsend-Ayush, D. McMillan, R. Attenborough, W. Rens, M. Ferguson-Smith, C. M. Lefčvre, J. A. Sharp, K. R. Nicholas, D. A. Ray, M. Kube, R. Reinhard, T. H. Pringle, J. Taylor, R. C. Jones, B. Nixon, J.-L. Dacheux, H. Niwa, Y. Sekita, X. Huang, A. Stark, P. Kheradpour, P. Flicek, Y. Chen, C. Webber, R. Hardison, J. Nelson, K. Hallsworth-Pepin, K. Delehaunty, C. Markovic, P. Minx, Y. Feng, C. Kremitzki, M. Mitreva, J. Glasscock, P. Wohldmann, P. Thiru, M. N. Nhan, C. S. Pohl, S. M. Smith, S. Hou, M. Renfree, E. R. Mardis and R. K. Wilson (2008) Genome analysis of the platypus reveals unique signatures of evolution. Nature 452: 175-183 [cover article]* These authors contributed equally to this work.
