Faculty & Research
- Contact Information
- Contact Thom Kaufman by kaufman [at] indiana [dot] edu
- By telephone: 812-855-3033/5-7674(lab)
- By fax: 812-855-2577
- JH A508 / JH A505 (lab)
- Genome, Cell & Developmental Biology
- Research Areas
- Chromatin, Chromosomes, and Genome Integrity
- Developmental Mechanisms and Regulation in Eukaryotic Systems
- Eukaryotic Cell Biology, Cytoskeleton and Signaling
Ph.D., University of Texas, 1970
Postdoctoral Fellow, University of British Columbia, Vancouver, 1971
Member, National Academy of Sciences
Fellow, American Academy of Arts & Sciences
Using the fruit fly Drosophila melanogaster, the long-term goal of our laboratory is to contribute to an understanding of the genetic basis of the developmental program of higher organisms. The homeotic genes, which play a crucial role in development, have been our principal locus.
Homeotic lesions cause one portion of the animal to be transformed into an identity normally found in another region. Thus mutations at the Antennapedia (Antp)locus cause a transformation of the antennae of the adult fly into a leg, and lesions in the proboscipedia (pb)gene result in the development of legs in place of the adult mouthparts.
The role of the homeotic loci are best viewed as a series of developmental switches for either/or decisions of cellular fate. The homeodomain, that endows the proteins with DNA-binding ability, indicates that the switch activity of the loci is reflected in their functioning as regulators of specific downstream target genes.
The Search for Downstream Genes. In order to gain further insights into the function of the homeotic transcription factor proteins we have cloned a group of targets of these genes. In the process of our analyses we found one the targets, based on the nature of its encoded protein, to be particularity interesting. We have therefore concentrated our recent efforts on understanding the role of this gene in development.
We have recovered cDNAs that encode a protein of 150 kD and the ORF predicts a novel hydrophilic coiled-coil polypeptide that contains three leucine zipper motifs. Antisera raised against the polypeptide were used to localize the protein to the centrosome and we have called the gene centrosomin (cnn).
We have found that the cnnlocus is expressed throughout embryogenesis as well as post embryonically. In order to define the role of Cnn in the cells in which it is accumulated we have recovered mutations in the gene. Surprisingly screens for cnnIesions have resulted in the recovery of sterile but not lethal mutations. Adult females homozygous for all the alleles are sterile and produce eggs in which the syncytial divisions proceed as far as the twelfth cycle, and embryos fail to cellularize. Examination of the cleavage mitotic figures shows that the embryos exhibit defects in chromosome segregation and spindle organization. Frequently, one observes apparently linked spindles that share poles, indicating that Cnn is required for the proper spacing and separation of mitotic spindles within the syncytium.
Males homozygous for these mutations are also sterile. Examination of mutant testes has shown that in developing spermatocytes, Cnn is required for meiotic cytokinesis. Additionally, axonemal morphology and elongation are abnormal. Since Cnn is also found in the basal body of the developing sperm it would appear that it functions in the organization of the axoneme. Taken together, these results indicate essential roles for Cnn in the organization of the cleavage and male meiotic spindle and cytoskeleton of the axoneme. The fact that apparent null mutations at cnncan complete normal post embryonic development implies that Cnn is dispensable for spindle function after cleavage and that there is a qualitative difference in the centrosome at these different stages of development.
Homeotic genes in Evolution and Development. By using the knowledge we have gained from Drosophila as a genetic framework, we are now able to examine the evolution of developmental processes within the arthropods. One of the most striking features of arthropods is their segmental organization along the anterior/posterior axis. One difference among the various arthropod taxa is the deployment and identities of these segments. Since HOX genes play a pivotal role in segmental identity, it is thought that they are responsible, in part, for arthropod diversity.
We have therefore begun to extend our analysis of HOX genes to other taxa. We have now cloned most of the homeotic genes from several insects and representative species from the Crustacea, Chelicerata and Myriapoda. HOX gene expression patterns in these other arthropods are offering tantalizing clues to developmental processes in this very diverse group of organisms. We have also begun to take a functional approach to studying HOX gene evolution. By using the technique of RNA-mediated gene inhibition (RNAi), we can now determine the functional and regulatory interactions between HOX genes.
Using this technique we have demonstrated that inhibition of the genes Deformed, Sex combs reduced, Antennapedia and proboscipedia in the milkweed bug Oncopeltus laciatus produces homeotic transformations similar to those found in Drosophila. There are however intriguing differences in the 0. faciatus transformations relative to what is seen in flies that indicate that the regulatory paradigm for these genes in the Diptera and the Hemiptera has evolved differently.
These approaches will allow us to both study the development of this very diverse group of organisms, and to understand how the process of development evolves.
- Eisman, R. C., M. A. S. Phelps and T. C. Kaufman. 2015 A Polo Kinase-Cnn Interaction Motif Regulates Centrosome Formation and Reveals a Novel Function for centrosomin (cnn) in Drosophila Embryos. Genetics (in revision).
- Brown J. B., N. Boley, R. Eisman, G. E. May, M. H. Stoiber, Michael O. Duff, B. W. Booth, J. Wen, S. Park, A. Maria Suzuki, K. H. Wan, C. Yu, D. Zhang, J. W. Carlsonb, L. Cherbas, B. D. Eads, D. Miller, K. Mockaitis, J. Roberts , Carrie A. Davis, E. Frise, A. S. Hammonds, S. Olson, S. Shenker, D. Sturgill, A. A. Samsonova, G. Robinson, J. Hernandez, J. Andrews, P. J. Bickel, P. Carninci, P. Cherbas, T. R. Gingeras, R. A. Hoskins, T.C. Kaufman, E. C. Lai, B. Oliver, N. Perrimon, B. R. Graveley and S. E. Celniker 2014 Diversity and dynamics of the Drosophila transcriptome. Nature 512(7515): 393-399.
- Mark B. Gerstein, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B. Brown, Carrie A. Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li, Baikang Pei, Arif O. Harmanci, Michael O. Duff, Sarah Djebali, Roger P. Alexander, Burak H. Alver, Raymond K. Auerbach, Kimberly Bell, Peter J. Bickel, Max E. Boeck, Nathan P. Boley, Benjamin W. Booth, Lucy Cherbas, Peter Cherbas, Chao Di, Alex Dobin, Jorg Drenkow, Brent Ewing, Gang Fang, Megan Fastuca, Elise A. Feingold, Adam Frankish, Guanjun Gao, Peter J. Good, Phil Green, Roderic Guigó, Ann Hammonds, Jen Harrow, Roger A. Hoskins, Cédric Howald, Long Hu, Haiyan Huang, Tim J. P. Hubbard, Chau Huynh, Sonali Jha, Dionna Kasper, Masaomi Kato, Thomas C. Kaufman, Rob Kitchen, Erik Ladewig, Julien Lagarde, Eric Lai, Jing Leng, Zhi Lu, Michael MacCoss, Gemma May, Rebecca McWhirter, Gennifer Merrihew, David M. Miller, Ali Mortazavi, Rabi Murad, Brian Oliver, Sara Olson, Peter Park, Michael J. Pazin, Norbert Perrimon, Dmitri Pervouchine, Valerie Reinke, Alexandre Reymond, Garrett Robinson, Anastasia Samsonova, Gary I. Saunders, Felix Schlesinger, Anurag Sethi, Frank J. Slack, William C. Spencer, Marcus H. Stoiber, Pnina Strasbourger, Andrea Tanzer, Owen A. Thompson, Kenneth H. Wan, Guilin Wang, Huaien Wang, Kathie L. Watkins, Jiayu Wen, Kejia Wen, Chenghai Xue, Li Yang, Kevin Yip, Chris Zaleski, Yan Zhang, Henry Zheng, Steven E. Brenner, Brenton R. Graveley, Susan E. Celniker, Thomas R Gingeras, Robert Waterston. 2014 The Comparative ENCODE RNA Resource Reveals Conserved Principles of Transcription. Nature 512(7515): 445-448.
- Wen, J., J. Mohammed, H. Tsai, N. Robine, J. O. Westholm, E. Ladewig, D. Bortolamiol-Becet, Q. Dai, K. Okamura, A. S. Flynt, D. Zhang, J. Andrews, L. Cherbas, T. C. Kaufman, P. Cherbas, A. Siepel and E. C. Lai 2014 Diversity of miRNAs, siRNAs and piRNAs surveyed across 25 Drosophila cell lines. Genome Res. 24(7): 1236-1250.
- Eisman, R. C. and T. C. Kaufman 2013 Probing the Boundaries of Orthology: The unanticipated rapid evolution of Drosophila centrosomin Genetics 194:903-926
- Robert J. Wilson, Joshua L. Goodman, Victor B. Strelets and The FlyBase Consortium* 2008 FlyBase: Integration and Improvements to Query Tools. Nucl. Acids Res. 36(Database issue): D588-D593; doi:10.1093/nar/gkm930
* W. Gelbart, L. Bitsoi, M. Crosby, A. Dirkmaat, D. Emmert, L. S. Gramates, K. Falls, R. Kulathinal, B. Matthews, M. Roark, S. Russo, A. Schroeder, S. St. Pierre, H. Zhang, P. Zhang, P. Zhou, M. Zytkovicz, M. Ashburner, N. Brown, P. Leyland, S. Marygold, P. McQuilton, G. Millburn, R. Seal, D. Sutherland, S. Tweedie, M. Williams, T. Kaufman, K. Matthews, G. Grumbling.
- Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. 2008 Quantitative Proteomics of a Presymptomatic A53T-Synuclein Drosophila Model of Parkinson Disease. Mol. Cell. Proteomics, 7, 1191-1203.
- Eisman, R., and T. C. Kaufman. 2008. Cytological investigation of the mechanism of parthenogenesis in Drosophila mercatorum. FLY 1: 317 - 329
- Schaeffer, S. W., A. Bhutkar, B. F. McAllister, M. Matsuda, L. M. Matzkin, P. M. O' Grady, C. Rohde, V. L. S. Valente, M. Aguadé, W. W. Anderson, K. Edwards, A. C. L. Garcia, J. Goodman, J. Hartigan, E. Kataoka, R. T. Lapoint, E. R. Lozovsky, C. A. Machado, M. A. F. Noor, M. Papaceit, L. K. Reed, S. Richards, T. T. Rieger, S. M. Russo, H. Sato, C. Segarra, D. R. Smith, T. F. Smith, V. Strelets, Y. N. Tobari, Y. Tomimura, M. Wasserman, T. Watts, R. Wilson, K. Yoshida, T. A. Markow, W. M. Gelbart and T. C. Kaufman. 2008. Polytene Chromosomal Maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics Genetics 179: 1601-1655.
- Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. 2007 Lifetime Proteomic Profiling of an A30P α-synuclein Drosophila Model of Parkinson's Disease J. Proteome Res., 6, 3729-3738.
- A. Stark, M. F. Lin, P. Kheradpour, J. S. Pedersen, L. Parts, J. W. Carlson, M. A. Crosby, M. D. Rasmussen, S. Roy, A. N. Deoras, J. G. Ruby, J. Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, E. Hodges, A. S. Hinrichs, A. Caspi, B. Paten, S.-W. Park, M. V. Han, M. L. Maeder, B. J. Polansky, B. E. Robson, S. Aerts, J. van Helden, B. Hassan, D. G. Gilbert, D. A. Eastman, Michael Rice, M. Weir, M. W. Hahn, Y. Park, C. N. Dewey, L. Pachter, W. J. Kent, D. Haussler, E. C. Lai, D. P. Bartel, G. J. Hannon, T. C. Kaufman, M. B. Eisen, A. G. Clark, D. Smith, S. E. Celniker, W. M. Gelbart and M. Kellis 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219-32.
- Steven J Marygold, Andrew Lambertsson, John Roote, Michael Ashburner, Gillian Millburn, Naoya Kenmochi, Paul Harrison, Zhan Yu, Thomas C Kaufman, Sally J Leevers and Kevin R Cook. 2007. The Ribosomal Protein Genes and Minute Loci of Drosophila melanogaster. Genome Biology 8(10):R216.
- Xun, Z.; Sowell, R. A.; Kaufman, T. C.; Clemmer, D. E. 2007 Protein Expression in a Drosophila Model of Parkinson's Disease, J. Proteome Research, 6, 348-357.
- Drosophila 12 Genomes Consortium* 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-18.
* Project Leaders A. G. Clark, M. B. Eisen, D. R. Smith, C. M. Bergman, B. Oliver, T. A. Markow, T. C. Kaufman, M. Kellis and William Gelbart
- Sowell, R. A., Hersberger, K. E., Kaufman, T. C., Clemmer, D. E. 2007 Examining the Proteome of Drosophila across Organism Lifespan J. Proteome Res., 6, 3637-3647.