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Damon Lisch

Damon Lisch Profile Picture
Associate Professor
Ph.D. in Genetics, U.C. Berkeley

Contact Info:
(765) 496-0197

Training Group(s):
Chromatin and Regulation of Gene Expression

Current Research Interests:

Dr. Lisch is interested in the regulation and evolution of plant transposable elements and the role that transposable elements have played in plant evolution.  Transposable elements, or transposons, are, by far, the most dynamic part of the eukaryotic genome, and the majority, often the vast majority, of plant genomes are composed of these genomic parasites.  Although they are an important source of genetic novelty, transposons can also be a significant source of detrimental mutations.  Because of this, plants (and indeed all eukaryotes) have evolved a sophisticated “immune system” whose function is to detect and epigenetically silence them.  Dr. Lisch’s research centers on determining the means by which transposons are detected and then maintained in a silenced state and the effect that this process has had on the trajectory of plant evolution.

Selected Publications:

Comet, P., D. Lisch, C. J. Hardeman, V. L. Chandler, and M. Freeling, 1991. Identification of a regulatory transposon that controls the Mutator system of transposable elements. Genetics 129: 261-270. Lisch, D., and M. Freeling, 1994. Loss of Mutator activity in a minimal line. M a y d i c a 39: 289-300 (13). Donlin, M. J., D. Lisch and M Freeling, 1995. Tissue-specific accumulation of MURB, a protein encoded by MuDR, the autonomous regulator of the Mutator transposable element family. The Plant Cell 7: 1989-2000. Lisch, D., P. Chomet, and M. Freeling, 1995. Genetic characterization of the Mutator system in maize: behavior and regulation of Mu elements in a minimal line. Genetics 139: 1777-1796. Kidwell, M., and D. Lisch, 1997. Transposable elements as sources of variation in animals and plants. PNAS 94: 7704-7711. Selinger, D.A., D. Lisch and V. L. Chandler, 1998. The Maize Regulatory Gene B-Peru contains a DNA rearrangement that specifies tissue-specific expression through both positive and negative promoter elements. Genetics 149:1125-1138. Kidwell, M. G. and D. Lisch, 1998. Hybrid genetics: transposons unbound. (Commentary) Nature 393:22-23. Lisch, D., L. Girard, M. Donlin and M. Freeling, 1999. Deletion derivatives of MuDR delineate functional roles for the MURA and MURB proteins. Genetics 151:331-341. Kidwell, M., and D. Lisch, 2000. Transposable elements and host gene evolution. Trends in Ecology and Evolution 15: 95-98. Kidwell, M., and D. Lisch, 2001. Perspective: Transposable Elements, parasitic DNA, and genome evolution. Evolution 55(1): 1-24

Lisch, D., R. Langham, M. Freeling, and M. Choy, 2001. The Mutator transposase is widespread in the grasses. Plant Physiology. 125: 1293-1303. M. Kidwell and D. Lisch, 2002. Transposable elements as sources of genomic variation. In: “Mobile DNA II”. Edited by Nancy L. Craig. Kaplinsky, N., D. Braun, D. Lisch, A. Hay, S. Hake, and M. Freeling, 2002. Biodiversity (Communications arising): maize transgene results in Mexico are artifacts. Nature (416): 601-2. Lisch, D., C. Carey, J. Dorweiler, and V.Chandler, 2002. A mutation that prevents paramutation in maize also reverses Mutator transposon methylation. P N A S . 99:6130-5. Lisch, D, 2002. The Mutator Transposons. Trends in Plant Science 7:498-504. Hudson, M., D. Lisch and P. Quail, 2003. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A signaling pathway. The Plant Journal 34:453-71 (16). Slotkin, R.K., M. Freeling, and D. Lisch, 2003. Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea mays. Genetics 165:781-97. Lisch, D. 2005. Pack-MULEs: Theft on a Massive Scale. BioEssays 27: 353-355. Slotkin, R.K., M. Freeling and D. Lisch, 2005 Heritable silencing of a transposon family is initiated by a naturally occurring inverted repeat derivative. Nature Genetics 137:641-644 Diao, X.M., M. Freeling and D. Lisch, 2006. Horizontal Transfer of a Plant Transposable element. PLoS Biology 4: 0119-0128. (Cover) Woodhouse, M., M. Freeling and D. Lisch, 2006. The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes enncoded by the MuDR transposon in maize. Genetics 172: 579-592. Diao, X. M. Freeling and D. Lisch, 2006. Mutator transposons in maize and MULEs in the plant genome. Yi Chuan Xue Bao 33: 477-87. Woodhouse, M., M. Freeling and D. Lisch, 2006, Initiation, establishment and maintenance of MuDR transposon silencing require distinct factors. PLoS Biology PMID: 16968137 (Editor’s Choice, Science 314:19) Lisch, D. and N. Jiang, 2008. Mutator and Pack-MULEs, in "The maize handbook - Volume II: Domestication, Genetics and Genomics of Maize". Edited by Sarah Hake and Jeff Bennetzen. Lyons, E., Castelletti, S., Brent Pedersen, B, Lisch, D. and M Freeling, 2008. Maize GEvo: A Comparative DNA Sequence Alignment Visualization and Research Tool in "The maize handbook - Volume II: Domestication, Genetics and Genomics of Maize". Edited by Sarah Hake and Jeff Bennetzen. Singh, J. Freeling, M. and D. Lisch, 2008. A position effect on the heritability of silencing. PLoS Genetics. PMID: 18846225

Lyons, E, Pedersen, B, Kane, J., Alam, M., Ming, R., Tang, H., Xiyin, H.T., Wang, R., Bowers, J., Paterson, Lisch, D., and M. Freeling, 2008. Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids. Plant Physiology. PMID: 18952863. Lisch, D, 2008. A new SPIN on horizontal transfer. Commentary. P N A S . PMID: 18974220 Freeling, M. Lyons, E., Pederson, B., Alam, B., Ming, R and D. Lisch, 2008. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research. PMID: 18836034 Lisch, D., 2009. Epigenetic regulation of transposons in plants. A n n u a l R e v i e w o f Plant Biology. PMID: 19007329. Hale, C., Erhard, L., Lisch, D., and J. Hollick, 2009. Distinct roles of RNA-directedDNA methylation factors in the processing of maize repetitive RNAs. P LoS Genetics. PMID: 19680464 Hanada, K., Vallejo, V., Nobuta, K., Slotkin, R.K., Lisch, D., Meyers, B.C., Shiu, S-H. and N. Jiang, 2009. Expression and evidence for function of Pack-MULEs in rice. Plant Cell. PMID: 19136648 Schnable, P.S et al. (Lisch, D., author 121 of 160), 2009. The B73 maize genome: complexity, diversity and dynamics. Science PMID: 19965430 (Cover) Jia, Y., Ohtsu, K, Lisch, D., Nettleton, D and P.S. Schnable, 2009. Loss of RNA- dependent RNA Polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons and genes in maize shoot apical meristems. PLoS Genetics PMID: 19936292 Ramirez, J., Bolduc, N., Lisch, D, and S. Hake, 2009. Position dependent effects of knotted1 on leaf shape in maize. Plant Physiology PMID: 19854860 Woodhouse, M. R., Schnable, J. C., Pedersen, B. S., Lyons, E., Lisch, D., Subramaniam, S. and M. Freeling, 2010. Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biology PMID: 20613864 (Cover) Li, Hong, Freeling, M. and D. Lisch, 2010. Epigenetic modifications are reprogrammed during vegetative phase change in maize. PNAS. PMID: 21135217 Jiang, N., Ferguson, A, Slotkin, R. K and D. Lisch, 2011. Pack-MULE transposable elements induce directional modification of genes through biased insertion and DNA acquisition. PNAS. PMID 21220310 Lisch, D. and J. Bennetzen, 2011. Transposable Element Origins of Epigenetic Gene Regulation. Current Opinion in Plant Biology, PMID: 21444239 Lisch, D. and R.K. Slotkin, 2011. Strategies for silencing and escape the ancient struggle between transposable elements and their hosts. International Review of Cell and Molecular Biology. PMID: 22078960

Ethalinda K. S., Cannon, Scott M., Birkett, Braun, B. L., Kodavali, S., Jennewein, D.M, Yilmaz, A., Antonescu, V., Antonescu, C., Harper, L.C., Gardiner, J.M., Schaeffer, M.L., Campbell, D. A., Andorf, C. M., Andorf, D., Lisch, D., Koch, K. E., and J. McCarty, 2012. POPcorn: an online resource providing access to distributed and diverse maize project data. International Journal of Plant Genomics. PMID: 22253616. Lisch, D., 2012. Regulation of transposable elements in maize. Current Opinion in Plant Biology. PMID: 22824142. Kidwell, M and D. Lisch, 2012. Hybrid Dysgenesis. In: “Encyclopedia of Genetics, 2nd edition.” Lisch, D., 2013. Regulation of the Mutator system of transposons in maize, in “Plant Transposable Elements” in the Methods in Molecular Biology series. Edited by Tom Peterson. Lisch, D., 2013. Transposons in Plant Gene Regulation. In: "Molecular Genetics and Epigenetics of Plant Transposons: Sculpting Genes and Genomes”. Edited by Nina Fedoroff. Lisch, D., 2013. How important are transposons for evolution? Nature Genetics Reviews. PMID: 23247435. Lisch, D., 2013. Transposable elements in plants. In: “McGraw-Hill Yearbook of Science & Technology”. Lisch, D., 2013. What is being written, and why?: comment on "How life changes itself: the Read-Write (RW) genome" by James Shapiro. PMID: 23891466 Woodhouse, M., Feng, C., Pires, J., Lisch, D. Freeling, M., and X. Wang, 2014. The origin, inheritance and gene regulatory consequences of genome dominance in polyploids. PNAS, PMID: 24706847. Mutator and MULE transposons. In: “Mobile DNA III”. In press. 

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