Damon Lisch

Damon Lisch Profile Picture

Associate Professor
Ph.D. in Genetics, U.C. Berkeley

Contact Info:

(765) 496-0197

Training Group(s):
Plant Biology
Chemical Biology

Active Mentor - currently hosting PULSe students for laboratory rotations and recruiting PULSe students into the laboratory; serves on preliminary exam committees

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:

Lee, S., Fu, F., Liao, C-J., Mewa, D.B., Adeyanju, A., Ejeta, G, Lisch, D., and T.  Mengiste †, 2022."Broad spectrum and complete fungal resistance in sorghum is conferred through a complex regulation of an immune receptor embedded in a natural antisense transcript". The Plant Cell. PMID 35018449 

Guo W.*, Dafang  W. and D. Lisch † RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays. PLoS Genetics, (Cover) PMID: 3412582 

Zhao M*., Rachel, Yanga, D., Yina, L., Ferrella, T., Stolla, C., Wang, C. R. and D. Lisch†. Loss of CHH methylation influences the recombination landscape in maize, 2021, PNAS. PMID: 33558228 

Zhang, X.*, Zhao, M*., McCarty, D. and D. Lisch †, 2020. Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes. Nucleic Acids Research, PMID 32442316 

Burgess, D. *, Li, H., Zhao, M. *, Kim. S.Y.*, and D. Lisch†, 2020. Silencing of Mu elements in maize involves distinct populations of small RNAs and distinct patterns of DNA methylation. Genetics (Cover) PMID: 32229532 

Wendel, J.F. , Lisch, D., Hu, G., and Mason, A.S., 2018.  The long and short of Doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation. Current Opinion in Genetics and Development. PMID: 29438956  

Zhao*, M., Zhang, B, Lisch, D.  and J. Ma . Patterns and consequences of subgenome differentiation provide insights into the nature of paleopolyploidy in plants. The Plant Cell, 2017. PMID 29180596 

Xu, J*., Wang, Q., Freeling, M., Zhang, X., Xu, Y., Mao, Y., Tang, X., Wu, F., Lan, H., Cao, M., Rong T, Lisch, D. , and Lu, Y †. Natural antisense transcripts are significantly involved in regulation of drought stress in maize. Nucleic Acids Research, 2017 PMID: 28175341  

Freeling, M., Xu, J., Woodhouse, M., and D. Lisch, 2015. A solution to the C-value paradox andfunction of junk DNA: The Genome Balance Hypothesis. Molecular Plant. PMID: 25743198.  

Lisch, D.†, 2013.  How important are transposons for plant evolution? Nature Reviews Genetics. PMID: 23247435  

Kidwell, M. , and D. Lisch, 2013.  Transposable elements as sources of variation in animals and plants. Reprinted in: “Essential Readings in Evolutionary Biology.” Edited by Francisco J. Ayala  and John C. Avise. ISBN-13: 978-1421413051 

Lisch, D. , 2013. Transposons in Plant Gene Regulation. In: " Plant Transposons and Genome Dynamics in Evolution”.  Edited by Nina Fedorof.  ISBN: 978-0-470-95994-7 

Freeling, M. , Woodhouse, M.R., Subramaniam, S., Turco, G., Lisch, D. and Schnable, J.  Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Current Opinion in Plant Biology.  PMID: 22824142  

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   

Lisch, D.  and J. Bennetzen, 2011. Transposable Element Origins of Epigenetic Gene Regulation.  Current Opinion in Plant Biology, PMID: 21444239  

Li, H. *, Freeling, M. and D. Lisch , 2010.  Epigenetic modifications are reprogrammed during vegetative phase change in maize. PNAS. PMID: 21135217  

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)  

Lisch, D. †, 2009.  Epigenetic regulation of transposons in plants. Annual Review of Plant Biology. PMID: 19007329  

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. ISBN: 97814419266 

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  

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  

Singh, J.*, Freeling, M. and D. Lisch , 2008. A position effect on the heritability of silencing. PLoS Genetics. PMID: 18846225 (Highlighted manuscript)  

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)   

Woodhouse, M.*, M. Freeling and D. Lisch , 2006. The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maize. Genetics 172: 579-592  

Diao, X.M., M. Freeling and D. Lisch , 2006.  Horizontal transfer of a plant transposable element.  PLoS Biology 4: 0119-0128. (Cover) 

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  

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 

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. Plant Journal 34:453-71 (16)  

Lisch, D., C. Carey, J. Dorweiler, and V. Chandler , 2002. A mutation that prevents paramutation in maize also reverses Mutator transposon methylation.  PNAS. 99:6130-5  

Kidwell, M. and D. Lisch, 2002.  Transposable elements as sources of genomic variation. In: “Mobile DNA II”.  Edited by Nancy L. Craig. ISBN: 9781555812096 

Lisch, D. †, R. Langham, M. Freeling, and M. Choy, 2001.  The Mutator transposase is widespread in the grasses.  Plant Physiology. 125: 1293-1303  

Kidwell, M. , and D. Lisch, 2001.  Perspective:  Transposable Elements, parasitic DNA, and genome evolution.  Evolution 55(1): 1-24   

Lisch, D., L. Girard, M. Donlin and M. Freeling , 1999.  Functional analysis of deletion derivatives of the maize transposon MuDR delineates roles for the MURA and MURB proteins.  Genetics 151:331-341  

Kidwell, M. , and D. Lisch, 1997.  Transposable elements as sources of variation in animals and plants.  PNAS 94: 7704-7711  

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  

Lisch, D., and M. Freeling , 1994.  Loss of Mutator activity in a minimal line.  Maydica 39: 289-300 (13)  

Chomet, 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   

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