Research Topics
Genomes and GenesSpecies | Damon LischSummaryAffiliation: University of California Country: USA Publications
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Publications
How important are transposons for plant evolution?Damon Lisch
Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California 94720, USA
Nat Rev Genet 14:49-61. 2013..Recent advances in genomics and phenomics for a range of plant species, particularly crops, have begun to allow the systematic assessment of these questions...- Regulation of transposable elements in maizeDamon Lisch
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States
Curr Opin Plant Biol 15:511-6. 2012..The available evidence from maize and other species suggests that these distinctions are made in order to generate information in somatic tissues that can be used to induce or reinforce silencing in germinal tissues... - Epigenetic regulation of transposable elements in plantsDamon Lisch
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Annu Rev Plant Biol 60:43-66. 2009..Together, these observations suggest that naturally occurring changes in transposon activity may have had an important impact on the causes and consequences of epigenetic silencing in plants... 
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosidsEric Lyons
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Plant Physiol 148:1772-81. 2008..This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically...- Initiation, establishment, and maintenance of heritable MuDR transposon silencing in maize are mediated by distinct factorsMargaret Roth Woodhouse
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
PLoS Biol 4:e339. 2006..Together, these data suggest that the establishment and maintenance of MuDR silencing have distinct requirements... - The mop1 (mediator of paramutation1) mutant progressively reactivates one of the two genes encoded by the MuDR transposon in maizeMargaret Roth Woodhouse
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Genetics 172:579-92. 2006..Conversely, mudrB expression is never restored, its TIR remains methylated, and new insertions of Mu elements are not observed. These data suggest that mudrA and mudrB silencing may be maintained via distinct mechanisms... 
Heritable transposon silencing initiated by a naturally occurring transposon inverted duplicationR Keith Slotkin
Department of Plant and Microbial Biology, 111 Koshland Hall, University of California Berkeley, Berkeley, California 94720, USA
Nat Genet 37:641-4. 2005..Further, transposon-generated inverted duplications may be important for the generation of double-stranded RNAs used in gene silencing...- Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plantsMichael Freeling
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
Curr Opin Plant Biol 15:131-9. 2012..Regulatory DNA deletion following polyploidy combined with abundant RNA-seq expression datasets are being used to generate testable hypothesizes regarding the function of specific cis-regulatory sequences... - Horizontal transfer of a plant transposonXianmin Diao
Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
PLoS Biol 4:e5. 2006..This is the first well-documented example of horizontal transfer of any nuclear-encoded genes between higher plants... - Distal expression of knotted1 in maize leaves leads to reestablishment of proximal/distal patterning and leaf dissectionJulio Ramirez
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Plant Physiol 151:1878-88. 2009.... - Production and processing of siRNA precursor transcripts from the highly repetitive maize genomeChristopher J Hale
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
PLoS Genet 5:e1000598. 2009.... - Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologsMargaret R Woodhouse
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
PLoS Biol 8:e1000409. 2010..Among the evolutionary benefits of this deletion/fractionation mechanism is bulk DNA removal and the generation of novel combinations of regulatory sequences and coding regions... - Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea maysR Keith Slotkin
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Genetics 165:781-97. 2003..MuDR elements silenced by Muk remain silenced even in plants that do not inherit Muk, suggesting that Muk is required for the initiation of MuDR silencing but not for its maintenance... - Strategies for silencing and escape: the ancient struggle between transposable elements and their hostsDamon Lisch
Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
Int Rev Cell Mol Biol 292:119-52. 2011..Here, we discuss TE activity in plants as the result of a constantly shifting balance between host strategies for TE silencing and TE strategies for escape and amplification... - Epigenetic reprogramming during vegetative phase change in maizeHong Li
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 107:22184-9. 2010..We demonstrate that a change in expression of a key component of the RNA silencing pathway is associated with both vegetative phase change and shifts in epigenetic regulation of a maize transposon... - Many or most genes in Arabidopsis transposed after the origin of the order BrassicalesMichael Freeling
Department of Plant and Microbial Biology, University of California at Berkeley, California 94720, USA
Genome Res 18:1924-37. 2008..The observed differences between gene families raise important questions concerning the causes and consequences of gene transposition... - Transposable element origins of epigenetic gene regulationDamon Lisch
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
Curr Opin Plant Biol 14:156-61. 2011.... - Biodiversity (Communications arising): maize transgene results in Mexico are artefactsNick Kaplinsky
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Nature 416:601-2; discussion 600, 602. 2002.... - Mutator transposonsDamon Lisch
Dept Plant and Microbial Biology, 111 Koshland Hall, University of California at Berkeley, 94720, USA
Trends Plant Sci 7:498-504. 2002..In addition to its utility, the means by which this widespread and highly mutagenic system is held in check should help us to address fundamental issues concerning the stability of genomes... - Pack-MULEs: theft on a massive scaleDamon Lisch
Department of Plant and Microbial Biology, University of California at Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
Bioessays 27:353-5. 2005..These results have fascinating implications for our understanding of the mode and tempo of gene evolution in plants...