Dr. William F. Thompson

Distinguished University Professor of Plant & Microbial Biology, Genetics, and Crop Science
Plant gene expression, chromatin structure, DNA replication, epigenetics

Research Interests

My two main research projects at present involve DNA replication and epigenetics.  One is a large collaboration involving colleagues at three major institutions that seeks to characterize DNA replication programs in Arabidopsis and maize under different developmental circumstances and elucidate the mechanism whereby epigenetic marks are transmitted to daughter chromosomes in mitosis.  The other is a local collaboration with Dr. George Allen in which we seek to clarify the molecular mechanism by which matrix attachment regions affect transgene expression and silencing.

Selected Publications (from 157 total)

Thompson, W. F. and R. Cleland, 1971.  Auxin and RNA synthesis in pea stem tissue as studied by DNA/RNA hybridization.  Plant Physiol. 48: 663-670.

Thompson, W. F. and R. Cleland, 1972.  Effect of light and gibberellin on RNA synthesis in pea stem tissue as studied by DNA/RNA hybridization.  Plant Physiol. 50:289-292.

Stein, D. B. and W. F. Thompson, 1975.  DNA hybridization and evolutionary relationships in three Osmunda species.  Science 189:888-890.

Cuellar, R. E., G. A. Ford, W. R. Briggs and W. F. Thompson, 1978.  Application of higher derivative techniques to analysis of high resolution thermal denaturation profiles of reassociated repetitive DNA.  Proc. Natl.  Acad. Sci., USA, 75:6026-6030.

Murray, M. G., R. E. Cuellar and W. F. Thompson, 1978.  DNA sequence organization in the pea genome.  Biochemistry 17:5781-5790.

Murray, M. G., J. D. Palmer, R. E. Cuellar and W. F. Thompson, 1979.  DNA sequence organization in the mung bean genome.  Biochemistry 18:5259-5266.

Stein, D. B., W. F. Thompson and H. S. Belford, 1979.  Studies on DNA sequence in the Osmundaceae.  J. Mol. Evol. 12:215-232.

Murray, M. G. and W. F. Thompson, 1980.  Rapid isolation of high molecular weight plant DNA.  Nucleic Acids Research 8:4321-4325.

Belford, H. S. and W. F. Thompson, 1981.  Single copy DNA homologies in Atriplex.  I. Cross reactivity estimates and the rate of deletions in genome evolution. Heredity 46:91-108.

Belford, H. S. and W. F. Thompson, 1981.  Single copy DNA homologies in Atriplex. II. Hybrid thermal stabilities and molecular phylogeny.  Heredity, 46:109-122.

Murray, M. G., D. L. Peters and W. F. Thompson, 1981.  Ancient repeated sequences in the pea and mung bean genomes and implications for genome evolution.  J. Mol. Evol. 17:31-42.

Palmer, J. D. and W. F. Thompson, 1981.  Rearrangements in the chloroplast genomes of mung bean and pea. Proc.  Natl. Acad. Sci. U. S. A., 78:5533-5537.

Thompson, W. F. and M. G. Murray, 1981.  The nuclear genome: Structure and Function.  In: The Biochemistry of Plants, Vol. 6, A. Marcus, (ed.), Academic Press, NY, 1-81.

Palmer, J. D. and W. F. Thompson, 1982.  Chloroplast DNA rearrangements are more frequent when a large inverted repeat is lost.  Cell 29:537-550.

Spiker, S., M. G. Murray, and W. F. Thompson, 1983.  DNase I sensitivity of transcriptionally active genes in intact nuclei and isolated chromatin of plants. Proc. Natl. Acad. Sci. U.S.A. 80:815-819.

Kaufman, L. S., W. F. Thompson and W. R. Briggs, 1984.Different red light requirements for phytochrome-induced accumulation of Cab RNA and RbcS RNA.  Science 226, 1447-1449.

Kaufman, L. S., W. R. Briggs and W. F. Thompson. 1985. Phytochrome control of specific mRNA levels in developing pea buds: The presence of both very low fluence and low fluence responses.  Plant Physiology 78, 388-393.

Polans, N. O., N. F. Weeden and W. F. Thompson. 1985. The inheritance, organization and mapping of RbcS and Cab multigene families in pea.  Proc.  Natl. Acad. Sci. USA 82, 5083-5087.

Kaufman, L. S., J. C. Watson, and W. F. Thompson. 1987. Light-regulated changes in DNase I hypersensitive sites in the rRNA genes of Pisum sativum.  Proc.Nat. Acad.Sci. USA 84, 1550-1554.

Palmer, J. D., B. Osorio, K. J. Aldrich, and W. F. Thompson. 1987.  Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements. Current Genetics 11, 275-286.

Watson, J. C., L. S. Kaufman, and W. F. Thompson. 1987. Developmental regulation of cytosine methylation in the nuclear ribosomal RNA genes of Pisum sativum.  J. Mol. Biol. 193, 15-26.

Flavell, R. B.,  M. O’Dell, and W. F. Thompson 1988 Cytosine methylation in ribosomal DNA and nucleolus organiser expression in wheat.   J. Mol. Biol. 204, (500-534).

Murphy, T. M. and W. F. Thompson. 1988. Molecular Plant Development, Prentice Hall, Englewood Cliffs, NJ

Thompson, W. F. and R. B. Flavell 1988 DNase I sensitivity of ribosomal RNA genes in chromatin and nucleolar dominance in wheat. J. Mol. Biol. 204, 535-548.

Thompson, W. F. 1988. Photoregulation: Diverse gene responses in greening seedlings.  Plant, Cell, and Environment 11, 319-328.

Woodbury, N. W., L. L. Roberts, J. D. Palmer, and W. F. Thompson. 1988. A transcription map of the pea chloroplast genome. Current Genetics 14, 75-89.

Elliott, R. C., T. J. Pedersen, B. Fristensky, M. J. White, L. F. Dickey, and W. F. Thompson. 1989  Characterization of a single copy gene encoding ferredoxin I from pea.  The Plant Cell, 1, 681-690.

Elliott, R. C.,  L. F. Dickey, M. J. White, and W. F. Thompson. 1989  Cis-acting elements for light regulation of pea ferredoxin I gene expression are located within transcribed sequences.  The Plant Cell, 1, 691-698.

Woodbury, N. W., M. S. Dobres and W. F. Thompson. 1989  The identification and localization of 33 pea chloroplast transcription initiation sites.  Current Genetics 16, 433-445.

Hall, G., G. C. Allen, D. S. Loer, W. F. Thompson and S. Spiker. (1991). Nuclear scaffold and scaffold attachment regions (SARs) in higher plants. Proc. Natl. Acad. Sci. USA 88, 9320-9324.

Thompson, W. F. and M. J. White. 1991. Physiological and molecular studies of light regulated nuclear genes in higher plants. Annu. Rev. Plant Physiol. Mol. Biol. 42: 423-466.

Dickey, L. F., M. Gallo-Meagher, and W. F. Thompson.  (1992) Light regulatory sequences are located within the 5′ portion of the Fed-1 message sequence. EMBO J. 11, 2311-2317.

Frances, S., M. J. White, M. D. Edgerton, A. M. Jones, R. C. Elliott and W. F. Thompson. (1992) Initial characterization of a pea mutant with light-independent photomorphogenesis.  Plant Cell 4, 1519-1530.

Gallo-Meagher, M., D. A. Sowinski and W. F. Thompson (1992)  The pea ferredoxin I gene exhibits different light responses in etiolated seedlings of pea and tobacco.  Plant Cell 4, 383-388.

Gallo-Meagher, M., D. A. Sowinski, R. C. Elliott and W. F. Thompson (1992)  Both internal and external elements control expression of the pea Fed-1 gene in etiolated seedlings.  Plant Cell 4, 389-395.

Allen, G. C., G. E. Hall, L. C. Childs, A. K. Weissinger, S. L. Spiker, and W. F. Thompson. (1993) Scaffold attachment regions increase reporter gene expresssion in stably transformed plant cells.  Plant Cell 5, 603-613.

Dickey, L. F. T.-T. Nguyen, G. C. Allen, and W. F. Thompson (1994) Light modulation of ferredoxin mRNA abundance requires an open reading frame.  Plant Cell 6, 1171-1176.

Allen, G. C., G. Hall, S. Michalowski, W. Newman, A. K. Weissinger, S. Spiker and W. F. Thompson. (1996). High level transgene expression in plant cells:  Effects of a strong SAR from tobacco.  Plant Cell 8, 899-913.

Petracek, M. E., L. F. Dickey, S. Huber, and W. F. Thompson (1997).  Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis.  Plant Cell 9:  2291-2300.

Tanzer, M. M., W. F. Thompson, M. D. Law, E. A. Wernsman and S. Uknes (1997).  Characterization of post-transcriptionally suppressed transgene expression that confers resistance to tobacco etch virus infection in tobacco. Plant Cell 9: 1411-1423.

Thompson, W. F., A. F. Bevan, B. Wells, and P. Shaw (1997).  Sites of rDNA transcription are widely disppersed through the nucleolus in Pisum sativum and can comprise single genes.  Plant J. 12: 571-581.

Dickey, L. F., M. E. Petracek, E. R. Hansen, and W. F. Thompson (1998).  Light regulation of Fed-1 mRNA requires an element in the 5′ untranslated region and correlates with differential polyribosome association.  Plant Cell 10: 475-484.

Petracek, M. E., L. F. Dickey, T. T. Nguyen, C. Gatz, D. A. Sowinski, G. C. Allen, and W. F. Thompson. (1998) Ferredoxin mRNA is destabilized by changes in photosynthetic electron transport.  Proc. Natl. Acad. Sci. USA 95, 9009-9013.

Fitzmaurice, W. P., L. V. Nguyen, E. A. Wernsman, W. F. Thompson, and M. A. Conkling (1999) Transposon tagging of the Sulfur gene of tobacco using engineered maize Ac/Ds elements.  Genetics 153, 1919-1928.

Michalowski, S.M., G. C. Allen, G. E. Hall, W. F. Thompson and S. Spiker (1999) Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants.  Biochemistry 38, 12795-12804.

Ulker, B., G. C. Allen, S. L. Spiker, W. F. Thompson, and A. K. Weissinger (1999)  A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants. Plant J. 18: 253-263.

Vain, P., B. Worland, A. Kohli, J. W. Snape, P. Christou, G. C. Allen and W. F. Thompson (1999)  Matrix attachment regions increase transgene expression levels and stability in transgenic rice plants and their progeny. Plant J. 18: 233-242.

Allen, G. C., S Spiker, and W. F. Thompson (2000)  Use of matrix attachment regions (MARs) to minimize transgene silencing.  Plant Molecular Biology 43, 361-376.  (Invited review in special issue)

Ling, J., Wells, D. R., Tanguay, R. L., Dickey, L. F., Thompson, W. F. and Gallie, D. R. (2000). Heat shock protein HSP101 binds to the Fed-1 internal light regulatory element and mediates its high translational activity. Plant Cell 12, 1213-1228.

Petracek, M. E., T. Nuygen, W. F. Thompson and L. F. Dickey (2000) Premature Termination codons destabilize Fed-1 mRNA when Fed-1 is translated.  Plant J. 21: 563-569.

Halweg, C., W. F. Thompson and S. Spiker (2005). The rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: a flow cytometric study. Plant Cell 17(2): 418-29.

Shultz, R. W., V. M. Tatineni, L. Hanley-Bowdoin and W. F. Thompson (2007). Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice. Plant Physiol 144(4): 1697-714.

Tanurdzic, M., M. Vaughn, H. Jiang, T.-J. Lee, R. K. Slotkin, B. Sosinski, W. F. Thompson, R. W. Doerge, and R. Martienssen (2008) Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol 6(12): e302. doi:10.1371/journal.pbio.0060302

Shultz, R. W., T. J. Lee, G. C. Allen, W. F. Thompson and L. Hanley-Bowdoin (2009). Dynamic localization of the DNA replication proteins MCM5 and MCM7 in plants. Plant Physiol. 150: 658-669.

Lee, T.J., Pascuzzi, P. E., Settlage, S. B., Shultz, R. W., Tanurdzic, M., Rabinowicz, P. D., Menges, M., Zheng, P., Main, D., Murray, J. A. H., Sosinski, B., Allen, G. C., Martienssen, R. A., Hanley-Bowdoin, L., Vaughn, M. W.. and Thompson, W. F. (2010). Arabidopsis Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State. PLoS Genetics 6: e1000982.

Bass, H.W., Wear, E.E., Lee, T.-J., Hoffman, G.G., Gumber, H.K., Allen, G.C., Thompson, W.F., and Hanley-Bowdoin, L. (2014 in press). A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development. Journal of Experimental Botany. doi:10.1093/jxb/ert470

Pascuzzi, E., Flores-Vergara, M. A., Lee, T.-J., Sosinski, B, Vaughn, M. W., Hanley-Bowdoin, L., Thompson, W. F. and Allen, G. C. (2014) In vivo mapping of Arabidopsis Scaffold/Matrix Attachment Regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts. Plant Cell 26: 102-120; doi:10.1105/tpc.113.121194