Karen Cone

Professor of Biological Sciences

PhD, 1984 Duke University

conek@missouri.edu
573-882-2118
101 Tucker Hall

http://www.biosci.missouri.edu/cone/index.html

Variegated pigmentation of PI-Blotched plant (left) compared to uniformly purple pigmentation of normal plant (right).

Research description

Epigenetics is the term used to described patterns of inheritance that involve changes in gene expression that do not result from classical mutation. For example, when genes are introduced into plants by genetic engineering, the genes become part of the genome by inserting at random into one of the plant chromosomes. Expression of the inserted gene depends, in part, on where the gene inserts. In some chromosomal sites, the gene may be expressed very well, but in other sites the gene may be expressed poorly or not at all. Because this differential expression is based on chromosomal context rather than DNA mutation, it can be considered to be under epigenetic control. Trying to understand epigenetic mechanisms of gene regulation is one of the goals of research in our lab. We are taking both genetics and genomics approaches.

Our genetic approach takes advantage of natural variants (mutants) in a regulatory gene, Purple, that controls purple anthocyanin pigment synthesis in maize. Plants carrying a normal allele of Purple develop intense purple pigmentation in virtually all of the vegetative tissues of the plant, but do not have pigmented kernels. By contrast, plants carrying the Blotched allele of Purple display a variegated pattern of pigmentation in all tissues of the plant, including the kernel. Molecular and genetic analyses indicate that Blotched is an “epimutation,” that is, a variant with altered gene expression but no substantive mutation at the DNA level. However, there are striking differences between the alleles in the level of genomic DNA methylation and in chromatin structure. To understand how these differences arise, we have isolated mutants that increase or decrease pigmentation in Blotched plants and that also change epigenetic patterns of methylation and/or chromatin structure. We are trying to isolate the genes responsible for altering Blotched as a way to dissect the mechanisms of epigenetic regulation.

In a genomics approach, we have joined forces with several colleagues across the country to identify and functionally analyze a large number of genes in maize that contribute to chromatin-based control of gene expression. Our strategy is to identify genes by their homology to known chromatin regulators, use genetic engineering to make mutations in these genes, and then ask what effect the mutations have on gene expression. One set of assays for the mutations involves crossing to Blotched to ask if any of the mutations cause Blotched to become more pigmented or less pigmented. Preliminary results indicate that several of the chromatin-gene mutations lead to altered levels of pigmentation in Blotched plants. This implicates these genes as players in the epigenetic regulation of Blotched gene. In the long term, we hope to learn not only how these chromatin genes influence Blotched expression, but also what effect they have on other genes that are controlled at the epigenetic level.

Selected publications

McGinnis, K., Chandler, V., Cone, K., Kaeppler, H., Kaeppler, S., Kerschen, A., Pikaard, C., Richards, E., Sidorenko, L., Smith, T., Springer, N., and Wulan, T. 2005. Transgene-induced RNA interference as a tool for plant functional genomics. Methods in Enzymology 392: 1-24.

Della Vedova, C. and Cone, K. 2004. Paramutation: the chromatin connection. The Plant Cell 16: 1358-1364.

Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C., Chandler, V.L., Kaeppler, H.F. and Kaeppler, S.M. 2003. Comparative analysis of SET domain proteins in maize (Zea mays) and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiology 132: 907-925.

Hoekenga, O.A., M.G. Musynski and K.C. Cone. 2000. Developmental patterns of chromatin structure and DNA methylation responsible for epigenetic expression of a maize regulatory gene. Genetics, 155: 1889-1902.

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