Interdisciplinary Life Science - PULSe Great research is a matter of choice

Joe Ogas

Joe  Ogas Profile Picture
Associate Professor of Biochemistry
Ph.D. - 1992 - University of California

Contact Info:

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

Current Research Interests:

We are interested in characterizing the factors and mechanisms that govern the flexible nature of plant cell identity. To accomplish this goal, we are utilizing a mutant of Arabidopsis thaliana, pickle (pkl), in which the primary root differentiates improperly and expresses embryonic characteristics after germination. Expression of the pickle root phenotype is dependent on gibberellin (GA), a plant growth regulator known to promote such diverse processes as germination, cell elongation, and initiation of flowering. We have cloned PKL, and it codes for a predicted CHD3-chromatin remodeling factor. CHD3 proteins from Xenopus and human cell lines have been shown to associate with histone deacetylase indicating that they may act as negative regulators of transcription. Consistent with such a role for PKL in Arabidopsis, we have shown that LEC1, a promoter of embryonic identity, is derepressed in germinating pkl seedlings.

Based on the phenotype of the pkl mutant and the function of proteins that are similar to PKL, our working model is that PKL regulates the transcription of genes in response to GA. Specifically, we propose that PKL establishes transcriptional repression of embryonic genes during germination by altering the structure of chromatin. This model will be tested by the following experimental strategies: examination of the expression of PKL, identification of genes that exhibit PKL-dependent transcription by microarray analysis, analysis of the promoters of those genes, identification of proteins that interact with PKL, and genetic screens for mutations that affect the phenotype of pkl plants.

Selected Publications:

Carter B, Henderson JT, Svedin E, Fiers M, McCarthy K, Smith A, Guo C, Bishop B, Zhang H, Riksen T, Shockley A, Dilkes BP, Boutilier K, and Ogas J. CHD3 chromatin remodelers promote crosstalk between sporophyte and gametophyte generations in A. thaliana. Genetics 203:817.

Bishop B, Ho KK, Tyler K, Smith A, Bonilla S, Leung YF, and Ogas J (2015). The chromatin remodeler chd5 is necessary for proper head development during embryogenesis of Danio rerio. Biochim Biophys Acta Gene Regulatory Mechanisms 1849, 1040-1050.

Harmeyer K, South PF, Bishop B, Ogas J, and Briggs S (2015). Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure. Nucleic Acids Research 43:e38.

Ho KK, Zhang H, Golden BL, Ogas J (2013). PICKLE is a CHD subfamily II ATP-dependent chromatin remodeling factor. Biochim Biophys Acta Gene Regulatory Mechanisms 1829:199.

Zhang H, Bishop B, Ringenberg W, Muir B, Ogas J (2012). The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone H3 lysine 27. Plant Physiology 159:418.

Muir WM, Rosa GJM, Pittendrigh BR, Xu Z, Rider SD, Fountain M, and Ogas J (2009). A mixture model approach for the analysis of small exploratory microarray experiments. Computational Statistics and Data Analysis 53:1566.

Zhang H, Rider SD, Henderson J, Fountain M, Chuang K, Kandachar K, Simons A, Edenberg HJ, Romero-Severson J, Muir WM, and Ogas J (2008). The CHD3 remodeler PICKLE promotes trimethylation of histone H3 lysine 27. J Biol Chem 283:22637.

Muir WM, Romero-Severson J, Rider SD, Simons A, and Ogas J (2006). Application of One Sided t-tests and a Generalized Experiment Wise Error Rate to High-Density Oligonucleotide Microarray Experiments: An Example Using Arabidopsis. J Data Sci 4:323.

Li H-C, Chuang K., Henderson JT, Rider Jr SD, Bai Y, Zhang H, Fountain M, Gerber J, and Ogas J (2005). PICKLE acts during germination to repress expression of embryonic traits. Plant Journal 44:1010.

Falcone DL, Ogas JP, and Somerville CR (2004). Regulation of membrane fatty acid composition by temperature in mutants of Arabidopsis with alterations in membrane lipid composition. BMC Plant Biology 4:17.

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