DNA methylation (5-methylcytosine) in mammals and plants silences transposons, retroviruses, and regulates gene imprinting. In mammals, DNA hypermethylation is associated with certain diseases including the onset and progression of cancer. We discovered that the Arabidopsis DEMETER (DME) protein regulates imprinting by DNA demethylation. DME is related to DNA glycosylases that excise damaged/mispaired bases in the base excision DNA repair pathway. DME excises 5-methylcytosine that is replaced with cytosine. DME is expressed primarily in the central cell, the progenitor of the placenta-like endosperm that supports embryo development. DME demethylates and activates maternal allele expression of genes that are imprinted in the endosperm. Arabidopsis has three DME-LIKE (DML) genes: ROS1, DML2, and DML3, which are broadly expressed in the plant. Like DME, they excise 5-methylcytosine and have a DNA glycosylase domain flanked by additional conserved domains that are essential for activity. DME and DML proteins specifically demethylate the 5'and 3'ends of at least 180 genes. ROS1 demethylates disease resistance genes and is required for resistance to a bacterial pathogen, Pseudomonas syringae. We will carry out the following experiments to understand the mechanisms and functions of DNA demethylation in the regulation of gene imprinting. 1) We will elucidate how expression of DME is restricted to the central cell, identify new genes imprinted by DME, and isolate mutations in genes that regulate DME expression, targeting, and/or DNA demethylation. 2) To understand the molecular mechanisms of DNA demethylation, we will identify and analyze the function of DME-binding proteins, determine if DME directly demethylates DNA by physical association with its target genes, and elucidate what changes in chromatin structure accompany DNA demethylation. 3) To understand how DNA demethylation regulates disease resistance, we will elucidate the function of plant defense genes that are demethylated by ROS1. Plants and animals have related mechanisms for controlling DNA methylation. Information about the basic mechanisms of DNA demethylation will provide valuable insights into the critical role DNA methylation plays in the regulation of gene imprinting and disease

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM069415-07
Application #
7804570
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
2004-02-01
Project End
2012-04-30
Budget Start
2010-05-01
Budget End
2011-04-30
Support Year
7
Fiscal Year
2010
Total Cost
$303,930
Indirect Cost
Name
University of California Berkeley
Department
Other Basic Sciences
Type
Schools of Earth Sciences/Natur
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Park, Jin-Sup; Frost, Jennifer M; Park, Kyunghyuk et al. (2017) Control of DEMETER DNA demethylase gene transcription in male and female gamete companion cells in Arabidopsis thaliana. Proc Natl Acad Sci U S A 114:2078-2083
Park, Kyunghyuk; Kim, M Yvonne; Vickers, Martin et al. (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proc Natl Acad Sci U S A 113:15138-15143
Hsieh, Ping-Hung; He, Shengbo; Buttress, Toby et al. (2016) Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proc Natl Acad Sci U S A 113:15132-15137
Park, Kyunghyuk; Frost, Jennifer M; Adair, Adam James et al. (2016) Optimized Methods for the Isolation of Arabidopsis Female Central Cells and Their Nuclei. Mol Cells 39:768-775
Rodrigues, Jessica A; Zilberman, Daniel (2015) Evolution and function of genomic imprinting in plants. Genes Dev 29:2517-31
Brooks, Sonja C; Fischer, Robert L; Huh, Jin Hoe et al. (2014) 5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3. Biochemistry 53:2525-32
Mérai, Zsuzsanna; Chumak, Nina; García-Aguilar, Marcelina et al. (2014) The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proc Natl Acad Sci U S A 111:16166-71
Park, Guen Tae; Frost, Jennifer M; Park, Jin-Sup et al. (2014) Nucleoporin MOS7/Nup88 is required for mitosis in gametogenesis and seed development in Arabidopsis. Proc Natl Acad Sci U S A 111:18393-8
Yu, Agnes; Lepere, Gersende; Jay, Florence et al. (2013) Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense. Proc Natl Acad Sci U S A 110:2389-94
Rodrigues, Jessica A; Ruan, Randy; Nishimura, Toshiro et al. (2013) Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proc Natl Acad Sci U S A 110:7934-9

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