DNA methylation is a crucial regulator of mammalian development. Mutations in DNA methyltransferases and methylcytosine binding protein genes cause genetic disease, and disrupted DNA methylation is a hallmark of cancer. Defects in DNA demethylation are associated with disorders of the central nervous system, tumor development, and failure to establish embryonic pluripotency. In addition, defective DNA demethylation prevents the in vitro derivation of induced pluripotent stem cells, a technology with the potential to be used in the clinic for the regeneration of cells, tissues and organs. Whereas most common model organisms lack DNA methylation, flowering plants, including Arabidopsis thaliana, share highly conserved methylation and demethylation pathways with mammals. Both plants and mammals use DNA methylation to regulate genomic imprinting - epigenetic marking and resultant gene expression only from an allele inherited from either the male or the female parent. We discovered that DNA demethylation catalyzed by the Arabidopsis DME DNA glycosylase occurs exclusively in companion cells, the central cell and the vegetative cell, which are adjacent to the gametes, the egg and sperm, respectively. One sperm fertilizes the central cell to generate the endosperm, a nutritive extra-embryonic tissue. A second sperm fertilizes the egg to form the embryo. We showed that gene imprinting occurs in the endosperm, which is established by DNA demethylation in the central cell. Moreover, our recent results suggest that DNA demethylation of central cell and vegetative cell genomes generates small RNAs that move to the adjacent gametes and silence transposable elements by the RNA-directed DNA methylation pathway.
In Aim 1, we will test our model that DME-mediated DNA demethylation in companion cells functions to reinforce TE silencing in gametes.
In Aim 2, we will elucidate the critical relationship between chromatin structure and targeted DNA demethylation.
In Aim 3, we will identify new genes required for DNA demethylation. Our studies will lead to a detailed understanding of the epigenetic reprogramming catalyzed by DNA demethylation during plant sexual reproduction.

Public Health Relevance

DNA methylation is an important mechanism for regulating human genes, the disruption of which contributes to the development of many cancers, congenital disorders, and syndromes associated with defects in gene imprinting. In early mammalian development, DNA demethylation is required for acquiring pluripotency, generating stem cells, and for gene imprinting. Defects in DNA demethylation are associated with disorders in the central nervous system associated with stress, as well as the development and progression of cancer. DNA demethylation is thought to be the rate-limiting step in generating induced pluripotent stem (iPS) cells, an emerging medical technology that offers the promise of patient-specific stem cell implantations that can potentially regenerate cells, tissues and organs. We are studying how DNA is actively demethylated by the DME DNA glycosylase;this will support the development of diagnostic and therapeutic interventions, detecting and potentially reversing the onset and progression of disease-causing aberrant DNA methylation. As described in a letter of support from Dr. George Martin (Director of Technology, Chief Technology Office, Roche Diagnostics), continued research into DME is invaluable for the study of epigenetics in human disease, and complements efforts to develop reagents to detect aberrant DNA methylation in clinical samples.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Molecular Genetics B Study Section (MGB)
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Carter, Anthony D
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University of California Berkeley
Other Basic Sciences
Schools of Earth Sciences/Natur
United States
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Frost, Jennifer M; Kim, M Yvonne; Park, Guen Tae et al. (2018) FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proc Natl Acad Sci U S A 115:E4720-E4729
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
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
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