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Zhang C, Hung YH, Rim HJ, Zhang D, Frost JM, Shin H, Jang H, Liu F, Xiao W, Iyer LM, Aravind L, Zhang XQ, Fischer RL, Huh JH, Hsieh TF. The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:17563-17571. [PMID: 31409710 PMCID: PMC6717269 DOI: 10.1073/pnas.1907290116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencing their expression and initiating plant gene imprinting. DME also targets intergenic and heterochromatic regions, but how it is recruited to these differing chromatin landscapes is unknown. The C-terminal half of DME consists of 3 conserved regions required for catalysis in vitro. We show that this catalytic core guides active demethylation at endogenous targets, rescuing dme developmental and genomic hypermethylation phenotypes. However, without the N terminus, heterochromatin demethylation is significantly impeded, and abundant CG-methylated genic sequences are ectopically demethylated. Comparative analysis revealed that the conserved DME N-terminal domains are present only in flowering plants, whereas the domain architecture of DME-like proteins in nonvascular plants mainly resembles the catalytic core, suggesting that it might represent the ancestral form of the 5mC DNA glycosylase found in plant lineages. We propose a bipartite model for DME protein action and suggest that the DME N terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets.
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Affiliation(s)
- Changqing Zhang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
| | - Yu-Hung Hung
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
| | - Hyun Jung Rim
- Department of Plant Science, Seoul National University, 08826 Seoul, Republic of Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, 08826 Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Republic of Korea
| | - Dapeng Zhang
- Department of Biology, St. Louis University, St. Louis, MO 63103
| | - Jennifer M Frost
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Hosub Shin
- Department of Plant Science, Seoul National University, 08826 Seoul, Republic of Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, 08826 Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Republic of Korea
| | - Hosung Jang
- Department of Plant Science, Seoul National University, 08826 Seoul, Republic of Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, 08826 Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Republic of Korea
| | - Fang Liu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004 Nanning, China
| | - Wenyan Xiao
- Department of Biology, St. Louis University, St. Louis, MO 63103
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Xiang-Qian Zhang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
- College of Forestry and Landscape Architecture, South China Agricultural University, 510642 Guangzhou, China
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, 08826 Seoul, Republic of Korea;
- Research Institute for Agriculture and Life Sciences, Seoul National University, 08826 Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Republic of Korea
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
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