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Hu J, Yang Y, Lv X, Lao Z, Yu L. Dichlorodiphenyltrichloroethane metabolites inhibit DNMT1 activity which confers methylation-specific modulation of the sex determination pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 279:116828. [PMID: 33765505 DOI: 10.1016/j.envpol.2021.116828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
Dichlorodiphenyltrichloroethane (DDT) poses a significant health risk to humans which is associated with genomic DNA hypomethylation. However, the mechanism and biological consequences remain poorly understood. In vitro assays confirmed that the DDT metabolites 2,2-bis(p-chlorophenyl)-acetic acid (DDA) and 1-chloro-2,2-bis-(p-chlorophenyl)ethylene (DDMU), but not other DDT metabolites, significantly inhibited DNA methyltransferase 1 (DNMT1) activity, leading to genomic hypomethylation in cell culture assays. DNMT1 as a target for DNA hypomethylation induced by DDT metabolites was also confirmed using cell cultures in which DNMT1 was silenced or highly expressed. DDA and DDMU can modify methylation markers in the promoter regions of sexual development-related genes, and change the expression of Sox9 and Oct4 in embryonic stem cells. Molecular docking indicated that DDA and DDMU bound to DNMT1 with high binding affinity. Molecular dynamic simulation revealed that DDA and DDMU acted as allosteric modulators that reshaped the conformation of the catalytic domain of DNMT1. These findings provide a new insight into DDT-induced abnormalities in sexual development and demonstrate that selective binding to DNMT1 by DDA and DDMU can interfere with human DNMT1 activity and regulate the expression of the Sox9 and Oct4 genes.
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Affiliation(s)
- Junjie Hu
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Yan Yang
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, PR China; Synergy Innovation Institute of GDUT, Shantou, 515041, China
| | - Xiaomei Lv
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Zhilang Lao
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Lili Yu
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Luohu District, Shenzhen, 518020, Guangdong, China.
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Gokhman D, Nissim-Rafinia M, Agranat-Tamir L, Housman G, García-Pérez R, Lizano E, Cheronet O, Mallick S, Nieves-Colón MA, Li H, Alpaslan-Roodenberg S, Novak M, Gu H, Osinski JM, Ferrando-Bernal M, Gelabert P, Lipende I, Mjungu D, Kondova I, Bontrop R, Kullmer O, Weber G, Shahar T, Dvir-Ginzberg M, Faerman M, Quillen EE, Meissner A, Lahav Y, Kandel L, Liebergall M, Prada ME, Vidal JM, Gronostajski RM, Stone AC, Yakir B, Lalueza-Fox C, Pinhasi R, Reich D, Marques-Bonet T, Meshorer E, Carmel L. Differential DNA methylation of vocal and facial anatomy genes in modern humans. Nat Commun 2020; 11:1189. [PMID: 32132541 PMCID: PMC7055320 DOI: 10.1038/s41467-020-15020-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Changes in potential regulatory elements are thought to be key drivers of phenotypic divergence. However, identifying changes to regulatory elements that underlie human-specific traits has proven very challenging. Here, we use 63 reconstructed and experimentally measured DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that likely emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes associated with face and vocal tract anatomy went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-associated genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Malka Nissim-Rafinia
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Lily Agranat-Tamir
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Swapan Mallick
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Heng Li
- Broad Institute, Cambridge, MA, 02138, USA
| | | | - Mario Novak
- Institute for Anthropological Research, 10000, Zagreb, Croatia
- Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
| | | | - Jason M Osinski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | | | - Pere Gelabert
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Iddi Lipende
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Deus Mjungu
- Gombe Stream Research Center, Jane Goodall Institute, Kigoma, Tanzania
| | - Ivanela Kondova
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands
| | - Ottmar Kullmer
- Department of Palaeoanthropology and Messel Research, Senckenberg Center of Human Evolution and Paleoecology, Frankfurt am Main, Germany
| | - Gerhard Weber
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Tal Shahar
- Department of Neurosurgery, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Mona Dvir-Ginzberg
- Laboratory of Cartilage Biology, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Marina Faerman
- Laboratory of Bioanthropology and Ancient DNA, Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, 91120, Jerusalem, Israel
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, 85287, USA
| | - Alexander Meissner
- Broad Institute, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yonatan Lahav
- Otolaryngology - Head & Neck Surgery Department, Laryngeal Surgery Unit, Kaplan Medical Center, Rehovot, Israel
- The Hebrew University Medical School, Jerusalem, Israel
| | - Leonid Kandel
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - Meir Liebergall
- Orthopaedic Department, Hadassah - Hebrew University Medical Center, Jerusalem, Israel
| | - María E Prada
- I.E.S.O. 'Los Salados'. Junta de Castilla y León, León, Spain
| | - Julio M Vidal
- Junta de Castilla y León, Servicio de Cultura de León, León, Spain
| | - Richard M Gronostajski
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
- Genetics, Genomics and Bioinformatics Program, New York State Center of Excellence in Bioinformatics and Life Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, 14203, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, 85281, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | - Benjamin Yakir
- Department of Statistics, The Hebrew University of Jerusalem, 91905, Jerusalem, Israel
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - David Reich
- Broad Institute, Cambridge, MA, 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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Jia Y, Zheng J, Chi M, Liu S, Jiang W, Cheng S, Gu Z, Chen L. Molecular identification of dmrt1 and its promoter CpG methylation in correlation with gene expression during gonad development in Culter alburnus. FISH PHYSIOLOGY AND BIOCHEMISTRY 2019; 45:245-252. [PMID: 30276577 DOI: 10.1007/s10695-018-0558-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 08/14/2018] [Indexed: 06/08/2023]
Abstract
Dmrt1, a member of the Dmrt family, is an important transcription regulator of gender determination. To study the biological function of dmrt1 in sexual differentiation and its potential implication in breeding technology, we obtained the full-length cDNA and proximal promoter sequence of dmrt1 in Culter alburnus, and analyzed the impact of promoter CpG methylation on the gene expression pattern of dmrt1 during gonad development. Dmrt1 was 922 bp in length and consisted a 150 bp 5'-UTR, a 28 bp 3'-UTR, and a 744 bp open reading frame (ORF). Based on the coding sequence of the dmrt1 gene, the deduced amino acid sequence was detected, and the protein structure of this gene was predicted in C. alburnus. The results indicate that the structure and function of dmrt1 were highly conservative compared to other vertebrates. The expression level of dmrt1 mRNA in different tissues was explored by qRT-PCR, which was only highly expressed in the testes and almost undetectable in other tissues. The CpG methylation pattern of the dmrt1 promoter was studied using DNA sequencing of sodium bisulfite in adult testes and ovaries, and it was found that dmrt1 promoter CpGs were not methylated in the testes, whereas hypermethylated in the ovaries. These findings demonstrate that DNA methylation can regulate sexual dimorphic expression of dmrt1, and therefore epigenetic modifications may play a critical role in the gonad differentiation of C. alburnus.
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Affiliation(s)
- Yongyi Jia
- School of Life Science, East China Normal University, ShangHai, 200000, China
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313000, China
| | - Jianbo Zheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313000, China
| | - Meili Chi
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313000, China
| | - Shili Liu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313000, China
| | - Wenping Jiang
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313000, China
| | - Shun Cheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313000, China
| | - Zhimi Gu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, 313000, China.
| | - Liqiao Chen
- School of Life Science, East China Normal University, ShangHai, 200000, China.
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