1
|
Toriyama K, Au Yeung WK, Inoue A, Kurimoto K, Yabuta Y, Saitou M, Nakamura T, Nakano T, Sasaki H. DPPA3 facilitates genome-wide DNA demethylation in mouse primordial germ cells. BMC Genomics 2024; 25:344. [PMID: 38580899 PMCID: PMC10996186 DOI: 10.1186/s12864-024-10192-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/05/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND Genome-wide DNA demethylation occurs in mammalian primordial germ cells (PGCs) as part of the epigenetic reprogramming important for gametogenesis and resetting the epigenetic information for totipotency. Dppa3 (also known as Stella or Pgc7) is highly expressed in mouse PGCs and oocytes and encodes a factor essential for female fertility. It prevents excessive DNA methylation in oocytes and ensures proper gene expression in preimplantation embryos: however, its role in PGCs is largely unexplored. In the present study, we investigated whether or not DPPA3 has an impact on CG methylation/demethylation in mouse PGCs. RESULTS We show that DPPA3 plays a role in genome-wide demethylation in PGCs even before sex differentiation. Dppa3 knockout female PGCs show aberrant hypermethylation, most predominantly at H3K9me3-marked retrotransposons, which persists up to the fully-grown oocyte stage. DPPA3 works downstream of PRDM14, a master regulator of epigenetic reprogramming in embryonic stem cells and PGCs, and independently of TET1, an enzyme that hydroxylates 5-methylcytosine. CONCLUSIONS The results suggest that DPPA3 facilitates DNA demethylation through a replication-coupled passive mechanism in PGCs. Our study identifies DPPA3 as a novel epigenetic reprogramming factor in mouse PGCs.
Collapse
Affiliation(s)
- Keisuke Toriyama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
| | - Azusa Inoue
- Laboratory for Epigenome Inheritance, Riken Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan
- Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Kazuki Kurimoto
- Department of Embryology, School of Medicine, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Yukihiro Yabuta
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe- cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Yoshida-Konoe- cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Toshinobu Nakamura
- Laboratory for Epigenetic Regulation, Department of Animal Bio-Science, Nagahama Institute of Bio-Science and Technology, Shiga, 526-0829, Japan
| | - Toru Nakano
- Graduate School of Frontier Biosciences, Osaka University, Osaka, 565-0871, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
| |
Collapse
|
2
|
Cuesta-Borràs E, Salvans C, Arqués O, Chicote I, Ramírez L, Cabellos L, Martínez-Quintanilla J, Mur-Espinosa A, García-Álvarez A, Hernando J, Tejedor JR, Mirallas O, Élez E, Fraga MF, Tabernero J, Nuciforo P, Capdevila J, Palmer HG, Puig I. DPPA3-HIF1α axis controls colorectal cancer chemoresistance by imposing a slow cell-cycle phenotype. Cell Rep 2023; 42:112927. [PMID: 37537841 DOI: 10.1016/j.celrep.2023.112927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 06/22/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Abstract
Tumor relapse is linked to rapid chemoresistance and represents a bottleneck for cancer therapy success. Engagement of a reduced proliferation state is a non-mutational mechanism exploited by cancer cells to bypass therapy-induced cell death. Through combining functional pulse-chase experiments in engineered cells and transcriptomic analyses, we identify DPPA3 as a master regulator of slow-cycling and chemoresistant phenotype in colorectal cancer (CRC). We find a vicious DPPA3-HIF1α feedback loop that downregulates FOXM1 expression via DNA methylation, thereby delaying cell-cycle progression. Moreover, downregulation of HIF1α partially restores a chemosensitive proliferative phenotype in DPPA3-overexpressing cancer cells. In cohorts of CRC patient samples, DPPA3 overexpression acts as a predictive biomarker of chemotherapeutic resistance that subsequently requires reduction in its expression to allow metastatic outgrowth. Our work demonstrates that slow-cycling cancer cells exploit a DPPA3/HIF1α axis to support tumor persistence under therapeutic stress and provides insights on the molecular regulation of disease progression.
Collapse
Affiliation(s)
- Estefania Cuesta-Borràs
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Cándida Salvans
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Oriol Arqués
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Irene Chicote
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; CIBERONC, 08029 Madrid, Spain
| | - Lorena Ramírez
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Laia Cabellos
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | | | - Alex Mur-Espinosa
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Alejandro García-Álvarez
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Jorge Hernando
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Juan Ramón Tejedor
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), Health Research Institute of the Principality of Asturias (ISPA), Spanish Biomedical Research Network in Rare Diseases (CIBERER), Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33011 Oviedo, Asturias, Spain
| | - Oriol Mirallas
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Elena Élez
- CIBERONC, 08029 Madrid, Spain; Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), Health Research Institute of the Principality of Asturias (ISPA), Spanish Biomedical Research Network in Rare Diseases (CIBERER), Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33011 Oviedo, Asturias, Spain
| | - Josep Tabernero
- CIBERONC, 08029 Madrid, Spain; Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; UVic-UCC, IOB-Quiron, 08023 Barcelona, Spain
| | - Paolo Nuciforo
- CIBERONC, 08029 Madrid, Spain; Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Jaume Capdevila
- Gastrointestinal and Endocrine Tumors Group, Medical Oncology Department, Vall d'Hebron University Hospital (HUVH), Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain; IOB-Teknon, 08023 Barcelona, Spain
| | - Héctor G Palmer
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; CIBERONC, 08029 Madrid, Spain.
| | - Isabel Puig
- Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain; CIBERONC, 08029 Madrid, Spain.
| |
Collapse
|
3
|
PGC7 Regulates Genome-Wide DNA Methylation by Regulating ERK-Mediated Subcellular Localization of DNMT1. Int J Mol Sci 2023; 24:ijms24043093. [PMID: 36834503 PMCID: PMC9958980 DOI: 10.3390/ijms24043093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 02/08/2023] Open
Abstract
DNA methylation is an epigenetic modification that plays a vital role in a variety of biological processes, including the regulation of gene expression, cell differentiation, early embryonic development, genomic imprinting, and X chromosome inactivation. PGC7 is a maternal factor that maintains DNA methylation during early embryonic development. One mechanism of action has been identified by analyzing the interactions between PGC7 and UHRF1, H3K9 me2, or TET2/TET3, which reveals how PGC7 regulates DNA methylation in oocytes or fertilized embryos. However, the mechanism by which PGC7 regulates the post-translational modification of methylation-related enzymes remains to be elucidated. This study focused on F9 cells (embryonic cancer cells), which display high levels of PGC7 expression. We found that both knockdown of Pgc7 and inhibition of ERK activity resulted in increased genome-wide DNA methylation levels. Mechanistic experiments confirmed that inhibition of ERK activity led to the accumulation of DNMT1 in the nucleus, ERK phosphorylated DNMT1 at ser717, and DNMT1 Ser717-Ala mutation promoted the nuclear localization of DNMT1. Moreover, knockdown of Pgc7 also caused downregulation of ERK phosphorylation and promoted the accumulation of DNMT1 in the nucleus. In conclusion, we reveal a new mechanism by which PGC7 regulates genome-wide DNA methylation via phosphorylation of DNMT1 at ser717 by ERK. These findings may provide new insights into treatments for DNA methylation-related diseases.
Collapse
|
4
|
Janssen SM, Lorincz MC. Interplay between chromatin marks in development and disease. Nat Rev Genet 2022; 23:137-153. [PMID: 34608297 DOI: 10.1038/s41576-021-00416-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have important roles in transcriptional regulation. Although many reports have characterized the functions of such chromatin marks in isolation, recent genome-wide studies reveal surprisingly complex interactions between them. Here, we focus on the interplay between DNAme and methylation of specific lysine residues on the histone H3 tail. We describe the impact of genetic perturbation of the relevant methyltransferases in the mouse on the landscape of chromatin marks as well as the transcriptome. In addition, we discuss the specific neurodevelopmental growth syndromes and cancers resulting from pathogenic mutations in the human orthologues of these genes. Integrating these observations underscores the fundamental importance of crosstalk between DNA and histone H3 methylation in development and disease.
Collapse
Affiliation(s)
- Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
5
|
UNOKI M, SASAKI H. The UHRF protein family in epigenetics, development, and carcinogenesis. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:401-415. [PMID: 36216533 PMCID: PMC9614205 DOI: 10.2183/pjab.98.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/14/2022] [Indexed: 05/31/2023]
Abstract
The UHRF protein family consists of multidomain regulatory proteins that sense modification status of DNA and/or proteins and catalyze the ubiquitylation of target proteins. Through their functional domains, they interact with other molecules and serve as a hub for regulatory networks of several important biological processes, including maintenance of DNA methylation and DNA damage repair. The UHRF family is conserved in vertebrates and plants but is missing from fungi and many nonvertebrate animals. Mammals commonly have UHRF1 and UHRF2, but, despite their high structural similarity, the two paralogues appear to have distinct functions. Furthermore, UHRF1 and UHRF2 show different expression patterns and different outcomes in gene knockout experiments. In this review, we summarize the current knowledge on the molecular function of the UHRF family in various biological pathways and discuss their roles in epigenetics, development, gametogenesis, and carcinogenesis, with a focus on the mammalian UHRF proteins.
Collapse
Affiliation(s)
- Motoko UNOKI
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Human Genetics, School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki SASAKI
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| |
Collapse
|
6
|
Greenberg MVC. Get Out and Stay Out: New Insights Into DNA Methylation Reprogramming in Mammals. Front Cell Dev Biol 2021; 8:629068. [PMID: 33490089 PMCID: PMC7817772 DOI: 10.3389/fcell.2020.629068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Vertebrate genomes are marked by notably high levels of 5-cytosine DNA methylation (5meC). The clearest function of DNA methylation among members of the subphylum is repression of potentially deleterious transposable elements (TEs). However, enrichment in the bodies of protein coding genes and pericentromeric heterochromatin indicate an important role for 5meC in those genomic compartments as well. Moreover, DNA methylation plays an important role in silencing of germline-specific genes. Impaired function of major components of DNA methylation machinery results in lethality in fish, amphibians and mammals. Despite such apparent importance, mammals exhibit a dramatic loss and regain of DNA methylation in early embryogenesis prior to implantation, and then again in the cells specified for the germline. In this minireview we will highlight recent studies that shine light on two major aspects of embryonic DNA methylation reprogramming: (1) The mechanism of DNA methylation loss after fertilization and (2) the protection of discrete loci from ectopic DNA methylation deposition during reestablishment. Finally, we will conclude with some extrapolations for the evolutionary underpinnings of such extraordinary events that seemingly put the genome under unnecessary risk during a particularly vulnerable window of development.
Collapse
Affiliation(s)
- Maxim V C Greenberg
- Centre National de la Recherche Scientifique, Institut Jacques Monod, Université de Paris, Paris, France
| |
Collapse
|
7
|
Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanishi M, Bultmann S, Leonhardt H. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun 2020; 11:5972. [PMID: 33235224 PMCID: PMC7686362 DOI: 10.1038/s41467-020-19603-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
Collapse
Affiliation(s)
- Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Joel Ryan
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Merve Yiğit
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ivo M Glück
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Franziska R Traube
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London, UK
| | - Aishwarya Acharya
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul Stolz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christoph Ziegenhain
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| |
Collapse
|
8
|
Cadmium-induced genome-wide DNA methylation changes in growth and oxidative metabolism in Drosophila melanogaster. BMC Genomics 2019; 20:356. [PMID: 31072326 PMCID: PMC6507226 DOI: 10.1186/s12864-019-5688-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Background Cadmium (Cd)-containing chemicals can cause serious damage to biological systems. In animals and plants, Cd exposure can lead to metabolic disorders or death. However, for the most part the effects of Cd on specific biological processes are not known. DNA methylation is an important mechanism for the regulation of gene expression. In this study we examined the effects of Cd exposure on global DNA methylation in a living organism by whole-genome bisulfite sequencing (WGBS) using Drosophila melanogaster as model. Results A total of 71 differentially methylated regions and 63 differentially methylated genes (DMGs) were identified by WGBS. A total of 39 genes were demethylated in the Cd treatment group but not in the control group, whereas 24 showed increased methylation in the former relative to the latter. In most cases, demethylation activated gene expression: genes such as Cdc42 and Mekk1 were upregulated as a result of demethylation. There were 37 DMGs that overlapped with differentially expressed genes from the digital expression library including baz, Act5C, and ss, which are associated with development, reproduction, and energy metabolism. Conclusions DNA methylation actively regulates the physiological response to heavy metal stress in Drosophila in part via activation of apoptosis. Electronic supplementary material The online version of this article (10.1186/s12864-019-5688-z) contains supplementary material, which is available to authorized users.
Collapse
|
9
|
do Amaral GCLS, Planello AC, Borgato G, de Lima DG, Guimarães GN, Marques MR, de Souza AP. 5-Aza-CdR promotes partial MGMT demethylation and modifies expression of different genes in oral squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2019; 127:425-432. [PMID: 30827853 DOI: 10.1016/j.oooo.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/03/2019] [Accepted: 01/06/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Treatment strategies for oral squamous cell carcinoma (OSCC) vary, depending on the stage of diagnosis. Surgery and radiotherapy are options for localized lesions for stage I patients, whereas chemotherapy is the main treatment for metastatic OSCC. However, aggressive tumors can relapse, frequently causing death. In an attempt to address this, novel treatment protocols using drugs that alter the epigenetic profile have emerged as an alternative to control tumor growth and metastasis. Therefore, the objective in this study was to investigate the effect of the demethylating drug 5-aza-CdR in SCC9 OSCC cells. STUDY DESIGN SCC9 cells were treated with 5-Aza-CdR at concentrations of 0.3μM and 2μM for 24hours and 48hours. DNA methylation of the MGMT, BRCA1, APC, c-MYC, and hTERT genes were investigated by using the methylation-specific high-resolution melting technique. Real time-polymerase chain reaction and quantitative polymerase chain reaction were performed to analyze gene expression. RESULTS 5-Aza-CdR promoted demethylation of MGMT and modified the transcription of all analyzed genes. Curiously, 5-aza-CdR at the concentration of 0.3μM was more efficient than 2μM in SCC9 cells. CONCLUSIONS We observed that 5-aza-CdR led to MGMT demethylation, upregulated the transcription of 3 important tumor suppressor genes, and promoted the downregulation of c-Myc.
Collapse
Affiliation(s)
- Guilherme C L S do Amaral
- Laboratory of Molecular Biology, Department of Morphology, Piracicaba Dental School, FOP, State University of Campinas, UNICAMP, Piracicaba-SP, Brazil
| | - Aline C Planello
- Laboratory of Molecular Biology, Department of Morphology, Piracicaba Dental School, FOP, State University of Campinas, UNICAMP, Piracicaba-SP, Brazil
| | - Gabriell Borgato
- Laboratory of Molecular Biology, Department of Morphology, Piracicaba Dental School, FOP, State University of Campinas, UNICAMP, Piracicaba-SP, Brazil
| | - Dieila Giomo de Lima
- Laboratory of Molecular Biology, Department of Morphology, Piracicaba Dental School, FOP, State University of Campinas, UNICAMP, Piracicaba-SP, Brazil
| | - Gustavo N Guimarães
- Laboratory of Molecular Biology, Department of Morphology, Piracicaba Dental School, FOP, State University of Campinas, UNICAMP, Piracicaba-SP, Brazil
| | - Marcelo Rocha Marques
- Laboratory of Molecular Biology, Department of Morphology, Piracicaba Dental School, FOP, State University of Campinas, UNICAMP, Piracicaba-SP, Brazil
| | - Ana Paula de Souza
- Laboratory of Molecular Biology, Department of Morphology, Piracicaba Dental School, FOP, State University of Campinas, UNICAMP, Piracicaba-SP, Brazil.
| |
Collapse
|
10
|
Zhao S, Xu J, Liu S, Cui K, Li Z, Liu N. Dppa3 in pluripotency maintenance of ES cells and early embryogenesis. J Cell Biochem 2018; 120:4794-4799. [PMID: 30417435 DOI: 10.1002/jcb.28063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/22/2018] [Indexed: 01/11/2023]
Abstract
Embryonic development is precisely regulated by a network of signal pathways and specific genes. Dppa3 (also known as Pgc7 or Stella) plays an important role in early embryonic development during the cleavage stage as a maternal effect gene. Dppa3 expresses in many species, and its homologous gene in human and rat genomes is located at the same chromosomal regions and have the same exon-intron structure. However, unlike mouse embryonic stem (ES) cells, in which the Dppa3 promoter maintains hypomethylation that allows a high transcription level, the DPPA3 promoter region in human ES cells is methylated, much like that of mouse epiblast stem cell. Dppa3 is essential for early embryogenesis and pluripotency maintenance; however, the precise mechanism and downstream passage remains unknown. In this review, we will summarize some important functions of Dppa3 in early embryogenesis and pluripotency maintenance of mouse ES cells.
Collapse
Affiliation(s)
- Shuang Zhao
- School of Medicine, Nankai University, Tianjin, China.,Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jia Xu
- School of Medicine, Nankai University, Tianjin, China
| | - Siying Liu
- School of Medicine, Nankai University, Tianjin, China
| | - Kaige Cui
- School of Medicine, Nankai University, Tianjin, China
| | - Zongjin Li
- School of Medicine, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Na Liu
- School of Medicine, Nankai University, Tianjin, China.,Key Laboratory of Bioactive Materials, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
11
|
Wang QQ, Zhang YM, Zhong X, Li JW, An XR, Hou J. Dimethylated histone H3 lysine 9 is dispensable for the interaction between developmental pluripotency-associated protein 3 (Dppa3) and ten-eleven translocation 3 (Tet3) in somatic cells. Reprod Fertil Dev 2018; 31:347-356. [PMID: 30099980 DOI: 10.1071/rd18062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 07/11/2018] [Indexed: 01/15/2023] Open
Abstract
Both developmental pluripotency-associated protein 3 (Dppa3/Stella/PGC7) and dioxygenase ten-eleven translocation 3 (Tet3) are maternal factors that regulate DNA methylation reprogramming during early embryogenesis. In the mouse zygote, dimethylated histone H3 lysine 9 (H3K9me2) attracts Dppa3 to prevent Tet3-mediated oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Here, we addressed the interplay between Dppa3 and Tet3 or H3K9me2 in somatic cells. In mouse NIH3T3 cells, the exogenously expressed Dppa3 preferentially accumulated in the cytoplasm and had no effect on Tet3-mediated 5hmC generation. In HeLa cells, the expressed Dppa3 was predominantly localised in the nucleus and could partially suppress Tet3-induced 5hmC accumulation, but this suppressive function was not correlated with H3K9me2. Co-immunoprecipitation assays further revealed an interaction of Dppa3 with Tet3 but not with H3K9me2 in HeLa cells. In cloned zygotes from somatic cells, Dppa3 distribution and 5hmC accumulation in nuclei were not affected by H3K9me2 levels. Taken together, these results suggest that H3K9me2 is not functionally associated with Dppa3 and Tet3 in somatic cells or somatic cell cloned embryos.
Collapse
Affiliation(s)
- Qian-Qian Wang
- State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, #2, Yuan-Ming-Yuan West Road, Haidian District, Beijing, 100193, China
| | - Yu-Mei Zhang
- State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, #2, Yuan-Ming-Yuan West Road, Haidian District, Beijing, 100193, China
| | - Xia Zhong
- State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, #2, Yuan-Ming-Yuan West Road, Haidian District, Beijing, 100193, China
| | - Jian-Wei Li
- State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, #2, Yuan-Ming-Yuan West Road, Haidian District, Beijing, 100193, China
| | - Xiao-Rong An
- State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, #2, Yuan-Ming-Yuan West Road, Haidian District, Beijing, 100193, China
| | - Jian Hou
- State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, #2, Yuan-Ming-Yuan West Road, Haidian District, Beijing, 100193, China
| |
Collapse
|
12
|
SanMiguel JM, Bartolomei MS. DNA methylation dynamics of genomic imprinting in mouse development. Biol Reprod 2018; 99:252-262. [PMID: 29462489 PMCID: PMC6044325 DOI: 10.1093/biolre/ioy036] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 01/05/2023] Open
Abstract
DNA methylation is an essential epigenetic mark crucial for normal mammalian development. This modification controls the expression of a unique class of genes, designated as imprinted, which are expressed monoallelically and in a parent-of-origin-specific manner. Proper parental allele-specific DNA methylation at imprinting control regions (ICRs) is necessary for appropriate imprinting. Processes that deregulate DNA methylation of imprinted loci cause disease in humans. DNA methylation patterns dramatically change during mammalian development: first, the majority of the genome, with the exception of ICRs, is demethylated after fertilization, and subsequently undergoes genome-wide de novo DNA methylation. Secondly, after primordial germ cells are specified in the embryo, another wave of demethylation occurs, with ICR demethylation occurring late in the process. Lastly, ICRs reacquire DNA methylation imprints in developing germ cells. We describe the past discoveries and current literature defining these crucial dynamics in relation to imprinted genes and the rest of the genome.
Collapse
Affiliation(s)
- Jennifer M SanMiguel
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
13
|
Farshchian M, Matin MM, Armant O, Geerts D, Dastpak M, Nakhaei-Rad S, Tajeran M, Jebelli A, Shahriyari M, Bahrami M, Fallah A, Yaghoobi V, Mirahmadi M, Abbaszadegan MR, Bahrami AR. Suppression of dsRNA response genes and innate immunity following Oct4, Stella, and Nanos2 overexpression in mouse embryonic fibroblasts. Cytokine 2018; 106:1-11. [DOI: 10.1016/j.cyto.2018.02.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/02/2018] [Accepted: 02/20/2018] [Indexed: 11/29/2022]
|
14
|
de Souza AF, Pieri NCG, Roballo KCS, Bressan FF, Casals JB, Ambrósio CE, Perecin F, Martins DS. Dynamics of male canine germ cell development. PLoS One 2018; 13:e0193026. [PMID: 29489867 PMCID: PMC5831030 DOI: 10.1371/journal.pone.0193026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 02/02/2018] [Indexed: 12/18/2022] Open
Abstract
Primordial germ cells (PGCs) are precursors of gametes that can generate new individuals throughout life in both males and females. Additionally, PGCs have been shown to differentiate into embryonic germ cells (EGCs) after in vitro culture. Most studies investigating germinative cells have been performed in rodents and humans but not dogs (Canis lupus familiaris). Here, we elucidated the dynamics of the expression of pluripotent (POU5F1 and NANOG), germline (DDX4, DAZL and DPPA3), and epigenetic (5mC, 5hmC, H3K27me3 and H3K9me2) markers that are important for the development of male canine germ cells during the early (22-30 days post-fertilization (dpf)), middle (35-40 dpf) and late (45-50 dpf) gestational periods. We performed sex genotype characterization, immunofluorescence, immunohistochemistry, and quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) analyses. Furthermore, in a preliminary study, we evaluated the capacity of canine embryo PGCs (30 dpf) to differentiate into EGCs. To confirm the canine EGCs phenotype, we performed alkaline phosphatase detection, immunohistochemistry, electron and transmission scanning microscopy and RT-qPCR analyses. The PGCs were positive for POU5F1 and H3K27me3 during all assessed developmental periods, including all periods between the gonadal tissue stage and foetal testes development. The number of NANOG, DDX4, DAZL, DPPA3 and 5mC-positive cells increased along with the developing cords from 35-50 dpf. Moreover, our results demonstrate the feasibility of inducing canine PGCs into putative EGCs that present pluripotent markers, such as POU5F1 and the NANOG gene, and exhibit reduced expression of germinative genes and increased expression of H3K27me3. This study provides new insight into male germ cell development mechanisms in dogs.
Collapse
Affiliation(s)
- Aline F. de Souza
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Naira C. Godoy Pieri
- Department of Reproduction, Faculty of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Kelly C. S. Roballo
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Fabiana F. Bressan
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Juliana B. Casals
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Carlos E. Ambrósio
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Felipe Perecin
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| | - Daniele S. Martins
- Department of Surgery, Faculty of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Veterinary Medicine, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, SP, Brazil
| |
Collapse
|
15
|
Liu H, Zhang L, Wei Q, Shi Z, Shi X, Du J, Huang C, Zhang Y, Guo Z. Comprehensive Proteomic Analysis of PGC7-Interacting Proteins. J Proteome Res 2017; 16:3113-3123. [PMID: 28712289 DOI: 10.1021/acs.jproteome.6b00883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Primordial germ cell 7 (PGC7), a maternal factor essential for early development, plays a critical role in the regulation of DNA methylation, transcriptional repression, chromatin condensation, and cell division and the maintenance of cell pluripotentiality. Despite the fundamental roles of PGC7 in these cellular processes, only a few molecular and functional interactions of PGC7 have been reported. Here, a streptavidin-biotin affinity purification technique combined with LC-MS/MS was used to analyze potential proteins that interact with PGC7. In total, 291 potential PGC7-interacting proteins were identified. Through an in-depth bioinformatic analysis of potential interactors, we linked PGC7 to critical cellular processes including translation, RNA processing, cell cycle, and regulation of heterochromatin structure. To better understand the functional interactions of PGC7 with its potential interactors, we constructed a protein-protein interaction network using the STRING database. In addition, we discussed in detail the interactions between PGC7 and some of its newly validated partners. The identification of these potential interactors of PGC7 expands our knowledge on the PGC7 interactome and provides a valuable resource for understanding the diverse functions of this protein.
Collapse
Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Lei Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Qing Wei
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Zhaopeng Shi
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Xiaoyan Shi
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China.,Medical Experiment Center of Shaanxi University of Chinese Medicine , Xianyang, Shaanxi 712000, China
| | - Juan Du
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China.,Medicine School of Yan'an University , Yan'an, Shaanxi 716000, China
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| |
Collapse
|
16
|
Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA. Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition. eLife 2017; 6:e22345. [PMID: 28323615 PMCID: PMC5404928 DOI: 10.7554/elife.22345] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/09/2017] [Indexed: 01/22/2023] Open
Abstract
The maternal-to-zygotic transition (MZT) marks the period when the embryonic genome is activated and acquires control of development. Maternally inherited factors play a key role in this critical developmental process, which occurs at the 2-cell stage in mice. We investigated the function of the maternally inherited factor Stella (encoded by Dppa3) using single-cell/embryo approaches. We show that loss of maternal Stella results in widespread transcriptional mis-regulation and a partial failure of MZT. Strikingly, activation of endogenous retroviruses (ERVs) is significantly impaired in Stella maternal/zygotic knockout embryos, which in turn leads to a failure to upregulate chimeric transcripts. Amongst ERVs, MuERV-L activation is particularly affected by the absence of Stella, and direct in vivo knockdown of MuERV-L impacts the developmental potential of the embryo. We propose that Stella is involved in ensuring activation of ERVs, which themselves play a potentially key role during early development, either directly or through influencing embryonic gene expression.
Collapse
Affiliation(s)
- Yun Huang
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Jong Kyoung Kim
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Dang Vinh Do
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Caroline Lee
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Christopher A Penfold
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Jan J Zylicz
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jamie A Hackett
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- European Molecular Biology Laboratory - Monterotondo, Rome, Italy
| | - M Azim Surani
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
17
|
Stage-Specific Demethylation in Primordial Germ Cells Safeguards against Precocious Differentiation. Dev Cell 2016; 39:75-86. [PMID: 27618282 DOI: 10.1016/j.devcel.2016.07.019] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/22/2016] [Accepted: 07/25/2016] [Indexed: 11/20/2022]
Abstract
Remodeling DNA methylation in mammalian genomes can be global, as seen in preimplantation embryos and primordial germ cells (PGCs), or locus specific, which can regulate neighboring gene expression. In PGCs, global and locus-specific DNA demethylation occur in sequential stages, with an initial global decrease in methylated cytosines (stage I) followed by a Tet methylcytosine dioxygenase (Tet)-dependent decrease in methylated cytosines that act at imprinting control regions (ICRs) and meiotic genes (stage II). The purpose of the two-stage mechanism is unclear. Here we show that Dnmt1 preserves DNA methylation through stage I at ICRs and meiotic gene promoters and is required for the pericentromeric enrichment of 5hmC. We discovered that the functional consequence of abrogating two-stage DNA demethylation in PGCs was precocious germline differentiation leading to hypogonadism and infertility. Therefore, bypassing stage-specific DNA demethylation has significant consequences for progenitor germ cell differentiation and the ability to transmit DNA from parent to offspring.
Collapse
|
18
|
Clark AT. DNA methylation remodeling in vitro and in vivo. Curr Opin Genet Dev 2015; 34:82-7. [PMID: 26451496 DOI: 10.1016/j.gde.2015.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/28/2015] [Accepted: 09/07/2015] [Indexed: 12/13/2022]
Abstract
In mammals, global DNA demethylation in vivo occurs in the pre-implantation embryo and in primordial germ cells (PGCs) where it is hypothesized to create a blank slate or 'tabula rasa' upon which new DNA methylation patterns are written. However, global DNA demethylation in vivo is far from complete with a small number of loci protected from demethylation. Failure to demethylate, or overt demethylation results in compromised differentiation. Recent work has shown that reversion of primed human pluripotent stem cells to the naïve state leads to unbridled DNA demethylation which has unknown consequences on the quality differentiated cells created in vitro. Taken together understanding DNA methylation remodeling is critical for understanding the epigenetic foundations of life, and the quality of stem cells for regenerative medicine.
Collapse
Affiliation(s)
- Amander T Clark
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, United States; Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, United States; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, United States.
| |
Collapse
|
19
|
Kimura T, Kaga Y, Sekita Y, Fujikawa K, Nakatani T, Odamoto M, Funaki S, Ikawa M, Abe K, Nakano T. Pluripotent stem cells derived from mouse primordial germ cells by small molecule compounds. Stem Cells 2015; 33:45-55. [PMID: 25186651 DOI: 10.1002/stem.1838] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 08/18/2014] [Indexed: 12/12/2022]
Abstract
Primordial germ cells (PGCs) can give rise to pluripotent stem cells known as embryonic germ cells (EGCs) when cultured with basic fibroblast growth factor (bFGF), stem cell factor (SCF), and leukemia inhibitory factor. Somatic cells can give rise to induced pluripotent stem cells (iPSCs) by introduction of the reprogramming transcription factors Oct4, Sox2, and Klf4. The effects of Sox2 and Klf4 on somatic cell reprogramming can be reproduced using the small molecule compounds, transforming growth factor-β receptor (TGFβR) inhibitor and Kempaullone, respectively. Here we examined the effects of TGFβR inhibitor and Kempaullone on EGC derivation from PGCs. Treatment of PGCs with TGFβR inhibitor and/or Kempaullone generated pluripotent stem cells under standard embryonic stem cell (ESC) culture conditions without bFGF and SCF, which we termed induced EGCs (iEGCs). The derivation efficiency of iEGCs was dependent on the differentiation stage and sex. DNA methylation levels of imprinted genes in iEGCs were reduced, with the exception of the H19 gene. The promoters of genes involved in germline development were generally hypomethylated in PGCs, but three germline genes showed comparable DNA methylation levels among iEGs, ESCs, and iPSCs. These results show that PGCs can be reprogrammed into pluripotent state using small molecule compounds, and that DNA methylation of these germline genes is not maintained in iEGCs.
Collapse
Affiliation(s)
- Tohru Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan; Department of Pathology, Osaka University, Suita, Osaka, Japan; Laboratory of Molecular Embryology, Kitasato University School of Science, Kitasato, Minami-ku, Sagamihara, Kanagawa, Japan; Laboratory of Stem Cell Biology, Kitasato University School of Science, Kitasato, Minami-ku, Sagamihara, Kanagawa, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Hahn MA, Szabó PE, Pfeifer GP. 5-Hydroxymethylcytosine: a stable or transient DNA modification? Genomics 2014; 104:314-23. [PMID: 25181633 DOI: 10.1016/j.ygeno.2014.08.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 12/16/2022]
Abstract
The DNA base 5-hydroxymethylcytosine (5hmC) is produced by enzymatic oxidation of 5-methylcytosine (5mC) by 5mC oxidases (the Tet proteins). Since 5hmC is recognized poorly by DNA methyltransferases, DNA methylation may be lost at 5hmC sites during DNA replication. In addition, 5hmC can be oxidized further by Tet proteins and converted to 5-formylcytosine and 5-carboxylcytosine, two bases that can be removed from DNA by base excision repair. The completed pathway represents a replication-independent DNA demethylation cycle. However, the DNA base 5hmC is also known to be rather stable and occurs at substantial levels, for example in the brain, suggesting that it represents an epigenetic mark by itself that may regulate chromatin structure and transcription. Focusing on a few well-studied tissues and developmental stages, we discuss the opposing views of 5hmC as a transient intermediate in DNA demethylation and as a modified DNA base with an instructive role.
Collapse
Affiliation(s)
- Maria A Hahn
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA
| | - Piroska E Szabó
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA
| | - Gerd P Pfeifer
- Beckman Research Institute, City of Hope, Duarte CA 91010, USA.
| |
Collapse
|