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Foong YH, Caldwell B, Thorvaldsen JL, Krapp C, Mesaros CA, Zhou W, Kohli RM, Bartolomei MS. TET1 displays catalytic and non-catalytic functions in the adult mouse cortex. Epigenetics 2024; 19:2374979. [PMID: 38970823 PMCID: PMC11229741 DOI: 10.1080/15592294.2024.2374979] [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: 01/23/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
TET1/2/3 dioxygenases iteratively demethylate 5-methylcytosine, beginning with the formation of 5-hydroxymethylcytosine (5hmC). The post-mitotic brain maintains higher levels of 5hmC than most peripheral tissues, and TET1 ablation studies have underscored the critical role of TET1 in brain physiology. However, deletion of Tet1 precludes the disentangling of the catalytic and non-catalytic functions of TET1. Here, we dissect these functions of TET1 by comparing adult cortex of Tet1 wildtype (Tet1 WT), a novel Tet1 catalytically dead mutant (Tet1 HxD), and Tet1 knockout (Tet1 KO) mice. Using DNA methylation array, we uncover that Tet1 HxD and KO mutations perturb the methylation status of distinct subsets of CpG sites. Gene ontology (GO) analysis on specific differential 5hmC regions indicates that TET1's catalytic activity is linked to neuronal-specific functions. RNA-Seq further shows that Tet1 mutations predominantly impact the genes that are associated with alternative splicing. Lastly, we performed High-performance Liquid Chromatography Mass-Spectrometry lipidomics on WT and mutant cortices and uncover accumulation of lysophospholipids lysophosphatidylethanolamine and lysophosphatidylcholine in Tet1 HxD cortex. In summary, we show that Tet1 HxD does not completely phenocopy Tet1 KO, providing evidence that TET1 modulates distinct cortical functions through its catalytic and non-catalytic roles.
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Affiliation(s)
- Yee Hoon Foong
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Blake Caldwell
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Joanne L. Thorvaldsen
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Christopher Krapp
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Clementina A. Mesaros
- Translational Biomarkers Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wanding Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Children’s Hospital of Philadelphia (CHOP), University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
| | - Rahul M. Kohli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
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2
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Bortel P, Hagn G, Skos L, Bileck A, Paulitschke V, Paulitschke P, Gleiter L, Mohr T, Gerner C, Meier-Menches SM. Memory effects of prior subculture may impact the quality of multiomic perturbation profiles. Proc Natl Acad Sci U S A 2024; 121:e2313851121. [PMID: 38976734 PMCID: PMC11260104 DOI: 10.1073/pnas.2313851121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Mass spectrometry-based omics technologies are increasingly used in perturbation studies to map drug effects to biological pathways by identifying significant molecular events. Significance is influenced by fold change and variation of each molecular parameter, but also by multiple testing corrections. While the fold change is largely determined by the biological system, the variation is determined by experimental workflows. Here, it is shown that memory effects of prior subculture can influence the variation of perturbation profiles using the two colon carcinoma cell lines SW480 and HCT116. These memory effects are largely driven by differences in growth states that persist into the perturbation experiment. In SW480 cells, memory effects combined with moderate treatment effects amplify the variation in multiple omics levels, including eicosadomics, proteomics, and phosphoproteomics. With stronger treatment effects, the memory effect was less pronounced, as demonstrated in HCT116 cells. Subculture homogeneity was controlled by real-time monitoring of cell growth. Controlled homogeneous subculture resulted in a perturbation network of 321 causal conjectures based on combined proteomic and phosphoproteomic data, compared to only 58 causal conjectures without controlling subculture homogeneity in SW480 cells. Some cellular responses and regulatory events were identified that extend the mode of action of arsenic trioxide (ATO) only when accounting for these memory effects. Controlled prior subculture led to the finding of a synergistic combination treatment of ATO with the thioredoxin reductase 1 inhibitor auranofin, which may prove useful in the management of NRF2-mediated resistance mechanisms.
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Affiliation(s)
- Patricia Bortel
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Vienna Doctoral School in Chemistry, University of Vienna, Vienna1090, Austria
| | - Gerhard Hagn
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Vienna Doctoral School in Chemistry, University of Vienna, Vienna1090, Austria
| | - Lukas Skos
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Vienna Doctoral School in Chemistry, University of Vienna, Vienna1090, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna1090, Austria
| | - Verena Paulitschke
- Department of Dermatology, Medical University of Vienna, Vienna1090, Austria
| | - Philipp Paulitschke
- PHIO scientific GmbH, Munich81371, Germany
- Faculty of Physics, Ludwig-Maximilians University of Munich, Munich80539, Germany
| | | | - Thomas Mohr
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Center of Cancer Research, Department of Medicine I, Medical University of Vienna and Comprehensive Cancer Center, Vienna1090, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna1090, Austria
| | - Samuel M. Meier-Menches
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna1090, Austria
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna1090, Austria
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3
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Wang M, Wang L, Huang Y, Qiao Z, Yi S, Zhang W, Wang J, Yang G, Cui X, Kou X, Zhao Y, Wang H, Jiang C, Gao S, Chen J. Loss of Tet hydroxymethylase activity causes mouse embryonic stem cell differentiation bias and developmental defects. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2631-x. [PMID: 39037697 DOI: 10.1007/s11427-024-2631-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 05/23/2024] [Indexed: 07/23/2024]
Abstract
The TET family is well known for active DNA demethylation and plays important roles in regulating transcription, the epigenome and development. Nevertheless, previous studies using knockdown (KD) or knockout (KO) models to investigate the function of TET have faced challenges in distinguishing its enzymatic and nonenzymatic roles, as well as compensatory effects among TET family members, which has made the understanding of the enzymatic role of TET not accurate enough. To solve this problem, we successfully generated mice catalytically inactive for specific Tet members (Tetm/m). We observed that, compared with the reported KO mice, mutant mice exhibited distinct developmental defects, including growth retardation, sex imbalance, infertility, and perinatal lethality. Notably, Tetm/m mouse embryonic stem cells (mESCs) were successfully established but entered an impaired developmental program, demonstrating extended pluripotency and defects in ectodermal differentiation caused by abnormal DNA methylation. Intriguingly, Tet3, traditionally considered less critical for mESCs due to its lower expression level, had a significant impact on the global hydroxymethylation, gene expression, and differentiation potential of mESCs. Notably, there were common regulatory regions between Tet1 and Tet3 in pluripotency regulation. In summary, our study provides a more accurate reference for the functional mechanism of Tet hydroxymethylase activity in mouse development and ESC pluripotency regulation.
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Affiliation(s)
- Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Liping Wang
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai, 200065, China
| | - Yanxin Huang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Zhibin Qiao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Shanru Yi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Weina Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Jing Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Guang Yang
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai, 200065, China
| | - Xinyu Cui
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai, 200065, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China
| | - Cizhong Jiang
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai, 200065, China.
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200092, China.
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4
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Fu Y, Jiang J, Wu Y, Cao D, Jia Z, Zhang Y, Li D, Cui Y, Zhang Y, Cao X. Genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA as noninvasive diagnostic markers for gastric cancer. Gastric Cancer 2024; 27:735-746. [PMID: 38584223 DOI: 10.1007/s10120-024-01493-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/14/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND 5-Hydroxymethylcytosine-enriched gene profiles and regions show tissue-specific and tumor specific. There is a potential value to explore cell-free DNA 5-hydroxymethylcytosine feature biomarkers for early gastric cancer detection. METHODS A matched case‒control study design with 50 gastric cancer patients and 50 controls was performed to sequence the different 5-hydroxymethylcytosine modification features of cell free DNA. Significantly differential 5-hydroxymethylcytosine modification genes were identified to construct a gastric cancer diagnostic model. Data set from GEO was used as an external testing set to test the robustness of the diagnostic model. RESULTS Accounting for more than 90% of 5-hydroxymethylcytosine peaks were distributed in the gene body in both the gastric cancer and control groups. The diagnostic model was developed based on five different 5-hydroxymethylcytosine modification genes, FBXL7, PDE3A, TPO, SNTG2 and STXBP5. The model could effectively distinguish gastric cancer patients from controls in the training (AUC = 0.95, sensitivity = 88.6%, specificity = 94.3%), validation (AUC = 0.87, sensitivity = 73.3%, specificity = 93.3%) and testing (AUC = 0.90, sensitivity = 81.9%, specificity = 90.2%) sets. The risk scores of the controls from the model were significantly lower than those of gastric cancer patients in both our own data (P < 0.001) and GEO external testing data (P < 0.001), and no significant difference between different TNM stage patients (P = 0.09 and 0.66). Furthermore, there was no significant difference between the healthy control and benign gastric disease patients in the testing set from GEO (P = 0.10). CONCLUSIONS The characteristics of 5-hydroxymethylcytosine in cell free DNA are specific to gastric cancer patients, and the diagnostic model constructed by five genes' 5-hydroxymethylcytosine features could effectively identify gastric cancer patients.
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Affiliation(s)
- Yingli Fu
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Jing Jiang
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Yanhua Wu
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Donghui Cao
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Zhifang Jia
- Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China
| | - Yangyu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Dongming Li
- Department of Hospital Infection Management, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yingnan Cui
- Department of Hospital Infection Management, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yuzheng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
- Department of Hospital Infection Management, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xueyuan Cao
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China.
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5
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Gilbert G, Renaud Y, Teste C, Anglaret N, Bertrand R, Hoehn S, Jurkowski TP, Schuettengruber B, Cavalli G, Waltzer L, Vandel L. Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity. SCIENCE ADVANCES 2024; 10:eadn5861. [PMID: 38701218 PMCID: PMC11068012 DOI: 10.1126/sciadv.adn5861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Enzymes of the ten-eleven translocation (TET) family play a key role in the regulation of gene expression by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark in many species. Yet, TET proteins also have less characterized noncanonical modes of action, notably in Drosophila, whose genome is devoid of 5mC. Here, we show that Drosophila TET activates the expression of genes required for larval central nervous system (CNS) development mainly in a catalytic-independent manner. Genome-wide profiling shows that TET is recruited to enhancer and promoter regions bound by Polycomb group complex (PcG) proteins. We found that TET interacts and colocalizes on chromatin preferentially with Polycomb repressor complex 1 (PRC1) rather than PRC2. Furthermore, PRC1 but not PRC2 is required for the activation of TET target genes. Last, our results suggest that TET and PRC1 binding to activated genes is interdependent. These data highlight the importance of TET noncatalytic function and the role of PRC1 for gene activation in the Drosophila larval CNS.
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Affiliation(s)
- Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Camille Teste
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Nadège Anglaret
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Romane Bertrand
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Sven Hoehn
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Tomasz P. Jurkowski
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Bernd Schuettengruber
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Laurence Vandel
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
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6
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Prashanth S, Radha Maniswami R, Rajajeyabalachandran G, Jegatheesan SK. SETDB1, an H3K9-specific methyltransferase: An attractive epigenetic target to combat cancer. Drug Discov Today 2024; 29:103982. [PMID: 38614159 DOI: 10.1016/j.drudis.2024.103982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) is an important epigenetic regulator catalyzing histone H3 lysine 9 (H3K9) methylation, specifically di-/tri-methylation. This regulation promotes gene silencing through heterochromatin formation. Aberrant SETDB1 expression, and its oncogenic role is evident in many cancers. Thus, SETDB1 is a valid target with novel therapeutic benefits. In this review, we explore the structural and biochemical features of SETDB1, its regulatory mechanisms, and its role in various cancers. We also discuss recent discoveries in small molecules targeting SETDB1 and provide suggestions for future research.
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Affiliation(s)
- Seema Prashanth
- Informatics, AI & ML, Jubilant Biosys Ltd., Bangalore, India
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7
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Tu R, Ping Z, Liu J, Tsoi ML, Song X, Liu W, Xie T. Niche Tet maintains germline stem cells independently of dioxygenase activity. EMBO J 2024; 43:1570-1590. [PMID: 38499787 PMCID: PMC11021519 DOI: 10.1038/s44318-024-00074-9] [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: 09/12/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are dioxygenases that convert 5-methylcytosine (5mC) into 5-hydroxylmethylcytosine (5hmC) in DNA and RNA. However, their involvement in adult stem cell regulation remains unclear. Here, we identify a novel enzymatic activity-independent function of Tet in the Drosophila germline stem cell (GSC) niche. Tet activates the expression of Dpp, the fly homologue of BMP, in the ovary stem cell niche, thereby controlling GSC self-renewal. Depletion of Tet disrupts Dpp production, leading to premature GSC loss. Strikingly, both wild-type and enzyme-dead mutant Tet proteins rescue defective BMP signaling and GSC loss when expressed in the niche. Mechanistically, Tet interacts directly with Bap55 and Stat92E, facilitating recruitment of the Polybromo Brahma associated protein (PBAP) complex to the dpp enhancer and activating Dpp expression. Furthermore, human TET3 can effectively substitute for Drosophila Tet in the niche to support BMP signaling and GSC self-renewal. Our findings highlight a conserved novel catalytic activity-independent role of Tet as a scaffold protein in supporting niche signaling for adult stem cell self-renewal.
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Affiliation(s)
- Renjun Tu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
| | - Zhaohua Ping
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA
| | - Jian Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Centre, Shenzhen, Guangdong, China
| | - Man Lung Tsoi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, New Territories, Hong Kong Special Administrative Region, China
| | - Xiaoqing Song
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Centre, Shenzhen, Guangdong, China
| | - Ting Xie
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, China.
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO, USA.
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8
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Wang J, Liu L, Li Z, Wang H, Ren Y, Wang K, Liu Y, Tao X, Zheng L. JMJD3 regulate H3K27me3 modification via interacting directly with TET1 to affect spermatogonia self-renewal and proliferation. BMC Genomics 2024; 25:225. [PMID: 38424516 PMCID: PMC10905883 DOI: 10.1186/s12864-024-10120-9] [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: 10/20/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND In epigenetic modification, histone modification and DNA methylation coordinate the regulation of spermatogonium. Not only can methylcytosine dioxygenase 1 (TET1) function as a DNA demethylase, converting 5-methylcytosine to 5-hydroxymethylcytosine, it can also form complexes with other proteins to regulate gene expression. H3K27me3, one of the common histone modifications, is involved in the regulation of stem cell maintenance and tumorigenesis by inhibiting gene transcription. METHODS we examined JMJD3 at both mRNA and protein levels and performed Chip-seq sequencing of H3K27me3 in TET1 overexpressing cells to search for target genes and signaling pathways of its action. RESULTS This study has found that JMJD3 plays a leading role in spermatogonia self-renewal and proliferation: at one extreme, the expression of the self-renewal gene GFRA1 and the proliferation-promoting gene PCNA was upregulated following the overexpression of JMJD3 in spermatogonia; at the other end of the spectrum, the expression of differentiation-promoting gene DAZL was down-regulated. Furthermore, the fact that TET1 and JMJD3 can form a protein complex to interact with H3K27me3 has also been fully proven. Then, through analyzing the sequencing results of CHIP-Seq, we found that TET1 targeted Pramel3 when it interacted with H3K27me3. Besides, TET1 overexpression not only reduced H3K27me3 deposition at Pramel3, but promoted its transcriptional activation as well, and the up-regulation of Pramel3 expression was verified in JMJD3-overexpressing spermatogonia. CONCLUSION In summary, our study identified a novel link between TET1 and H3K27me3 and established a Tet1-JMJD3-H3K27me3-Pramel3 axis to regulate spermatogonia self-renewal and proliferation. Judging from the evidence offered above, we can safely conclude that this study provides new ideas for further research regarding the mechanism of spermatogenesis and spermatogenesis disorders on an apparent spectrum.
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Affiliation(s)
- Jin Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Lingling Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zebin Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Haoyu Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yuanyuan Ren
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Kaisheng Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yang Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xinjie Tao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Liming Zheng
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
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9
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Di Giorgio E, Ranzino L, Tolotto V, Dalla E, Burelli M, Gualandi N, Brancolini C. Transcription of endogenous retroviruses in senescent cells contributes to the accumulation of double-stranded RNAs that trigger an anti-viral response that reinforces senescence. Cell Death Dis 2024; 15:157. [PMID: 38383514 PMCID: PMC10882003 DOI: 10.1038/s41419-024-06548-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
An important epigenetic switch marks the onset and maintenance of senescence. This allows transcription of the genetic programs that arrest the cell cycle and alter the microenvironment. Transcription of endogenous retroviruses (ERVs) is also a consequence of this epigenetic switch. In this manuscript, we have identified a group of ERVs that are epigenetically silenced in proliferating cells but are upregulated during replicative senescence or during various forms of oncogene-induced senescence, by RAS and Akt, or after HDAC4 depletion. In a HDAC4 model of senescence, removal of the repressive histone mark H3K27me3 is the plausible mechanism that allows the transcription of intergenic ERVs during senescence. We have shown that ERVs contribute to the accumulation of dsRNAs in senescence, which can initiate the antiviral response via the IFIH1-MAVS signaling pathway and thus contribute to the maintenance of senescence. This pathway, and MAVS in particular, plays an active role in shaping the microenvironment and maintaining growth arrest, two essential features of the senescence program.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Liliana Ranzino
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Vanessa Tolotto
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Matteo Burelli
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Nicolò Gualandi
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy.
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10
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Du X, Yang D, Yu X, Wei Y, Chen W, Zhai Y, Ma F, Zhang M, Wan S, Li Y, Yang X, Aierken A, Zhang N, Xu W, Meng Y, Li N, Liao M, Yuan X, Zhu H, Qu L, Zhou N, Bai X, Peng S, Yang F, Hua J. PLZF protein forms a complex with protein TET1 to target TCF7L2 in undifferentiated spermatogonia. Theriogenology 2024; 215:321-333. [PMID: 38128225 DOI: 10.1016/j.theriogenology.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/18/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
The transcription factor promyelocytic leukemia zinc finger (PLZF, also known as ZBTB16) is critical for the self-renewal of spermatogonial stem cells (SSCs). However, the function of PLZF in SSCs is not clear. Here, we found that PLZF acted as an epigenetic regulator of stem cell maintenance and self-renewal of germ cells. The PLZF protein interacts with the ten-eleven translocation 1 (TET1) protein and subsequently acts as a modulator to regulate the expression of self-renewal-related genes. Furthermore, Transcription Factor 7-like 2 (TCF7L2) is promoted by the coordination of PLZF and Tri-methylation of lysine 4 on histone H3 (H3K4me3). In addition, testicular single-cell sequencing indicated that TCF7L2 is commonly expressed in the PLZF cluster. We demonstrated that PLZF directly targets TCF7L2 and alters the landscape of histone methylation in the SSCs nucleus. Meanwhile, the RD domain and Zn finger domain of PLZF synergize with H3K4me3 and directly upregulate TCF7L2 expression at the transcriptional level. Additionally, we identified a new association between PLZF and the histone methyltransferase EZH2 at the genomic level. Our study identified a new association between PLZF and H3K4me3, established the novel PLZF&TET1-H3K4me3-TCF7L2 axis at the genomic level which regulates undifferentiated spermatogonia, and provided a platform for studying germ cell development in male domestic animals.
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Affiliation(s)
- Xiaomin Du
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China; Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, China
| | - Donghui Yang
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Xiuwei Yu
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China; Department of Histo-embryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yudong Wei
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Wenbo Chen
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Yuanxin Zhai
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Fanglin Ma
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Mengfei Zhang
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Shicheng Wan
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Yunxiang Li
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Xinchun Yang
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Aili Aierken
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Ning Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenjing Xu
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Yuan Meng
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Na Li
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaole Yuan
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, China
| | - Na Zhou
- People's Hospital of Jingbian County, Ningxia Medical University, Yuling, Shaanxi, 718500, China
| | - Xue Bai
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, M13 9PL, UK
| | - Sha Peng
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China.
| | - Fan Yang
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China.
| | - Jinlian Hua
- College of Veterinary Medicine, Northwest A&F University, Shaanxi Centre of Stem Cells Engineering & Technology, Yangling, 712100, China.
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11
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Armstrong MJ, Jin Y, Vattathil SM, Huang Y, Schroeder JP, Bennet DA, Qin ZS, Wingo TS, Jin P. Role of TET1-mediated epigenetic modulation in Alzheimer's disease. Neurobiol Dis 2023; 185:106257. [PMID: 37562656 PMCID: PMC10530206 DOI: 10.1016/j.nbd.2023.106257] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder influenced by a complex interplay of environmental, epigenetic, and genetic factors. DNA methylation (5mC) and hydroxymethylation (5hmC) are DNA modifications that serve as tissue-specific and temporal regulators of gene expression. TET family enzymes dynamically regulate these epigenetic modifications in response to environmental conditions, connecting environmental factors with gene expression. Previous epigenetic studies have identified 5mC and 5hmC changes associated with AD. In this study, we performed targeted resequencing of TET1 on a cohort of early-onset AD (EOAD) and control samples. Through gene-wise burden analysis, we observed significant enrichment of rare TET1 variants associated with AD (p = 0.04). We also profiled 5hmC in human postmortem brain tissues from AD and control groups. Our analysis identified differentially hydroxymethylated regions (DhMRs) in key genes responsible for regulating the methylome: TET3, DNMT3L, DNMT3A, and MECP2. To further investigate the role of Tet1 in AD pathogenesis, we used the 5xFAD mouse model with a Tet1 KO allele to examine how Tet1 loss influences AD pathogenesis. We observed significant changes in neuropathology, 5hmC, and RNA expression associated with Tet1 loss, while the behavioral alterations were not significant. The loss of Tet1 significantly increased amyloid plaque burden in the 5xFAD mouse (p = 0.044) and lead to a non-significant trend towards exacerbated AD-associated stress response in 5xFAD mice. At the molecular level, we found significant DhMRs enriched in genes involved in pathways responsible for neuronal projection organization, dendritic spine development and organization, and myelin assembly. RNA-Seq analysis revealed a significant increase in the expression of AD-associated genes such as Mpeg1, Ctsd, and Trem2. In conclusion, our results suggest that TET enzymes, particularly TET1, which regulate the methylome, may contribute to AD pathogenesis, as the loss of TET function increases AD-associated pathology.
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Affiliation(s)
- Matthew J Armstrong
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yulin Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Selina M Vattathil
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yanting Huang
- Department of Computer Science, Emory University, Atlanta, GA 30322, USA
| | - Jason P Schroeder
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David A Bennet
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
| | - Thomas S Wingo
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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12
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Agredo A, Kasinski AL. Histone 4 lysine 20 tri-methylation: a key epigenetic regulator in chromatin structure and disease. Front Genet 2023; 14:1243395. [PMID: 37671044 PMCID: PMC10475950 DOI: 10.3389/fgene.2023.1243395] [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: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 09/07/2023] Open
Abstract
Chromatin is a vital and dynamic structure that is carefully regulated to maintain proper cell homeostasis. A great deal of this regulation is dependent on histone proteins which have the ability to be dynamically modified on their tails via various post-translational modifications (PTMs). While multiple histone PTMs are studied and often work in concert to facilitate gene expression, here we focus on the tri-methylation of histone H4 on lysine 20 (H4K20me3) and its function in chromatin structure, cell cycle, DNA repair, and development. The recent studies evaluated in this review have shed light on how H4K20me3 is established and regulated by various interacting partners and how H4K20me3 and the proteins that interact with this PTM are involved in various diseases. Through analyzing the current literature on H4K20me3 function and regulation, we aim to summarize this knowledge and highlights gaps that remain in the field.
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Affiliation(s)
- Alejandra Agredo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Life Sciences Interdisciplinary Program (PULSe), Purdue University, West Lafayette, IN, United States
| | - Andrea L. Kasinski
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
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13
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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14
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van der Veer BK, Chen L, Custers C, Athanasouli P, Schroiff M, Cornelis R, Chui JSH, Finnell R, Lluis F, Koh K. Dual functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation. Nucleic Acids Res 2023; 51:5469-5498. [PMID: 37021585 PMCID: PMC10287924 DOI: 10.1093/nar/gkad231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/12/2023] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
Gastrulation begins when the epiblast forms the primitive streak or becomes definitive ectoderm. During this lineage bifurcation, the DNA dioxygenase TET1 has bipartite functions in transcriptional activation and repression, but the mechanisms remain unclear. By converting mouse embryonic stem cells (ESCs) into neuroprogenitors, we defined how Tet1-/- cells switch from neuroectoderm fate to form mesoderm and endoderm. We identified the Wnt repressor Tcf7l1 as a TET1 target that suppresses Wnt/β-catenin and Nodal signalling. ESCs expressing catalytic dead TET1 retain neural potential but activate Nodal and subsequently Wnt/β-catenin pathways to generate also mesoderm and endoderm. At CpG-poor distal enhancers, TET1 maintains accessible chromatin at neuroectodermal loci independently of DNA demethylation. At CpG-rich promoters, DNA demethylation by TET1 affects the expression of bivalent genes. In ESCs, a non-catalytic TET1 cooperation with Polycomb represses primitive streak genes; post-lineage priming, the interaction becomes antagonistic at neuronal genes, when TET1's catalytic activity is further involved by repressing Wnt signalling. The convergence of repressive DNA and histone methylation does not inhibit neural induction in Tet1-deficient cells, but some DNA hypermethylated loci persist at genes with brain-specific functions. Our results reveal versatile switching of non-catalytic and catalytic TET1 activities based on genomic context, lineage and developmental stage.
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Affiliation(s)
- Bernard K van der Veer
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Lehua Chen
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Colin Custers
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Paraskevi Athanasouli
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell Signaling, B-3000 Leuven, Belgium
| | - Mariana Schroiff
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Riet Cornelis
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
| | - Jonathan Sai-Hong Chui
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell Signaling, B-3000 Leuven, Belgium
| | - Richard H Finnell
- Baylor College of Medicine, Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Houston, TX 77030, USA
- Baylor College of Medicine, Department of Molecular and Human Genetics, Department of Medicine, Houston, TX 77030, USA
| | - Frederic Lluis
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell Signaling, B-3000 Leuven, Belgium
| | - Kian Peng Koh
- KU Leuven, Department of Development and Regeneration, Laboratory of Stem Cell and Developmental Epigenetics, B-3000 Leuven, Belgium
- Baylor College of Medicine, Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Houston, TX 77030, USA
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15
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Yuita H, López-Moyado IF, Jeong H, Cheng AX, Scott-Browne J, An J, Nakayama T, Onodera A, Ko M, Rao A. Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch. Proc Natl Acad Sci U S A 2023; 120:e2214824120. [PMID: 37406303 PMCID: PMC9963276 DOI: 10.1073/pnas.2214824120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/29/2022] [Indexed: 08/03/2023] Open
Abstract
The three mammalian TET dioxygenases oxidize the methyl group of 5-methylcytosine in DNA, and the oxidized methylcytosines are essential intermediates in all known pathways of DNA demethylation. To define the in vivo consequences of complete TET deficiency, we inducibly deleted all three Tet genes in the mouse genome. Tet1/2/3-inducible TKO (iTKO) mice succumbed to acute myeloid leukemia (AML) by 4 to 5 wk. Single-cell RNA sequencing of Tet iTKO bone marrow cells revealed the appearance of new myeloid cell populations characterized by a striking increase in expression of all members of the stefin/cystatin gene cluster on mouse chromosome 16. In patients with AML, high stefin/cystatin gene expression correlates with poor clinical outcomes. Increased expression of the clustered stefin/cystatin genes was associated with a heterochromatin-to-euchromatin compartment switch with readthrough transcription downstream of the clustered stefin/cystatin genes as well as other highly expressed genes, but only minor changes in DNA methylation. Our data highlight roles for TET enzymes that are distinct from their established function in DNA demethylation and instead involve increased transcriptional readthrough and changes in three-dimensional genome organization.
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Affiliation(s)
- Hiroshi Yuita
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA92037
| | - Isaac F. López-Moyado
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA92037
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92093
| | - Hyeongmin Jeong
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
| | - Arthur Xiuyuan Cheng
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA92037
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92093
| | - James Scott-Browne
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO80206
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO80045
| | - Jungeun An
- Department of Life Sciences, Jeonbuk National University, Jeonju54896, Republic of Korea
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
- Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Chiba260-8670, Japan
| | - Atsushi Onodera
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA92037
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba260-8670, Japan
- Institute for Advanced Academic Research, Chiba University, Inage-ku, Chiba263-8522, Japan
| | - Myunggon Ko
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan44919, Republic of Korea
- Center for Genomic Integrity, Institute for Basic Science, Ulsan44919, Republic of Korea
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA92037
- Sanford Consortium for Regenerative Medicine, La Jolla, CA92093
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16
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Tsagaratou A. TET Proteins in the Spotlight: Emerging Concepts of Epigenetic Regulation in T Cell Biology. Immunohorizons 2023; 7:106-115. [PMID: 36645853 PMCID: PMC10152628 DOI: 10.4049/immunohorizons.2200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Ten-eleven translocation (TET) proteins are dioxygenases that oxidize 5-methylcytosine to form 5-hydroxymethylcytosine and downstream oxidized modified cytosines. In the past decade, intensive research established that TET-mediated DNA demethylation is critical for immune cell development and function. In this study, we discuss major advances regarding the role of TET proteins in regulating gene expression in the context of T cell lineage specification, function, and proliferation. Then, we focus on open questions in the field. We discuss recent findings regarding the diverse roles of TET proteins in other systems, and we ask how these findings might relate to T cell biology. Finally, we ask how this tremendous progress on understanding the multifaceted roles of TET proteins in shaping T cell identity and function can be translated to improve outcomes of human disease, such as hematological malignancies and immune response to cancer.
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Affiliation(s)
- Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; and Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC
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17
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Kaluscha S, Domcke S, Wirbelauer C, Stadler MB, Durdu S, Burger L, Schübeler D. Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation. Nat Genet 2022; 54:1895-1906. [PMID: 36471082 PMCID: PMC9729108 DOI: 10.1038/s41588-022-01241-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 10/24/2022] [Indexed: 12/12/2022]
Abstract
Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indirect inhibition via recruitment of methyl-CpG-binding domain (MBD) proteins is unclear. Here we show that combinatorial genetic deletions of all four proteins with functional MBDs in mouse embryonic stem cells, derived neurons or a human cell line do not reactivate genes or repeats with methylated promoters. These do, however, become activated by methylation-restricted TFs if DNA methylation is removed. We identify several causal TFs in neurons, including ONECUT1, which is methylation sensitive only at a motif variant. Rampantly upregulated retrotransposons in methylation-free neurons feature a CRE motif, which activates them in the absence of DNA methylation via methylation-sensitive binding of CREB1. Our study reveals methylation-sensitive TFs in vivo and argues that direct inhibition, rather than indirect repression by the tested MBD proteins, is the prevailing mechanism of methylation-mediated repression at regulatory regions and repeats.
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Affiliation(s)
- Sebastian Kaluscha
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Faculty of Sciences, Basel, Switzerland
| | - Silvia Domcke
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- University of Basel, Faculty of Sciences, Basel, Switzerland
| | - Sevi Durdu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Faculty of Sciences, Basel, Switzerland.
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