1
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Kim A, Benavente CA. Oncogenic Roles of UHRF1 in Cancer. EPIGENOMES 2024; 8:26. [PMID: 39051184 PMCID: PMC11270427 DOI: 10.3390/epigenomes8030026] [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: 04/10/2024] [Revised: 05/29/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is an essential protein involved in the maintenance of repressive epigenetic marks, ensuring epigenetic stability and fidelity. As an epigenetic regulator, UHRF1 comprises several functional domains (UBL, TTD, PHD, SRA, RING) that are collectively responsible for processes like DNA methylation, histone modification, and DNA repair. UHRF1 is a downstream effector of the RB/E2F pathway, which is nearly universally deregulated in cancer. Under physiological conditions, UHRF1 protein levels are cell cycle-dependent and are post-translationally regulated by proteasomal degradation. Conversely, UHRF1 is overexpressed and serves as an oncogenic driver in multiple cancers. This review focuses on the functional domains of UHRF1, highlighting its key interacting proteins and oncogenic roles in solid tumors including retinoblastoma, osteosarcoma, lung cancer, and breast cancer. Additionally, current therapeutic strategies targeting UHRF1 domains or its interactors are explored, providing an insight on potential clinical applications.
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Affiliation(s)
- Ahhyun Kim
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Claudia A. Benavente
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92697, USA
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2
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Shiraishi N, Konuma T, Chiba Y, Hokazono S, Nakamura N, Islam MH, Nakanishi M, Nishiyama A, Arita K. Structure of human DPPA3 bound to the UHRF1 PHD finger reveals its functional and structural differences from mouse DPPA3. Commun Biol 2024; 7:746. [PMID: 38898124 PMCID: PMC11187062 DOI: 10.1038/s42003-024-06434-9] [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: 11/29/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
DNA methylation maintenance is essential for cell fate inheritance. In differentiated cells, this involves orchestrated actions of DNMT1 and UHRF1. In mice, the high-affinity binding of DPPA3 to the UHRF1 PHD finger regulates UHRF1 chromatin dissociation and cytosolic localization, which is required for oocyte maturation and early embryo development. However, the human DPPA3 ortholog functions during these stages remain unclear. Here, we report the structural basis for human DPPA3 binding to the UHRF1 PHD finger. The conserved human DPPA3 85VRT87 motif binds to the acidic surface of UHRF1 PHD finger, whereas mouse DPPA3 binding additionally utilizes two unique α-helices. The binding affinity of human DPPA3 for the UHRF1 PHD finger was weaker than that of mouse DPPA3. Consequently, human DPPA3, unlike mouse DPPA3, failed to inhibit UHRF1 chromatin binding and DNA remethylation in Xenopus egg extracts effectively. Our data provide novel insights into the distinct function and structure of human DPPA3.
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Affiliation(s)
- Nao Shiraishi
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tsuyoshi Konuma
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sayaka Hokazono
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Nao Nakamura
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Md Hadiul Islam
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, 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
| | - 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
| | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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3
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Dasgupta A, Nandi S, Gupta S, Roy S, Das C. To Ub or not to Ub: The epic dilemma of histones that regulate gene expression and epigenetic cross-talk. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195033. [PMID: 38750882 DOI: 10.1016/j.bbagrm.2024.195033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 01/04/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
A dynamic array of histone post-translational modifications (PTMs) regulate diverse cellular processes in the eukaryotic chromatin. Among them, histone ubiquitination is particularly complex as it alters nucleosome surface area fostering intricate cross-talk with other chromatin modifications. Ubiquitin signaling profoundly impacts DNA replication, repair, and transcription. Histones can undergo varied extent of ubiquitination such as mono, multi-mono, and polyubiquitination, which brings about distinct cellular fates. Mechanistic studies of the ubiquitin landscape in chromatin have unveiled a fascinating tapestry of events that orchestrate gene regulation. In this review, we summarize the key contributors involved in mediating different histone ubiquitination and deubiquitination events, and discuss their mechanism which impacts cell transcriptional identity and DNA damage response. We also focus on the proteins bearing epigenetic reader modules critical in discerning site-specific histone ubiquitination, pivotal for establishing complex epigenetic crosstalk. Moreover, we highlight the role of histone ubiquitination in different human diseases including neurodevelopmental disorders and cancer. Overall the review elucidates the intricate orchestration of histone ubiquitination impacting diverse cellular functions and disease pathogenesis, and provides insights into the current challenges of targeting them for therapeutic interventions.
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Affiliation(s)
- Anirban Dasgupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sayan Gupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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4
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Gu L, Fu Y, Li X. Roles of post-translational modifications of UHRF1 in cancer. Epigenetics Chromatin 2024; 17:15. [PMID: 38725075 PMCID: PMC11080273 DOI: 10.1186/s13072-024-00540-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
UHRF1 as a member of RING-finger type E3 ubiquitin ligases family, is an epigenetic regulator with five structural domains. It has been involved in the regulation of a series of biological functions, such as DNA replication, DNA methylation, and DNA damage repair. Additionally, aberrant overexpression of UHRF1 has been observed in over ten cancer types, indicating that UHRF1 is a typical oncogene. The overexpression of UHRF1 repressed the transcription of such tumor-suppressor genes as CDKN2A, BRCA1, and CDH1 through DNMT1-mediated DNA methylation. In addition to the upstream transcription factors regulating gene transcription, post-translational modifications (PTMs) also contribute to abnormal overexpression of UHRF1 in cancerous tissues. The types of PTM include phosphorylation, acetylation, methylationand ubiquitination, which regulate protein stability, histone methyltransferase activity, intracellular localization and the interaction with binding partners. Recently, several novel PTM types of UHRF1 have been reported, but the detailed mechanisms remain unclear. This comprehensive review summarized the types of UHRF1 PTMs, as well as their biological functions. A deep understanding of these crucial mechanisms of UHRF1 is pivotal for the development of novel UHRF1-targeted anti-cancer therapeutic strategies in the future.
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Affiliation(s)
- Lili Gu
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, 510699, Guangdong, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, 510699, Guangdong, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China
| | - Yongming Fu
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, 510699, Guangdong, China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, 510699, Guangdong, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China
| | - Xiong Li
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, 510699, Guangdong, China.
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, 510699, Guangdong, China.
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China.
- School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China.
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5
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Nguyen K, Karn J. The sounds of silencing: dynamic epigenetic control of HIV latency. Curr Opin HIV AIDS 2024; 19:102-109. [PMID: 38547337 PMCID: PMC10990033 DOI: 10.1097/coh.0000000000000850] [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] [Indexed: 04/04/2024]
Abstract
PURPOSE OF REVIEW This review highlights advances in understanding the epigenetic control mechanisms that regulate HIV-1 latency mechanisms in T-cells and microglial cells and describes the potential of current therapeutic approaches targeting the epigenetic machinery to eliminate or block the HIV-1 latent reservoir. RECENT FINDINGS Large-scale unbiased CRISPR-Cas9 library-based screenings, coupled with biochemical studies, have comprehensively identified the epigenetic factors pivotal in regulating HIV-1 latency, paving the way for potential novel targets in therapeutic development. These studies also highlight how the bivalency observed at the HIV-1 5'LTR primes latent proviruses for rapid reactivation. SUMMARY The HIV-1 latent is established very early during infection, and its persistence is the major obstacle to achieving an HIV-1 cure. Here, we present a succinct summary of the latest research findings, shedding light on the pivotal roles played by host epigenetic machinery in the control of HIV-1 latency. Newly uncovered mechanisms permitting rapid reversal of epigenetic restrictions upon viral reactivation highlight the formidable challenges of achieving enduring and irreversible epigenetic silencing of HIV-1.
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Affiliation(s)
- Kien Nguyen
- Department of Molecular Biology & Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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6
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Yamaguchi K, Chen X, Rodgers B, Miura F, Bashtrykov P, Bonhomme F, Salinas-Luypaert C, Haxholli D, Gutekunst N, Aygenli BÖ, Ferry L, Kirsh O, Laisné M, Scelfo A, Ugur E, Arimondo PB, Leonhardt H, Kanemaki MT, Bartke T, Fachinetti D, Jeltsch A, Ito T, Defossez PA. Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells. Nat Commun 2024; 15:2960. [PMID: 38580649 PMCID: PMC10997609 DOI: 10.1038/s41467-024-47314-4] [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: 07/09/2023] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
DNA methylation is an essential epigenetic chromatin modification, and its maintenance in mammals requires the protein UHRF1. It is yet unclear if UHRF1 functions solely by stimulating DNA methylation maintenance by DNMT1, or if it has important additional functions. Using degron alleles, we show that UHRF1 depletion causes a much greater loss of DNA methylation than DNMT1 depletion. This is not caused by passive demethylation as UHRF1-depleted cells proliferate more slowly than DNMT1-depleted cells. Instead, bioinformatics, proteomics and genetics experiments establish that UHRF1, besides activating DNMT1, interacts with DNMT3A and DNMT3B and promotes their activity. In addition, we show that UHRF1 antagonizes active DNA demethylation by TET2. Therefore, UHRF1 has non-canonical roles that contribute importantly to DNA methylation homeostasis; these findings have practical implications for epigenetics in health and disease.
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Affiliation(s)
- Kosuke Yamaguchi
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France.
| | - Xiaoying Chen
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Brianna Rodgers
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, Epigenetic Chemical Biology, CNRS, UMR 3523, Chem4Life, Paris, France
| | | | - Deis Haxholli
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicole Gutekunst
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | | | - Laure Ferry
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Olivier Kirsh
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Marthe Laisné
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Andrea Scelfo
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
| | - Enes Ugur
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paola B Arimondo
- Institut Pasteur, Université Paris Cité, Epigenetic Chemical Biology, CNRS, UMR 3523, Chem4Life, Paris, France
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
- Department of Biological Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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Tiedemann RL, Hrit J, Du Q, Wiseman AK, Eden HE, Dickson BM, Kong X, Chomiak AA, Vaughan RM, Hebert JM, David Y, Zhou W, Baylin SB, Jones PA, Clark SJ, Rothbart SB. UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580169. [PMID: 38405904 PMCID: PMC10888769 DOI: 10.1101/2024.02.13.580169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The RING E3 ubiquitin ligase UHRF1 is an established cofactor for DNA methylation inheritance. Nucleosomal engagement through histone and DNA interactions directs UHRF1 ubiquitin ligase activity toward lysines on histone H3 tails, creating binding sites for DNMT1 through ubiquitin interacting motifs (UIM1 and UIM2). Here, we profile contributions of UHRF1 and DNMT1 to genome-wide DNA methylation inheritance and dissect specific roles for ubiquitin signaling in this process. We reveal DNA methylation maintenance at low-density CpGs is vulnerable to disruption of UHRF1 ubiquitin ligase activity and DNMT1 ubiquitin reading activity through UIM1. Hypomethylation of low-density CpGs in this manner induces formation of partially methylated domains (PMD), a methylation signature observed across human cancers. Furthermore, disrupting DNMT1 UIM2 function abolishes DNA methylation maintenance. Collectively, we show DNMT1-dependent DNA methylation inheritance is a ubiquitin-regulated process and suggest a disrupted UHRF1-DNMT1 ubiquitin signaling axis contributes to the development of PMDs in human cancers.
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8
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Song Y, Liu H, Xian Q, Gui C, Xu M, Zhou Y. Mechanistic insights into UHRF1‑mediated DNA methylation by structure‑based functional clarification of UHRF1 domains (Review). Oncol Lett 2023; 26:542. [PMID: 38020304 PMCID: PMC10660443 DOI: 10.3892/ol.2023.14129] [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: 03/04/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Epigenetic modification is crucial for transmitting genetic information, while abnormalities in DNA methylation modification are primarily associated with cancer and neurological diseases. As a multifunctional epigenetic modifier, ubiquitin like with PHD and ring finger domains 1 (UHRF1) mainly affects cell energy metabolism and cell cycle control. It also inhibits the transcription of tumor suppressor genes through DNA and/or histone methylation modifications, promoting the occurrence and development of cancer. Therefore, comprehensively understanding the molecular mechanism of the epigenetic modification of UHRF1 in tumors will help identify targets for inhibiting the expression and function of UHRF1. Notably, each domain of UHRF1 functions as a whole and differently. Thus, the abnormality of any domain can lead to a change in phenotype or disease. However, the specific regulatory mechanism and proteins of each domain have not been fully elucidated. The present review aimed to contribute to the study of the regulatory mechanism of UHRF1 to a greater extent in different cancers and provide ideas for drug research by clarifying the function of UHRF1 domains.
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Affiliation(s)
- Yiying Song
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Haiting Liu
- Department of Critical Care Medicine, Jinan Zhangqiu Hospital of Traditional Chinese Medicine, Jinan, Shandong 250200, P.R. China
| | - Qingqing Xian
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
| | - Chengzhi Gui
- Department of Clinical Laboratory Diagnosis, Shandong First Medical University, Jinan, Shandong 250012, P.R. China
| | - Mingjie Xu
- Medical Research and Laboratory Diagnostic Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
| | - Yunying Zhou
- Department of Clinical Laboratory Diagnosis, Jinan Central Hospital, Shandong University, Jinan, Shandong 250012, P.R. China
- Department of Clinical Laboratory Diagnosis, Shandong First Medical University, Jinan, Shandong 250012, P.R. China
- Medical Research and Laboratory Diagnostic Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250013, P.R. China
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9
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Irwin RE, Scullion C, Thursby SJ, Sun M, Thakur A, Hilman L, Callaghan B, Thompson PD, McKenna DJ, Rothbart SB, Xu G, Walsh CP. The UHRF1 protein is a key regulator of retrotransposable elements and innate immune response to viral RNA in human cells. Epigenetics 2023; 18:2216005. [PMID: 37246786 PMCID: PMC10228402 DOI: 10.1080/15592294.2023.2216005] [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: 05/09/2022] [Accepted: 04/14/2023] [Indexed: 05/30/2023] Open
Abstract
While epigenetic mechanisms such as DNA methylation and histone modification are known to be important for gene suppression, relatively little is still understood about the interplay between these systems. The UHRF1 protein can interact with both DNA methylation and repressive chromatin marks, but its primary function in humans has been unclear. To determine what that was, we first established stable UHRF1 knockdowns (KD) in normal, immortalized human fibroblasts using targeting shRNA, since CRISPR knockouts (KO) were lethal. Although these showed a loss of DNA methylation across the whole genome, transcriptional changes were dominated by the activation of genes involved in innate immune signalling, consistent with the presence of viral RNA from retrotransposable elements (REs). We confirmed using mechanistic approaches that 1) REs were demethylated and transcriptionally activated; 2) this was accompanied by activation of interferons and interferon-stimulated genes and 3) the pathway was conserved across other adult cell types. Restoring UHRF1 in either transient or stable KD systems could abrogate RE reactivation and the interferon response. Notably, UHRF1 itself could also re-impose RE suppression independent of DNA methylation, but not if the protein contained point mutations affecting histone 3 with trimethylated lysine 9 (H3K9me3) binding. Our results therefore show for the first time that UHRF1 can act as a key regulator of retrotransposon silencing independent of DNA methylation.
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Affiliation(s)
- RE Irwin
- Biomedical Sciences, Ulster University, Coleraine, UK
| | - C Scullion
- Biomedical Sciences, Ulster University, Coleraine, UK
- Precision Nanosystems Inc, Vancouver, BC, Canada
| | - SJ Thursby
- Biomedical Sciences, Ulster University, Coleraine, UK
- State Key Laboratory of Molecular Biology, Shanghai Institutes of Biological Sciences, Shanghai, China
| | - M Sun
- Cellular and Molecular Medicine Program, Division of Oncology, Johns Hopkins School of Medicine, St., Baltimore, MD, USA
| | - A Thakur
- Biomedical Sciences, Ulster University, Coleraine, UK
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - L Hilman
- Biomedical Sciences, Ulster University, Coleraine, UK
| | - B Callaghan
- Biomedical Sciences, Ulster University, Coleraine, UK
| | - PD Thompson
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - DJ McKenna
- Biomedical Sciences, Ulster University, Coleraine, UK
| | - SB Rothbart
- Nutrition Innovation Centre for Food and Health, Biomedical Sciences, Ulster University, Coleraine, UK
| | - Guoliang Xu
- Cellular and Molecular Medicine Program, Division of Oncology, Johns Hopkins School of Medicine, St., Baltimore, MD, USA
| | - CP Walsh
- Biomedical Sciences, Ulster University, Coleraine, UK
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10
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Ashraf W, Ahmad T, Reynoird N, Hamiche A, Mély Y, Bronner C, Mousli M. Natural and Synthetic Anticancer Epidrugs Targeting the Epigenetic Integrator UHRF1. Molecules 2023; 28:5997. [PMID: 37630248 PMCID: PMC10459542 DOI: 10.3390/molecules28165997] [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: 06/21/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide, and its incidence and mortality are increasing each year. Improved therapeutic strategies against cancer have progressed, but remain insufficient to invert this trend. Along with several other risk factors, abnormal genetic and epigenetic regulations play a critical role in the initiation of cellular transformation, as well as tumorigenesis. The epigenetic regulator UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is a multidomain protein with oncogenic abilities overexpressed in most cancers. Through the coordination of its multiple domains and other epigenetic key players, UHRF1 regulates DNA methylation and histone modifications. This well-coordinated dialogue leads to the silencing of tumor-suppressor genes (TSGs) and facilitates tumor cells' resistance toward anticancer drugs, ultimately promoting apoptosis escape and uncontrolled proliferation. Several studies have shown that the downregulation of UHRF1 with natural compounds in tumor cells induces the reactivation of various TSGs, inhibits cell growth, and promotes apoptosis. In this review, we discuss the underlying mechanisms and the potential of various natural and synthetic compounds that can inhibit/minimize UHRF1's oncogenic activities and/or its expression.
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Affiliation(s)
- Waseem Ashraf
- Department of Pharmacology, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60800, Pakistan;
| | - Tanveer Ahmad
- Institut Pour L’avancée des Biosciences, Centre de Recherche UGA, INSERM U1209, CNRS 5309, Université Grenoble Alpes, 38058 Grenoble, France; (T.A.); (N.R.)
| | - Nicolas Reynoird
- Institut Pour L’avancée des Biosciences, Centre de Recherche UGA, INSERM U1209, CNRS 5309, Université Grenoble Alpes, 38058 Grenoble, France; (T.A.); (N.R.)
| | - Ali Hamiche
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR 7104, Université de Strasbourg, Equipe Labellisée Ligue Contre le Cancer, 67401 Illkirch, France;
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch, France;
| | - Christian Bronner
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR 7104, Université de Strasbourg, Equipe Labellisée Ligue Contre le Cancer, 67401 Illkirch, France;
| | - Marc Mousli
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch, France;
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11
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Uemura S, Maenohara S, Inoue K, Ogonuki N, Matoba S, Ogura A, Kurumizaka M, Yamagata K, Sharif J, Koseki H, Ueda K, Unoki M, Sasaki H. UHRF1 is essential for proper cytoplasmic architecture and function of mouse oocytes and derived embryos. Life Sci Alliance 2023; 6:e202301904. [PMID: 37225425 PMCID: PMC10209520 DOI: 10.26508/lsa.202301904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 05/26/2023] Open
Abstract
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is a protein essential for the maintenance of DNA methylation in somatic cells. However, UHRF1 is predominantly localized in the cytoplasm of mouse oocytes and preimplantation embryos, where it may play a role unrelated to the nuclear function. We herein report that oocyte-specific Uhrf1 KO results in impaired chromosome segregation, abnormal cleavage division, and preimplantation lethality of derived embryos. Our nuclear transfer experiment showed that the phenotype is attributable to cytoplasmic rather than nuclear defects of the zygotes. A proteomic analysis of KO oocytes revealed the down-regulation of proteins associated with microtubules including tubulins, which occurred independently of transcriptomic changes. Intriguingly, cytoplasmic lattices were disorganized, and mitochondria, endoplasmic reticulum, and components of the subcortical maternal complex were mislocalized. Thus, maternal UHRF1 regulates the proper cytoplasmic architecture and function of oocytes and preimplantation embryos, likely through a mechanism unrelated to DNA methylation.
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Affiliation(s)
- Shuhei Uemura
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Shoji Maenohara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, RIKEN BioResource Research Center (BRC), Ibaraki, Japan
| | - Narumi Ogonuki
- Bioresource Engineering Division, RIKEN BioResource Research Center (BRC), Ibaraki, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, RIKEN BioResource Research Center (BRC), Ibaraki, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN BioResource Research Center (BRC), Ibaraki, Japan
| | - Mayuko Kurumizaka
- Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Kazuo Yamagata
- Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Faculty of Biology-Oriented Science and Technology, KINDAI University, Wakayama, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - 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
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12
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Miyashita R, Nishiyama A, Qin W, Chiba Y, Kori S, Kato N, Konishi C, Kumamoto S, Kozuka-Hata H, Oyama M, Kawasoe Y, Tsurimoto T, Takahashi TS, Leonhardt H, Arita K, Nakanishi M. The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5. eLife 2023; 12:79013. [PMID: 36734974 PMCID: PMC9943068 DOI: 10.7554/elife.79013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 02/02/2023] [Indexed: 02/04/2023] Open
Abstract
UHRF1-dependent ubiquitin signaling plays an integral role in the regulation of maintenance DNA methylation. UHRF1 catalyzes transient dual mono-ubiquitylation of PAF15 (PAF15Ub2), which regulates the localization and activation of DNMT1 at DNA methylation sites during DNA replication. Although the initiation of UHRF1-mediated PAF15 ubiquitin signaling has been relatively well characterized, the mechanisms underlying its termination and how they are coordinated with the completion of maintenance DNA methylation have not yet been clarified. This study shows that deubiquitylation by USP7 and unloading by ATAD5 (ELG1 in yeast) are pivotal processes for the removal of PAF15 from chromatin. On replicating chromatin, USP7 specifically interacts with PAF15Ub2 in a complex with DNMT1. USP7 depletion or inhibition of the interaction between USP7 and PAF15 results in abnormal accumulation of PAF15Ub2 on chromatin. Furthermore, we also find that the non-ubiquitylated form of PAF15 (PAF15Ub0) is removed from chromatin in an ATAD5-dependent manner. PAF15Ub2 was retained at high levels on chromatin when the catalytic activity of DNMT1 was inhibited, suggesting that the completion of maintenance DNA methylation is essential for the termination of UHRF1-mediated ubiquitin signaling. This finding provides a molecular understanding of how the maintenance DNA methylation machinery is disassembled at the end of the S phase.
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Affiliation(s)
- Ryota Miyashita
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Satomi Kori
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Norie Kato
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Chieko Konishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Yoshitaka Kawasoe
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | - Toshiki Tsurimoto
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | - Tatsuro S Takahashi
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | | | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
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13
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Ngan KCH, Hoenig SM, Kwok HS, Lue NZ, Gosavi PM, Tanner DA, Garcia EM, Lee C, Liau BB. Activity-based CRISPR scanning uncovers allostery in DNA methylation maintenance machinery. eLife 2023; 12:80640. [PMID: 36762644 PMCID: PMC9946446 DOI: 10.7554/elife.80640] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Allostery enables dynamic control of protein function. A paradigmatic example is the tightly orchestrated process of DNA methylation maintenance. Despite the fundamental importance of allosteric sites, their identification remains highly challenging. Here, we perform CRISPR scanning on the essential maintenance methylation machinery-DNMT1 and its partner UHRF1-with the activity-based inhibitor decitabine to uncover allosteric mechanisms regulating DNMT1. In contrast to non-covalent DNMT1 inhibition, activity-based selection implicates numerous regions outside the catalytic domain in DNMT1 function. Through computational analyses, we identify putative mutational hotspots in DNMT1 distal from the active site that encompass mutations spanning a multi-domain autoinhibitory interface and the uncharacterized BAH2 domain. We biochemically characterize these mutations as gain-of-function, exhibiting increased DNMT1 activity. Extrapolating our analysis to UHRF1, we discern putative gain-of-function mutations in multiple domains, including key residues across the autoinhibitory TTD-PBR interface. Collectively, our study highlights the utility of activity-based CRISPR scanning for nominating candidate allosteric sites, and more broadly, introduces new analytical tools that further refine the CRISPR scanning framework.
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Affiliation(s)
- Kevin Chun-Ho Ngan
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Samuel M Hoenig
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Hui Si Kwok
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Pallavi M Gosavi
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - David A Tanner
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Emma M Garcia
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Ceejay Lee
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
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14
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Ren Y. Regulatory mechanism and biological function of UHRF1–DNMT1-mediated DNA methylation. Funct Integr Genomics 2022; 22:1113-1126. [DOI: 10.1007/s10142-022-00918-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
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15
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Zhang H, Liu Y, Xie Y, Zhu Y, Liu J, Lu F. H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1685-1700. [PMID: 35831553 DOI: 10.1007/s11427-022-2155-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation and histone lysine tri-methylation at H3K27 (H3K27me3) are two chromatin modifications for transcriptional gene silencing, which play important roles in diverse biological processes, including cell fate determination and cell lineage commitment. These two marks are largely mutually exclusive and target distinct sets of genes in the mammalian genome. However, how H3K27me3 shapes the DNA methylome remains elusive. Here, we report that the loss of H3K27me3 modification leads to increased DNA methylation at previously marked H3K27me3 sites, indicating that H3K27me3 negatively regulates DNA methylation. Genome-wide analysis of H3 ubiquitination, essential for recruitment and activation of DNA methyltransferase DNMT1, reveals the absence of H3 ubiquitination at H3K27me3 marked nucleosomes. Moreover, loss of H3K27me3 modification induces an increase in H3K18 ubiquitination at the corresponding hyper-methylated loci. Importantly, we show that H3K27me3 directly inhibits UHRF1-mediated H3 ubiquitination toward nucleosomes in a defined biochemical assay. Taken together, our findings reveal a general mechanism for H3K27me3-mediated shaping of the mammalian DNA methylome via modulation of H3 ubiquitination.
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Affiliation(s)
- Honglian Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yali Xie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunji Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingwen Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Mandal P, Eswara K, Yerkesh Z, Kharchenko V, Zandarashvili L, Szczepski K, Bensaddek D, Jaremko Ł, Black BE, Fischle W. Molecular basis of hUHRF1 allosteric activation for synergistic histone modification binding by PI5P. SCIENCE ADVANCES 2022; 8:eabl9461. [PMID: 36001657 PMCID: PMC9401617 DOI: 10.1126/sciadv.abl9461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Chromatin marks are recognized by distinct binding modules, many of which are embedded in multidomain proteins. How the different functionalities of such complex chromatin modulators are regulated is often unclear. Here, we delineated the interplay of the H3 amino terminus- and K9me-binding activities of the multidomain hUHRF1 protein. We show that the phosphoinositide PI5P interacts simultaneously with two distant flexible linker regions connecting distinct domains of hUHRF1. The binding is dependent on both, the polar head group, and the acyl part of the phospholipid and induces a conformational rearrangement juxtaposing the H3 amino terminus and K9me3 recognition modules of the protein. In consequence, the two features of the H3 tail are bound in a multivalent, synergistic manner. Our work highlights a previously unidentified molecular function for PI5P outside of the context of lipid mono- or bilayers and establishes a molecular paradigm for the allosteric regulation of complex, multidomain chromatin modulators by small cellular molecules.
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Affiliation(s)
- Papita Mandal
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Karthik Eswara
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Zhadyra Yerkesh
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Vladlena Kharchenko
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Levani Zandarashvili
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kacper Szczepski
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- Core Laboratories, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Łukasz Jaremko
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Ben E. Black
- Department of Biochemistry and Biophysics, Penn Center for Genome Integrity, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wolfgang Fischle
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
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17
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Comprehensive Pan-Cancer Analysis Reveals the Role of UHRF1-Mediated DNA Methylation and Immune Infiltration in Renal Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:3842547. [PMID: 35656341 PMCID: PMC9152404 DOI: 10.1155/2022/3842547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/17/2022]
Abstract
Ubiquitin-like PHD and ring finger domain protein 1 (UHRF1) are members of the multifunctional UHRF family, which can participate in DNA methylation change and histone posttranslational change through particular domains and participate in the event and development of tumors. The purpose of this study was to decide the molecular traits and potential medicine-based importance of UHRF1 that helped settle methylated immune infiltration in generalized cancer by carefully studying the relationship between UHRF1 expression and a variety of tumors and to further check for truth the functional role of UHRF1 in kidney-related cancer. A comprehensive analysis of UHRF1 in 33 cancers was performed based on TCGA database. This research involves analysis of mRNA expression profiles, prognostic value, immune infiltration, immune neoantigens, TMB, microsatellite instability, DNA methylation, and gene set enrichment analysis (GSEA). Both immune infiltration and DNA methylation were used to evaluate the importance and method of UHRF1 in renal cancer. The results showed that tumor tissue had higher expression level of UHRF1 than usual tissue. The high expression level of UHRF1 is related to the survival rate of renal cancer. UHRF1 expression was associated with tumor mutation load and microsatellite instability in different cancer types, and enrichment analysis identified terminology and pathways associated with UHRF1. This study showed that UHRF1 plays an important role in the group of objects and development of 33 tumors. UHRF1 may serve as a biomarker of immune infiltration and poor outlook of cancer.
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18
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Verdikt R, Bendoumou M, Bouchat S, Nestola L, Pasternak AO, Darcis G, Avettand-Fenoel V, Vanhulle C, Aït-Ammar A, Santangelo M, Plant E, Douce VL, Delacourt N, Cicilionytė A, Necsoi C, Corazza F, Passaes CPB, Schwartz C, Bizet M, Fuks F, Sáez-Cirión A, Rouzioux C, De Wit S, Berkhout B, Gautier V, Rohr O, Van Lint C. Novel role of UHRF1 in the epigenetic repression of the latent HIV-1. EBioMedicine 2022; 79:103985. [PMID: 35429693 PMCID: PMC9038550 DOI: 10.1016/j.ebiom.2022.103985] [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: 09/02/2021] [Revised: 03/11/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The multiplicity, heterogeneity, and dynamic nature of human immunodeficiency virus type-1 (HIV-1) latency mechanisms are reflected in the current lack of functional cure for HIV-1. Accordingly, all classes of latency-reversing agents (LRAs) have been reported to present variable ex vivo potencies. Here, we investigated the molecular mechanisms underlying the potency variability of one LRA: the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-AzadC). METHODS We employed epigenetic interrogation methods (electrophoretic mobility shift assays, chromatin immunoprecipitation, Infinium array) in complementary HIV-1 infection models (latently-infected T-cell line models, primary CD4+ T-cell models and ex vivo cultures of PBMCs from HIV+ individuals). Extracellular staining of cell surface receptors and intracellular metabolic activity were measured in drug-treated cells. HIV-1 expression in reactivation studies was explored by combining the measures of capsid p24Gag protein, green fluorescence protein signal, intracellular and extracellular viral RNA and viral DNA. FINDINGS We uncovered specific demethylation CpG signatures induced by 5-AzadC in the HIV-1 promoter. By analyzing the binding modalities to these CpG, we revealed the recruitment of the epigenetic integrator Ubiquitin-like with PHD and RING finger domain 1 (UHRF1) to the HIV-1 promoter. We showed that UHRF1 redundantly binds to the HIV-1 promoter with different binding modalities where DNA methylation was either non-essential, essential or enhancing UHRF1 binding. We further demonstrated the role of UHRF1 in the epigenetic repression of the latent viral promoter by a concerted control of DNA and histone methylations. INTERPRETATION A better understanding of the molecular mechanisms of HIV-1 latency allows for the development of innovative antiviral strategies. As a proof-of-concept, we showed that pharmacological inhibition of UHRF1 in ex vivo HIV+ patient cell cultures resulted in potent viral reactivation from latency. Together, we identify UHRF1 as a novel actor in HIV-1 epigenetic silencing and highlight that it constitutes a new molecular target for HIV-1 cure strategies. FUNDING Funding was provided by the Belgian National Fund for Scientific Research (F.R.S.-FNRS, Belgium), the « Fondation Roi Baudouin », the NEAT (European AIDS Treatment Network) program, the Internationale Brachet Stiftung, ViiV Healthcare, the Télévie, the Walloon Region (« Fonds de Maturation »), « Les Amis des Instituts Pasteur à Bruxelles, asbl », the University of Brussels (Action de Recherche Concertée ULB grant), the Marie Skodowska Curie COFUND action, the European Union's Horizon 2020 research and innovation program under grant agreement No 691119-EU4HIVCURE-H2020-MSCA-RISE-2015, the French Agency for Research on AIDS and Viral Hepatitis (ANRS), the Sidaction and the "Alsace contre le Cancer" Foundation. This work is supported by 1UM1AI164562-01, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Roxane Verdikt
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Maryam Bendoumou
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Sophie Bouchat
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Lorena Nestola
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Alexander O Pasternak
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Virology, Amsterdam 1105 AZ, the Netherland
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, Liège 4000, Belgium
| | - Véronique Avettand-Fenoel
- AP-HP, Hôpital Necker-Enfants-Malades, Service de Microbiologie clinique, Paris 75015, France; Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France; INSERM, U1016, Institut Cochin, Paris, 75014, France; CNRS, UMR8104, Paris 75014, France
| | - Caroline Vanhulle
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Amina Aït-Ammar
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Marion Santangelo
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Valentin Le Douce
- Centre for Research in Infectious Diseases, University College Dublin, Dublin 4, Ireland
| | - Nadège Delacourt
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Aurelija Cicilionytė
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Virology, Amsterdam 1105 AZ, the Netherland
| | - Coca Necsoi
- Service des Maladies Infectieuses, CHU St-Pierre, Université Libre de Bruxelles (ULB), Brussels 1000, Belgium
| | - Francis Corazza
- Laboratory of Immunology, IRISLab, CHU Brugmann, Université Libre de Bruxelles (ULB), Brussels 1020, Belgium
| | | | - Christian Schwartz
- Laboratoire DHPI EA7292, Université de Strasbourg, Schiltigheim, 67300, France; IUT Louis Pasteur, Université de Strasbourg, Schiltigheim, 67300, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels 1070, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels 1070, Belgium
| | - Asier Sáez-Cirión
- Départements de Virologie et Immunologie, Institut Pasteur, Unité HIV, Inflammation et Persistance, Paris 75015, France
| | - Christine Rouzioux
- AP-HP, Hôpital Necker-Enfants-Malades, Service de Microbiologie clinique, Paris 75015, France
| | - Stéphane De Wit
- Service des Maladies Infectieuses, CHU St-Pierre, Université Libre de Bruxelles (ULB), Brussels 1000, Belgium
| | - Ben Berkhout
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Laboratory of Experimental Virology, Amsterdam 1105 AZ, the Netherland
| | - Virginie Gautier
- Centre for Research in Infectious Diseases, University College Dublin, Dublin 4, Ireland
| | - Olivier Rohr
- Laboratoire DHPI EA7292, Université de Strasbourg, Schiltigheim, 67300, France; IUT Louis Pasteur, Université de Strasbourg, Schiltigheim, 67300, France
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium.
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19
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Roman-Trufero M, Dillon N. The UBE2D ubiquitin conjugating enzymes: Potential regulatory hubs in development, disease and evolution. Front Cell Dev Biol 2022; 10:1058751. [PMID: 36578786 PMCID: PMC9790923 DOI: 10.3389/fcell.2022.1058751] [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: 09/30/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination of cellular proteins plays critical roles in key signalling pathways and in the regulation of protein turnover in eukaryotic cells. E2 ubiquitin conjugating enzymes function as essential intermediates in ubiquitination reactions by acting as ubiquitin donors for the E3 ubiquitin ligase enzymes that confer substrate specificity. The members of the UBE2D family of E2 enzymes are involved in regulating signalling cascades through ubiquitination of target proteins that include receptor tyrosine kinases (RTKs) and components of the Hedgehog, TGFβ and NFκB pathways. UBE2D enzymes also function in transcriptional control by acting as donors for ubiquitination of histone tails by the Polycomb protein Ring1B and the DNA methylation regulator UHRF1 as well as having roles in DNA repair and regulation of the level of the tumour suppressor p53. Here we review the functional roles and mechanisms of regulation of the UBE2D proteins including recent evidence that regulation of the level of UBE2D3 is critical for controlling ubiquitination of specific targets during development. Cellular levels of UBE2D3 have been shown to be regulated by phosphorylation, which affects folding of the protein, reducing its stability. Specific variations in the otherwise highly conserved UBE2D3 protein sequence in amniotes and in a subgroup of teleost fishes, the Acanthomorpha, suggest that the enzyme has had important roles during vertebrate evolution.
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Affiliation(s)
- Monica Roman-Trufero
- Centre for Haematology, Department of Immunology and Inflammation, Imperial College, Hammersmith Hospital Campus, London, United Kingdom
| | - Niall Dillon
- MRC London Institute of Medical Sciences, Imperial College, Hammersmith Hospital Campus, London, United Kingdom
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20
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Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:111-136. [PMID: 36350508 PMCID: PMC9815518 DOI: 10.1007/978-3-031-11454-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytosine methylation at the C5-position-generating 5-methylcytosine (5mC)-is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80%) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation and genetic alterations in enzymes and regulators involved in DNA methylation are associated with various human diseases, including cancer and developmental disorders. In mammals, DNA methylation is mediated by two families of DNA methyltransferases (Dnmts), namely Dnmt1 and Dnmt3 proteins. Over the last three decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and human diseases.
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21
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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.
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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
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22
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Petell CJ, Randene K, Pappas M, Sandoval D, Strahl BD, Harrison JS, Steimel JP. Mechanically transduced immunosorbent assay to measure protein-protein interactions. eLife 2021; 10:67525. [PMID: 34581668 PMCID: PMC8479797 DOI: 10.7554/elife.67525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus producing a mechanical signal when a binding event occurs. The METRIS assay uses as little as 20 pmols of reagents to measure a wide range of affinities while exhibiting a high resolution and sensitivity. We use METRIS to measure several PPIs that were previously inaccessible using traditional methods, providing new insights into epigenetic recognition.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Kathyrn Randene
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Michael Pappas
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Diego Sandoval
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Joshua P Steimel
- Department of Mechanical Engineering, University of the Pacific, Stockton, United States
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23
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Newkirk SJ, An W. UHRF1: a jack of all trades, and a master epigenetic regulator during spermatogenesis. Biol Reprod 2021; 102:1147-1152. [PMID: 32101289 DOI: 10.1093/biolre/ioaa026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Affiliation(s)
- Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
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24
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Mancini M, Magnani E, Macchi F, Bonapace IM. The multi-functionality of UHRF1: epigenome maintenance and preservation of genome integrity. Nucleic Acids Res 2021; 49:6053-6068. [PMID: 33939809 PMCID: PMC8216287 DOI: 10.1093/nar/gkab293] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
During S phase, the cooperation between the macromolecular complexes regulating DNA synthesis, epigenetic information maintenance and DNA repair is advantageous for cells, as they can rapidly detect DNA damage and initiate the DNA damage response (DDR). UHRF1 is a fundamental epigenetic regulator; its ability to coordinate DNA methylation and histone code is unique across proteomes of different species. Recently, UHRF1’s role in DNA damage repair has been explored and recognized to be as important as its role in maintaining the epigenome. UHRF1 is a sensor for interstrand crosslinks and a determinant for the switch towards homologous recombination in the repair of double-strand breaks; its loss results in enhanced sensitivity to DNA damage. These functions are finely regulated by specific post-translational modifications and are mediated by the SRA domain, which binds to damaged DNA, and the RING domain. Here, we review recent studies on the role of UHRF1 in DDR focusing on how it recognizes DNA damage and cooperates with other proteins in its repair. We then discuss how UHRF1’s epigenetic abilities in reading and writing histone modifications, or its interactions with ncRNAs, could interlace with its role in DDR.
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Affiliation(s)
- Monica Mancini
- Department of Biotechnology and Life Sciences, University of Insubria, Busto Arsizio, VA 21052, Italy
| | - Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, United Arab Emirates
| | - Ian Marc Bonapace
- Department of Biotechnology and Life Sciences, University of Insubria, Busto Arsizio, VA 21052, Italy
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25
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Nishiyama A, Nakanishi M. Navigating the DNA methylation landscape of cancer. Trends Genet 2021; 37:1012-1027. [PMID: 34120771 DOI: 10.1016/j.tig.2021.05.002] [Citation(s) in RCA: 291] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/11/2022]
Abstract
DNA methylation is a chemical modification that defines cell type and lineage through the control of gene expression and genome stability. Disruption of DNA methylation control mechanisms causes a variety of diseases, including cancer. Cancer cells are characterized by aberrant DNA methylation (i.e., genome-wide hypomethylation and site-specific hypermethylation), mainly targeting CpG islands in gene expression regulatory elements. In particular, the early findings that a variety of tumor suppressor genes (TSGs) are targets of DNA hypermethylation in cancer led to the proposal of a model in which aberrant DNA methylation promotes cellular oncogenesis through TSGs silencing. However, recent genome-wide analyses have revealed that this classical model needs to be reconsidered. In this review, we will discuss the molecular mechanisms of DNA methylation abnormalities in cancer as well as their therapeutic potential.
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Affiliation(s)
- Atsuya Nishiyama
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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26
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Bacheva AV, Gotmanova NN, Belogurov AA, Kudriaeva AA. Control of Genome through Variative Nature of Histone-Modifying Ubiquitin Ligases. BIOCHEMISTRY (MOSCOW) 2021; 86:S71-S95. [PMID: 33827401 DOI: 10.1134/s0006297921140066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Covalent attachment of ubiquitin residue is not only the proteasomal degradation signal, but also a widespread posttranslational modification of cellular proteins in eukaryotes. One of the most important targets of the regulatory ubiquitination are histones. Localization of ubiquitin residue in different regions of the nucleosome attracts a strictly determined set of cellular factors with varied functionality. Depending on the type of histone and the particular lysine residue undergoing modification, histone ubiquitination can lead both to transcription activation and to gene repression, as well as contribute to DNA repair via different mechanisms. An extremely interesting feature of the family of RING E3 ubiquitin ligases catalyzing histone ubiquitination is the striking structural diversity of the domains providing high specificity of modification very similar initial targets. It is obvious that further elucidation of peculiarities of the ubiquitination system involved in histone modification, as well as understanding of physiological role of this process in the maintenance of homeostasis of both single cells and the entire organism, will substantially expand the possibilities of treating a number of socially significant diseases.
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Affiliation(s)
- Anna V Bacheva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | | | - Alexey A Belogurov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Anna A Kudriaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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27
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Unoki M. Chromatin remodeling in replication-uncoupled maintenance DNA methylation and chromosome stability: Insights from ICF syndrome studies. Genes Cells 2021; 26:349-359. [PMID: 33960584 PMCID: PMC9292322 DOI: 10.1111/gtc.12850] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022]
Abstract
Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is characterized by frequent appearance of multiradial chromosomes, which are distinctive chromosome fusions that occur at hypomethylated pericentromeric regions comprising repetitive sequences, in activated lymphocytes. The syndrome is caused by mutations in DNMT3B, ZBTB24, CDCA7, or HELLS. De novo DNA methylation is likely defective in patients with ICF syndrome harboring mutations in DNMT3B, whereas accumulating evidence suggests that replication‐uncoupled maintenance DNA methylation of late‐replicating regions is impaired in patients with ICF syndrome harboring mutations in ZBTB24, CDCA7, or HELLS. ZBTB24 is a transcriptional activator of CDCA7, and CDCA7 and HELLS compose a chromatin remodeling complex and are involved in the maintenance DNA methylation through an interaction with UHRF1 in a feed‐forward manner. Furthermore, our recent studies possibly provided the missing link between DNA hypomethylation and the formation of the abnormal chromosomes; it could occur via aberrant transcription from the hypomethylated regions, followed by pathological R‐loop formation. The homologous‐recombination dominant condition caused by a defect in nonhomologous end joining observed in several types of ICF syndrome could facilitate the formation of multiradial chromosomes. Here, the latest knowledge regarding maintenance DNA methylation and chromosome stability provided by those studies is reviewed.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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28
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Li Y, Chen X, Lu C. The interplay between DNA and histone methylation: molecular mechanisms and disease implications. EMBO Rep 2021; 22:e51803. [PMID: 33844406 PMCID: PMC8097341 DOI: 10.15252/embr.202051803] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Methylation of cytosine in CpG dinucleotides and histone lysine and arginine residues is a chromatin modification that critically contributes to the regulation of genome integrity, replication, and accessibility. A strong correlation exists between the genome-wide distribution of DNA and histone methylation, suggesting an intimate relationship between these epigenetic marks. Indeed, accumulating literature reveals complex mechanisms underlying the molecular crosstalk between DNA and histone methylation. These in vitro and in vivo discoveries are further supported by the finding that genes encoding DNA- and histone-modifying enzymes are often mutated in overlapping human diseases. Here, we summarize recent advances in understanding how DNA and histone methylation cooperate to maintain the cellular epigenomic landscape. We will also discuss the potential implication of these insights for understanding the etiology of, and developing biomarkers and therapies for, human congenital disorders and cancers that are driven by chromatin abnormalities.
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Affiliation(s)
- Yinglu Li
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Xiao Chen
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
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29
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A tri-functional amino acid enables mapping of binding sites for posttranslational-modification-mediated protein-protein interactions. Mol Cell 2021; 81:2669-2681.e9. [PMID: 33894155 DOI: 10.1016/j.molcel.2021.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/01/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022]
Abstract
Posttranslational modification (PTM), through the recruitment of effector proteins (i.e., "readers") that signal downstream events, plays key roles in regulating a variety of cellular processes. To understand how a PTM is recognized, it is necessary to find its readers and, importantly, the location of the binding pockets responsible for PTM recognition. Although various methods have been developed to identify PTM readers, it remains a challenge to directly map the PTM-binding regions, especially for intrinsically disordered domains. Here, we demonstrate a photo-crosslinkable, clickable, and cleavable tri-functional amino acid, ADdis-Cys, that when coupled with mass spectrometry (ADdis-Cys-MS) can not only identify PTM readers from complex proteomes but also simultaneously map their PTM-recognition modules. Using ADdis-Cys-MS, we successfully identify the binding sites of several reader-PTM interactions, among which we discover human C1QBP as a histone chaperone. This robust method should find wide applications in examining other histone or non-histone PTM-mediated protein-protein interactions.
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30
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Petryk N, Bultmann S, Bartke T, Defossez PA. Staying true to yourself: mechanisms of DNA methylation maintenance in mammals. Nucleic Acids Res 2021; 49:3020-3032. [PMID: 33300031 PMCID: PMC8034647 DOI: 10.1093/nar/gkaa1154] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022] Open
Abstract
DNA methylation is essential to development and cellular physiology in mammals. Faulty DNA methylation is frequently observed in human diseases like cancer and neurological disorders. Molecularly, this epigenetic mark is linked to other chromatin modifications and it regulates key genomic processes, including transcription and splicing. Each round of DNA replication generates two hemi-methylated copies of the genome. These must be converted back to symmetrically methylated DNA before the next S-phase, or the mark will fade away; therefore the maintenance of DNA methylation is essential. Mechanistically, the maintenance of this epigenetic modification takes place during and after DNA replication, and occurs within the very dynamic context of chromatin re-assembly. Here, we review recent discoveries and unresolved questions regarding the mechanisms, dynamics and fidelity of DNA methylation maintenance in mammals. We also discuss how it could be regulated in normal development and misregulated in disease.
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Affiliation(s)
- Nataliya Petryk
- Epigenetics and Cell Fate Centre, UMR7216 CNRS, Université de Paris, F-75013 Paris, France
| | - Sebastian Bultmann
- Department of Biology II, Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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31
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Osborne HC, Irving E, Forment JV, Schmidt CK. E2 enzymes in genome stability: pulling the strings behind the scenes. Trends Cell Biol 2021; 31:628-643. [PMID: 33685796 DOI: 10.1016/j.tcb.2021.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
Ubiquitin and ubiquitin-like proteins (UBLs) function as critical post-translational modifiers in the maintenance of genome stability. Ubiquitin/UBL-conjugating enzymes (E2s) are responsible, as part of a wider enzymatic cascade, for transferring single moieties or polychains of ubiquitin/UBLs to one or multiple residues on substrate proteins. Recent advances in structural and mechanistic understanding of how ubiquitin/UBL substrate attachment is orchestrated indicate that E2s can exert control over chain topology, substrate-site specificity, and downstream physiological effects to help maintain genome stability. Drug discovery efforts have typically focussed on modulating other members of the ubiquitin/UBL cascades or the ubiquitin-proteasome system. Here, we review the current standing of E2s in genome stability and revisit their potential as pharmacological targets for developing novel anti-cancer therapies.
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Affiliation(s)
- Hugh C Osborne
- Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
| | - Elsa Irving
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Josep V Forment
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Christine K Schmidt
- Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK.
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32
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Ming X, Zhu B, Li Y. Mitotic inheritance of DNA methylation: more than just copy and paste. J Genet Genomics 2021; 48:1-13. [PMID: 33771455 DOI: 10.1016/j.jgg.2021.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Decades of investigation on DNA methylation have led to deeper insights into its metabolic mechanisms and biological functions. This understanding was fueled by the recent development of genome editing tools and our improved capacity for analyzing the global DNA methylome in mammalian cells. This review focuses on the maintenance of DNA methylation patterns during mitotic cell division. We discuss the latest discoveries of the mechanisms for the inheritance of DNA methylation as a stable epigenetic memory. We also highlight recent evidence showing the rapid turnover of DNA methylation as a dynamic gene regulatory mechanism. A body of work has shown that altered DNA methylomes are common features in aging and disease. We discuss the potential links between methylation maintenance mechanisms and disease-associated methylation changes.
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Affiliation(s)
- Xuan Ming
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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33
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Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery. Sci Rep 2021; 11:1121. [PMID: 33441849 PMCID: PMC7806715 DOI: 10.1038/s41598-020-80588-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
Despite the established roles of the epigenetic factor UHRF1 in oncogenesis, no UHRF1-targeting therapeutics have been reported to date. In this study, we use fragment-based ligand discovery to identify novel scaffolds for targeting the isolated UHRF1 tandem Tudor domain (TTD), which recognizes the heterochromatin-associated histone mark H3K9me3 and supports intramolecular contacts with other regions of UHRF1. Using both binding-based and function-based screens of a ~ 2300-fragment library in parallel, we identified 2,4-lutidine as a hit for follow-up NMR and X-ray crystallography studies. Unlike previous reported ligands, 2,4-lutidine binds to two binding pockets that are in close proximity on TTD and so has the potential to be evolved into more potent inhibitors using a fragment-linking strategy. Our study provides a useful starting point for developing potent chemical probes against UHRF1.
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34
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Okechukwu C. Targeting epigenetic alterations in the treatment of glioma. MGM JOURNAL OF MEDICAL SCIENCES 2021. [DOI: 10.4103/mgmj.mgmj_3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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35
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Vaughan RM, Kupai A, Rothbart SB. Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications. Trends Biochem Sci 2020; 46:258-269. [PMID: 33308996 DOI: 10.1016/j.tibs.2020.11.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/27/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Chromatin functions are influenced by the addition, removal, and recognition of histone post-translational modifications (PTMs). Ubiquitin and ubiquitin-like (UBL) PTMs on histone proteins can function as signaling molecules by mediating protein-protein interactions. Fueled by the identification of novel ubiquitin and UBL sites and the characterization of the writers, erasers, and readers, the breadth of chromatin functions associated with ubiquitin signaling is emerging. Here, we highlight recently appreciated roles for histone ubiquitination in DNA methylation control, PTM crosstalk, nucleosome structure, and phase separation. We also discuss the expanding diversity and functions associated with histone UBL modifications. We conclude with a look toward the future and pose key questions that will drive continued discovery at the interface of epigenetics and ubiquitin signaling.
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Affiliation(s)
- Robert M Vaughan
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ariana Kupai
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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36
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Han M, Li J, Cao Y, Huang Y, Li W, Zhu H, Zhao Q, Han JDJ, Wu Q, Li J, Feng J, Wong J. A role for LSH in facilitating DNA methylation by DNMT1 through enhancing UHRF1 chromatin association. Nucleic Acids Res 2020; 48:12116-12134. [PMID: 33170271 PMCID: PMC7708066 DOI: 10.1093/nar/gkaa1003] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/25/2022] Open
Abstract
LSH, a SNF2 family DNA helicase, is a key regulator of DNA methylation in mammals. How LSH facilitates DNA methylation is not well defined. While previous studies with mouse embryonic stem cells (mESc) and fibroblasts (MEFs) derived from Lsh knockout mice have revealed a role of Lsh in de novo DNA methylation by Dnmt3a/3b, here we report that LSH contributes to DNA methylation in various cell lines primarily by promoting DNA methylation by DNMT1. We show that loss of LSH has a much bigger effect in DNA methylation than loss of DNMT3A and DNMT3B. Mechanistically, we demonstrate that LSH interacts with UHRF1 but not DNMT1 and facilitates UHRF1 chromatin association and UHRF1-catalyzed histone H3 ubiquitination in an ATPase activity-dependent manner, which in turn promotes DNMT1 recruitment to replication fork and DNA methylation. Notably, UHRF1 also enhances LSH association with the replication fork. Thus, our study identifies LSH as an essential factor for DNA methylation by DNMT1 and provides novel insight into how a feed-forward loop between LSH and UHRF1 facilitates DNMT1-mediated maintenance of DNA methylation in chromatin.
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Affiliation(s)
- Mengmeng Han
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Room122, 320 Yue Yang Road, Shanghai 200031, China
| | - Yuanyong Huang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Haijun Zhu
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China
| | - Qian Zhao
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jing-Dong Jackie Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Room122, 320 Yue Yang Road, Shanghai 200031, China
| | - Qihan Wu
- NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Fudan University, Shanghai 200032, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jing Feng
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
- Department of Laboratory Medicine & Central Laboratory, Southern Medical University Affiliated Fengxian Hospital, Shanghai 201499, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
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Mognato M, Burdak-Rothkamm S, Rothkamm K. Interplay between DNA replication stress, chromatin dynamics and DNA-damage response for the maintenance of genome stability. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108346. [PMID: 34083038 DOI: 10.1016/j.mrrev.2020.108346] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
DNA replication stress is a major source of DNA damage, including double-stranded breaks that promote DNA damage response (DDR) signaling. Inefficient repair of such lesions can affect genome integrity. During DNA replication different factors act on chromatin remodeling in a coordinated way. While recent studies have highlighted individual molecular mechanisms of interaction, less is known about the orchestration of chromatin changes under replication stress. In this review we attempt to explore the complex relationship between DNA replication stress, DDR and genome integrity in mammalian cells, taking into account the role of chromatin disposition as an important modulator of DNA repair. Recent data on chromatin restoration and epigenetic re-establishment after DNA replication stress are reviewed.
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Affiliation(s)
| | - Susanne Burdak-Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
| | - Kai Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
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Vaughan RM, Kupai A, Foley CA, Sagum CA, Tibben BM, Eden HE, Tiedemann RL, Berryhill CA, Patel V, Shaw KM, Krajewski K, Strahl BD, Bedford MT, Frye SV, Dickson BM, Rothbart SB. The histone and non-histone methyllysine reader activities of the UHRF1 tandem Tudor domain are dispensable for the propagation of aberrant DNA methylation patterning in cancer cells. Epigenetics Chromatin 2020; 13:44. [PMID: 33097091 PMCID: PMC7585203 DOI: 10.1186/s13072-020-00366-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
The chromatin-binding E3 ubiquitin ligase ubiquitin-like with PHD and RING finger domains 1 (UHRF1) contributes to the maintenance of aberrant DNA methylation patterning in cancer cells through multivalent histone and DNA recognition. The tandem Tudor domain (TTD) of UHRF1 is well-characterized as a reader of lysine 9 di- and tri-methylation on histone H3 (H3K9me2/me3) and, more recently, lysine 126 di- and tri-methylation on DNA ligase 1 (LIG1K126me2/me3). However, the functional significance and selectivity of these interactions remain unclear. In this study, we used protein domain microarrays to search for additional readers of LIG1K126me2, the preferred methyl state bound by the UHRF1 TTD. We show that the UHRF1 TTD binds LIG1K126me2 with high affinity and selectivity compared to other known methyllysine readers. Notably, and unlike H3K9me2/me3, the UHRF1 plant homeodomain (PHD) and its N-terminal linker (L2) do not contribute to multivalent LIG1K126me2 recognition along with the TTD. To test the functional significance of this interaction, we designed a LIG1K126me2 cell-penetrating peptide (CPP). Consistent with LIG1 knockdown, uptake of the CPP had no significant effect on the propagation of DNA methylation patterning across the genomes of bulk populations from high-resolution analysis of several cancer cell lines. Further, we did not detect significant changes in DNA methylation patterning from bulk cell populations after chemical or genetic disruption of lysine methyltransferase activity associated with LIG1K126me2 and H3K9me2. Collectively, these studies identify UHRF1 as a selective reader of LIG1K126me2 in vitro and further implicate the histone and non-histone methyllysine reader activity of the UHRF1 TTD as a dispensable domain function for cancer cell DNA methylation maintenance.
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Affiliation(s)
- Robert M Vaughan
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Ariana Kupai
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Caroline A Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Cari A Sagum
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Bailey M Tibben
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Hope E Eden
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | | | | | - Varun Patel
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Kevin M Shaw
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina At Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bradley M Dickson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA.
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39
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Yuan Z, Li H. Molecular mechanisms of eukaryotic origin initiation, replication fork progression, and chromatin maintenance. Biochem J 2020; 477:3499-3525. [PMID: 32970141 PMCID: PMC7574821 DOI: 10.1042/bcj20200065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
Eukaryotic DNA replication is a highly dynamic and tightly regulated process. Replication involves several dozens of replication proteins, including the initiators ORC and Cdc6, replicative CMG helicase, DNA polymerase α-primase, leading-strand DNA polymerase ε, and lagging-strand DNA polymerase δ. These proteins work together in a spatially and temporally controlled manner to synthesize new DNA from the parental DNA templates. During DNA replication, epigenetic information imprinted on DNA and histone proteins is also copied to the daughter DNA to maintain the chromatin status. DNA methyltransferase 1 is primarily responsible for copying the parental DNA methylation pattern into the nascent DNA. Epigenetic information encoded in histones is transferred via a more complex and less well-understood process termed replication-couple nucleosome assembly. Here, we summarize the most recent structural and biochemical insights into DNA replication initiation, replication fork elongation, chromatin assembly and maintenance, and related regulatory mechanisms.
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Affiliation(s)
- Zuanning Yuan
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
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Rennie ML, Chaugule VK, Walden H. Modes of allosteric regulation of the ubiquitination machinery. Curr Opin Struct Biol 2020; 62:189-196. [PMID: 32305021 DOI: 10.1016/j.sbi.2020.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/29/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Ubiquitination is a post-translational modification crucial for cellular signaling. A diverse range of enzymes constitute the machinery that mediates attachment of ubiquitin onto target proteins. This diversity allows the targeting of various proteins in a highly regulated fashion. Many of the enzymes have multiple domains or subunits that bind allosteric effectors and exhibit large conformational rearrangements to facilitate regulation. Here we consider recent examples of ubiquitin itself as an allosteric effector of RING and RBR E3 ligases, as well as advances in the understanding of allosteric regulatory elements within HECT E3 ligases.
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Affiliation(s)
- Martin L Rennie
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Viduth K Chaugule
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Helen Walden
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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Kori S, Jimenji T, Ekimoto T, Sato M, Kusano F, Oda T, Unoki M, Ikeguchi M, Arita K. Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain. J Mol Biol 2020; 432:4061-4075. [PMID: 32428527 DOI: 10.1016/j.jmb.2020.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 01/26/2023]
Abstract
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is an essential factor for the maintenance of mammalian DNA methylation and harbors several reader modules for recognizing epigenetic marks. The tandem Tudor domain (TTD) of UHRF1 has a peptide-binding groove that functions as a binding platform for intra- or intermolecular interactions. Besides the groove interacting with unphosphorylated linker 2 and spacer of UHRF1, it also interacts with di/tri-methylated histone H3 at Lys9 and DNA ligase 1 (LIG1) at Lys126. Here we focus on the phosphorylation of Ser298 in linker 2, which was implied to regulate the ligand-binding property of the TTD. Although the protein expression level of UHRF1 is unchanged throughout the cell cycle, Ser298 phosphorylated form of UHRF1 is notably increased in the G2/M phase, which is revealed by immunoprecipitation followed by Western blotting. Molecularly, while unphosphorylated linker 2 covers the peptide-binding groove to prevent access of other interactors, small-angle X-ray scattering, thermal stability assay and molecular dynamics simulation revealed that the phosphate group of Ser298 dissociates linker 2 from the peptide-binding groove of the TTD to permit the other interactors to access to the groove. Our data reveal a mechanism in which Ser298 phosphorylation in linker 2 triggers a change of the TTD's structure and may affect multiple functions of UHRF1 by facilitating associations with LIG1 at DNA replication sites and histone H3K9me2/me3 at heterochromatic regions.
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Affiliation(s)
- Satomi Kori
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Jimenji
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Ekimoto
- Computational Life Science Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Miwa Sato
- Mitsui Knowledge Industry, 2-5-1 Atago, Minato-ku, Tokyo 105-6215, Japan
| | - Fumie Kusano
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Oda
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mitsunori Ikeguchi
- Computational Life Science Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; RIKEN Medical Sciences Innovation Hub Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kyohei Arita
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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42
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Zhang Y, Chen Y, Ma R, Jiang Y, Liu J, Lin Y, Chen S, Xia M, Zou F, Zhang J, Pan T, Wang L, Wei L, Zhang H. UHRF1 Controls Thymocyte Fate Decisions through the Epigenetic Regulation of EGR1 Expression. THE JOURNAL OF IMMUNOLOGY 2020; 204:3248-3261. [DOI: 10.4049/jimmunol.1901471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/06/2020] [Indexed: 12/14/2022]
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Nishiyama A, Mulholland CB, Bultmann S, Kori S, Endo A, Saeki Y, Qin W, Trummer C, Chiba Y, Yokoyama H, Kumamoto S, Kawakami T, Hojo H, Nagae G, Aburatani H, Tanaka K, Arita K, Leonhardt H, Nakanishi M. Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation. Nat Commun 2020; 11:1222. [PMID: 32144273 PMCID: PMC7060239 DOI: 10.1038/s41467-020-15006-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 02/10/2020] [Indexed: 12/31/2022] Open
Abstract
Stable inheritance of DNA methylation is critical for maintaining differentiated phenotypes in multicellular organisms. We have recently identified dual mono-ubiquitylation of histone H3 (H3Ub2) by UHRF1 as an essential mechanism to recruit DNMT1 to chromatin. Here, we show that PCNA-associated factor 15 (PAF15) undergoes UHRF1-dependent dual mono-ubiquitylation (PAF15Ub2) on chromatin in a DNA replication-coupled manner. This event will, in turn, recruit DNMT1. During early S-phase, UHRF1 preferentially ubiquitylates PAF15, whereas H3Ub2 predominates during late S-phase. H3Ub2 is enhanced under PAF15 compromised conditions, suggesting that H3Ub2 serves as a backup for PAF15Ub2. In mouse ES cells, loss of PAF15Ub2 results in DNA hypomethylation at early replicating domains. Together, our results suggest that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are prerequisite for high fidelity DNA methylation inheritance. Ubiquitylation of histone H3 (H3Ub2) by UHRF1 recruits DNMT1 to chromatin, which is essential for DNA methylation inheritance. Here, the authors provide evidence that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are required for high fidelity DNA methylation inheritance.
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Affiliation(s)
- Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.
| | - Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Satomi Kori
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Akinori Endo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Haruka Yokoyama
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Toru Kawakami
- Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Hironobu Hojo
- Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Genta Nagae
- The Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Hiroyuki Aburatani
- The Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Kyohei Arita
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.
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UHRF1-repressed 5'-hydroxymethylcytosine is essential for the male meiotic prophase I. Cell Death Dis 2020; 11:142. [PMID: 32081844 PMCID: PMC7035279 DOI: 10.1038/s41419-020-2333-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 12/23/2022]
Abstract
5’-hydroxymethylcytosine (5hmC), an important 5’-cytosine modification, is altered highly in order in male meiotic prophase. However, the regulatory mechanism of this dynamic change and the function of 5hmC in meiosis remain largely unknown. Using a knockout mouse model, we showed that UHRF1 regulated male meiosis. UHRF1 deficiency led to failure of meiosis and male infertility. Mechanistically, the deficiency of UHRF1 altered significantly the meiotic gene profile of spermatocytes. Uhrf1 knockout induced an increase of the global 5hmC level. The enrichment of hyper-5hmC at transcriptional start sites (TSSs) was highly associated with gene downregulation. In addition, the elevated level of the TET1 enzyme might have contributed to the higher 5hmC level in the Uhrf1 knockout spermatocytes. Finally, we reported Uhrf1, a key gene in male meiosis, repressed hyper-5hmC by downregulating TET1. Furthermore, UHRF1 facilitated RNA polymerase II (RNA-pol2) loading to promote gene transcription. Thus our study demonstrated a potential regulatory mechanism of 5hmC dynamic change and its involvement in epigenetic regulation in male meiosis.
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Abstract
DNA methylation at the 5-position of cytosine (5mC) plays vital roles in mammalian development. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), and the two DNMT families, DNMT3 and DNMT1, are responsible for methylation establishment and maintenance, respectively. Since their discovery, biochemical and structural studies have revealed the key mechanisms underlying how DNMTs catalyze de novo and maintenance DNA methylation. In particular, recent development of low-input genomic and epigenomic technologies has deepened our understanding of DNA methylation regulation in germ lines and early stage embryos. In this review, we first describe the methylation machinery including the DNMTs and their essential cofactors. We then discuss how DNMTs are recruited to or excluded from certain genomic elements. Lastly, we summarize recent understanding of the regulation of DNA methylation dynamics in mammalian germ lines and early embryos with a focus on both mice and humans.
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Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA; , .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA; , .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA
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46
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Zhang Y, Ying JB, Hong JJ, Li FC, Fu TT, Yang FY, Zheng GX, Yao XJ, Lou Y, Qiu Y, Xue WW, Zhu F. How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics. ACS Chem Neurosci 2019; 10:2467-2480. [PMID: 30784262 DOI: 10.1021/acschemneuro.8b00729] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Histone deacetylase 6 (HDAC6) plays a key role in a variety of neurological disorders, which makes it attractive drug target for the treatment of Alzheimer's disease, Parkinson's disease, and memory/learning impairment. The selectivity of HDAC6 inhibitors (sHDAC6Is) are widely considered to be susceptible to the sizes of their Cap group and the physicochemical properties of their linker or zinc-binding group, which makes the discovery of new sHDAC6Is extremely difficult. With the discovery of the distinct selectivity between Trichostatin A (TSA) enantiomers, the chirality residing in the connective units between TSA's Cap and linker shows a great impact on its selectivity. However, the mechanism underlining ( S)-TSA's selectivity is still elusive, and the way chirality switches the selective ( S)-TSA to nonselective ( R)-TSA is unknown. In this study, multiple computational approaches were collectively applied to explore, validate, and differentiate the binding modes of two TSA enantiomers in HDACs (especially the HDAC6) at atomic level. First, two nonconservative residues (G200/M205 and Y197/F202 in HDAC1/6) in loop3 and four conservative residues deep inside the hydrophobic binding pocket were discovered as the decisive residues of ( S)-TSA's selectivity toward HDAC6. Then, a novel mechanism underlying the selectivity of ( S)-TSA toward HDAC6 was proposed, which was composed of the trigger by two nonconservative residues F202 and M205 in HDAC6 and a subsequently improved fit of ( S)-TSA deep inside HDAC6's hydrophobic binding pocket. TSA enantiomers were used as a molecular probe to explore the mechanism underlying sHDAC6Is' selectivity in this study. Because of their decisive roles in ( S)-TSA's selectivity to HDAC6, both F202 and M205 in HDAC6 should be especially considered in the discovery of novel sHDAC6Is.
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Affiliation(s)
- Yang Zhang
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Jun Biao Ying
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jia Jun Hong
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Cheng Li
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ting Ting Fu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Yuan Yang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Guo Xun Zheng
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Xiao Jun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Yunqing Qiu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Wei Wei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Lab of Innovative Drug Research and Bioinformatics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
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Kong X, Chen J, Xie W, Brown SM, Cai Y, Wu K, Fan D, Nie Y, Yegnasubramanian S, Tiedemann RL, Tao Y, Chiu Yen RW, Topper MJ, Zahnow CA, Easwaran H, Rothbart SB, Xia L, Baylin SB. Defining UHRF1 Domains that Support Maintenance of Human Colon Cancer DNA Methylation and Oncogenic Properties. Cancer Cell 2019; 35:633-648.e7. [PMID: 30956060 PMCID: PMC6521721 DOI: 10.1016/j.ccell.2019.03.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/22/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022]
Abstract
UHRF1 facilitates the establishment and maintenance of DNA methylation patterns in mammalian cells. The establishment domains are defined, including E3 ligase function, but the maintenance domains are poorly characterized. Here, we demonstrate that UHRF1 histone- and hemimethylated DNA binding functions, but not E3 ligase activity, maintain cancer-specific DNA methylation in human colorectal cancer (CRC) cells. Disrupting either chromatin reader activity reverses DNA hypermethylation, reactivates epigenetically silenced tumor suppressor genes (TSGs), and reduces CRC oncogenic properties. Moreover, an inverse correlation between high UHRF1 and low TSG expression tracks with CRC progression and reduced patient survival. Defining critical UHRF1 domain functions and its relationship with CRC prognosis suggests directions for, and value of, targeting this protein to develop therapeutic DNA demethylating agents.
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Affiliation(s)
- Xiangqian Kong
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jie Chen
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province 430030, China; State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province 710032, China
| | - Wenbing Xie
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephen M Brown
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yi Cai
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province 710032, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province 710032, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province 710032, China
| | - Srinivasan Yegnasubramanian
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rochelle L Tiedemann
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Yong Tao
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ray-Whay Chiu Yen
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michael J Topper
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Cynthia A Zahnow
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hariharan Easwaran
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
| | - Limin Xia
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province 430030, China; State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, Shaanxi Province 710032, China.
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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Zeng Y, Chen T. DNA Methylation Reprogramming during Mammalian Development. Genes (Basel) 2019; 10:E257. [PMID: 30934924 PMCID: PMC6523607 DOI: 10.3390/genes10040257] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
DNA methylation (5-methylcytosine, 5mC) is a major form of DNA modification in the mammalian genome that plays critical roles in chromatin structure and gene expression. In general, DNA methylation is stably maintained in somatic tissues. However, DNA methylation patterns and levels show dynamic changes during development. Specifically, the genome undergoes two waves of global demethylation and remethylation for the purpose of producing the next generation. The first wave occurs in the germline, initiated with the erasure of global methylation in primordial germ cells (PGCs) and completed with the establishment of sex-specific methylation patterns during later stages of germ cell development. The second wave occurs after fertilization, including the erasure of most methylation marks inherited from the gametes and the subsequent establishment of the embryonic methylation pattern. The two waves of DNA methylation reprogramming involve both distinct and shared mechanisms. In this review article, we provide an overview of the key reprogramming events, focusing on the important players in these processes, including DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) family of 5mC dioxygenases.
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Affiliation(s)
- Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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49
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Coordinated Dialogue between UHRF1 and DNMT1 to Ensure Faithful Inheritance of Methylated DNA Patterns. Genes (Basel) 2019; 10:genes10010065. [PMID: 30669400 PMCID: PMC6360023 DOI: 10.3390/genes10010065] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/22/2018] [Accepted: 01/11/2019] [Indexed: 12/19/2022] Open
Abstract
DNA methylation, catalyzed by DNA methyltransferases (DNMTs), is an epigenetic mark that needs to be faithfully replicated during mitosis in order to maintain cell phenotype during successive cell divisions. This epigenetic mark is located on the 5′-carbon of the cytosine mainly within cytosine–phosphate–guanine (CpG) dinucleotides. DNA methylation is asymmetrically positioned on both DNA strands, temporarily generating a hemi-methylated state after DNA replication. Hemi-methylation is a particular status of DNA that is recognized by ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1 (UHRF1) through its SET- (Su(var)3-9, Enhancer-of-zeste and Trithorax) and RING-associated (SRA) domain. This interaction is considered to be involved in the recruitment of DNMT1 to chromatin in order to methylate the adequate cytosine on the newly synthetized DNA strand. The UHRF1/DNMT1 tandem plays a pivotal role in the inheritance of DNA methylation patterns, but the fine-tuning mechanism remains a mystery. Indeed, because DNMT1 experiences difficulties in finding the cytosine to be methylated, it requires the help of a guide, i.e., of UHRF1, which exhibits higher affinity for hemi-methylated DNA vs. non-methylated DNA. Two models of the UHRF1/DNMT1 dialogue were suggested to explain how DNMT1 is recruited to chromatin: (i) an indirect communication via histone H3 ubiquitination, and (ii) a direct interaction of UHRF1 with DNMT1. In the present review, these two models are discussed, and we try to show that they are compatible with each other.
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Xue B, Zhao J, Feng P, Xing J, Wu H, Li Y. Epigenetic mechanism and target therapy of UHRF1 protein complex in malignancies. Onco Targets Ther 2019; 12:549-559. [PMID: 30666134 PMCID: PMC6334784 DOI: 10.2147/ott.s192234] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ubiquitin-like with plant homeodomain and really interesting new gene finger domains 1 (UHRF1) functions as an epigenetic regulator recruiting PCNA, DNMT1, histone deacetylase 1, G9a, SuV39H, herpes virus-associated ubiquitin-specific protease, and Tat-interactive protein by multiple corresponding domains of DNA and H3 to maintain DNA methylation and histone modifications. Overexpression of UHRF1 has been found as a potential biomarker in various cancers resulting in either DNA hypermethylation or global DNA hypo-methylation, which participates in the occurrence, progression, and invasion of cancer. The role of UHRF1 in the reciprocal interaction between DNA methylation and histone modifications, the dynamic structural transformation of UHRF1 protein within epigenetic code replication machinery in epigenetic regulations, as well as modifications during cell cycle and chemotherapy targeting UHRF1 are evaluated in this study.
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Affiliation(s)
- Busheng Xue
- Department of Spine and Joint Surgery, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
| | - Jiansong Zhao
- Department of Spine and Joint Surgery, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
| | - Penghui Feng
- Department of Obstetrics and Gynecology-Reproductive Medical Center, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Jia Xing
- Department of Histology and Embryology, Basic Medicine College, China Medical University, Shenyang, People's Republic of China
| | - Hongliang Wu
- Department of Spine and Joint Surgery, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
| | - Yan Li
- Department of Spine and Joint Surgery, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
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