1
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Cheng S, Guo H, Bai M, Cui Y, Tian H, Mei X. Inhibition of UHRF1 Improves Motor Function in Mice with Spinal Cord Injury. Cell Mol Neurobiol 2024; 44:39. [PMID: 38649645 PMCID: PMC11035417 DOI: 10.1007/s10571-024-01474-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Spinal-cord injury (SCI) is a severe condition that can lead to limb paralysis and motor dysfunction, and its pathogenesis is not fully understood. The objective of this study was to characterize the differential gene expression and molecular mechanisms in the spinal cord of mice three days after spinal cord injury. By analyzing RNA sequencing data, we identified differentially expressed genes and discovered that the immune system and various metabolic processes play crucial roles in SCI. Additionally, we identified UHRF1 as a key gene that plays a significant role in SCI and found that SCI can be improved by suppressing UHRF1. These findings provide important insights into the molecular mechanisms of SCI and identify potential therapeutic targets that could greatly contribute to the development of new treatment strategies for SCI.
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Affiliation(s)
- Shuai Cheng
- School of Basic Medicine, Jinzhou Medical University, Jinzhou, China
- Liaoning Provincial Collaborative Innovation Center for Medical Testing and Drug Research, Jinzhou Medical University, Jinzhou, Liaoning, China
- Jinzhou Medical University, Jinzhou, China
| | - Hui Guo
- School of Basic Medicine, Jinzhou Medical University, Jinzhou, China
- Liaoning Provincial Collaborative Innovation Center for Medical Testing and Drug Research, Jinzhou Medical University, Jinzhou, Liaoning, China
- Jinzhou Medical University, Jinzhou, China
| | - Mingyu Bai
- Liaoning Provincial Collaborative Innovation Center for Medical Testing and Drug Research, Jinzhou Medical University, Jinzhou, Liaoning, China
- Jinzhou Medical University, Jinzhou, China
| | - Yang Cui
- Liaoning Provincial Collaborative Innovation Center for Medical Testing and Drug Research, Jinzhou Medical University, Jinzhou, Liaoning, China
- Jinzhou Medical University, Jinzhou, China
| | - He Tian
- School of Basic Medicine, Jinzhou Medical University, Jinzhou, China.
- Liaoning Provincial Collaborative Innovation Center for Medical Testing and Drug Research, Jinzhou Medical University, Jinzhou, Liaoning, China.
- Jinzhou Medical University, Jinzhou, China.
- Jinzhou Medical University, Linghe District, No. 40, Section 3, Songpo Road, Jinzhou, Liaoning Province, China.
| | - Xifan Mei
- School of Basic Medicine, Jinzhou Medical University, Jinzhou, China.
- Liaoning Provincial Collaborative Innovation Center for Medical Testing and Drug Research, Jinzhou Medical University, Jinzhou, Liaoning, China.
- Jinzhou Medical University, Jinzhou, China.
- Jinzhou Medical University, Linghe District, No. 40, Section 3, Songpo Road, Jinzhou, Liaoning Province, China.
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2
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Zuo Z, Zhou Z, Chang Y, Liu Y, Shen Y, Li Q, Zhang L. Ribonucleotide reductase M2 (RRM2): Regulation, function and targeting strategy in human cancer. Genes Dis 2024; 11:218-233. [PMID: 37588202 PMCID: PMC10425756 DOI: 10.1016/j.gendis.2022.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/26/2022] [Accepted: 11/14/2022] [Indexed: 12/29/2022] Open
Abstract
Ribonucleotide reductase M2 (RRM2) is a small subunit in ribonucleotide reductases, which participate in nucleotide metabolism and catalyze the conversion of nucleotides to deoxynucleotides, maintaining the dNTP pools for DNA biosynthesis, repair, and replication. RRM2 performs a critical role in the malignant biological behaviors of cancers. The structure, regulation, and function of RRM2 and its inhibitors were discussed. RRM2 gene can produce two transcripts encoding the same ORF. RRM2 expression is regulated at multiple levels during the processes from transcription to translation. Moreover, this gene is associated with resistance, regulated cell death, and tumor immunity. In order to develop and design inhibitors of RRM2, appropriate strategies can be adopted based on different mechanisms. Thus, a greater appreciation of the characteristics of RRM2 is a benefit for understanding tumorigenesis, resistance in cancer, and tumor microenvironment. Moreover, RRM2-targeted therapy will be more attention in future therapeutic approaches for enhancement of treatment effects and amelioration of the dismal prognosis.
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Affiliation(s)
- Zanwen Zuo
- Innovative Drug R&D Center, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), and School of Food and Biological Engineering, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Zerong Zhou
- Innovative Drug R&D Center, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), and School of Food and Biological Engineering, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Yuzhou Chang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
| | - Yan Liu
- School of Agriculture and Biology, and Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuping Shen
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan 425199, China
| | - Qizhang Li
- Innovative Drug R&D Center, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), and School of Food and Biological Engineering, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Lei Zhang
- Innovative Drug R&D Center, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China
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3
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Choudalakis M, Kungulovski G, Mauser R, Bashtrykov P, Jeltsch A. Refined read-out: The hUHRF1 Tandem-Tudor domain prefers binding to histone H3 tails containing K4me1 in the context of H3K9me2/3. Protein Sci 2023; 32:e4760. [PMID: 37593997 PMCID: PMC10464304 DOI: 10.1002/pro.4760] [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: 07/13/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/19/2023]
Abstract
UHRF1 is an essential chromatin protein required for DNA methylation maintenance, mammalian development, and gene regulation. We investigated the Tandem-Tudor domain (TTD) of human UHRF1 that is known to bind H3K9me2/3 histones and is a major driver of UHRF1 localization in cells. We verified binding to H3K9me2/3 but unexpectedly discovered stronger binding to H3 peptides and mononucleosomes containing K9me2/3 with additional K4me1. We investigated the combined binding of TTD to H3K4me1-K9me2/3 versus H3K9me2/3 alone, engineered mutants with specific and differential changes of binding, and discovered a novel read-out mechanism for H3K4me1 in an H3K9me2/3 context that is based on the interaction of R207 with the H3K4me1 methyl group and on counting the H-bond capacity of H3K4. Individual TTD mutants showed up to a 10,000-fold preference for the double-modified peptides, suggesting that after a conformational change, WT TTD could exhibit similar effects. The frequent appearance of H3K4me1-K9me2 regions in human chromatin demonstrated in our TTD chromatin pull-down and ChIP-western blot data suggests that it has specific biological roles. Chromatin pull-down of TTD from HepG2 cells and full-length murine UHRF1 ChIP-seq data correlate with H3K4me1 profiles indicating that the H3K4me1-K9me2/3 interaction of TTD influences chromatin binding of full-length UHRF1. We demonstrate the H3K4me1-K9me2/3 specific binding of UHRF1-TTD to enhancers and promoters of cell-type-specific genes at the flanks of cell-type-specific transcription factor binding sites, and provided evidence supporting an H3K4me1-K9me2/3 dependent and TTD mediated downregulation of these genes by UHRF1. All these findings illustrate the important physiological function of UHRF1-TTD binding to H3K4me1-K9me2/3 double marks in a cellular context.
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Affiliation(s)
- Michel Choudalakis
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Goran Kungulovski
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Rebekka Mauser
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Pavel Bashtrykov
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
| | - Albert Jeltsch
- Department of BiochemistryInstitute of Biochemistry and Technical Biochemistry, University of StuttgartStuttgartGermany
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4
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Hou J, Li W, Zhang S, Tan D, Lv K, Zhu Y, Hou Y, Guo H, Jiang L. UHRF1 plays an oncogenic role in small cell lung cancer. Mol Carcinog 2023; 62:385-397. [PMID: 36537722 DOI: 10.1002/mc.23493] [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: 07/21/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Small cell lung cancer (SCLC) is a malignant tumor characterized by aggressiveness and dismal prognosis. The specific role of ubiquitin-like PHD and RING finger domain (UHRF1), a frequently overexpressed cancer-promoting gene in various tumors, is poorly understood in SCLC. Herein, we explored the potential carcinogenic role of UHRF1 in SCLC. First, public databases were used to analyze the expression of UHRF1 in SCLC, and tissue specimens in our center were examined to confirm the results while clinical outcomes were collected to analyze its relationship with UHRF1. Then, UHRF1 knockdown and overexpression cell lines were established to evaluate the carcinogenic function of UHRF1 in vitro and in vivo. The mechanism of the biological consequences was determined by co-inmunoprecipitation. Moreover, we also analyzed the influence of UHRF1 on cisplatin (DDP) sensitivity of SCLC. The expression of UHRF1 was significantly higher in SCLC tissues than in normal tissues, and high levels of UHRF1 suggested a poor prognosis for SCLC. Mechanistically, UHRF1 promoted SCLC growth through yes-associated protein 1 (YAP1). Specifically, UHRF1 bound to YAP1 and inhibited YAP1 ubiquitin degradation, thus stabilizing the YAP1 protein in SCLC cells. UHRF1 downregulation enhanced DDP sensitivity in SCLC cells and was correlated with a favorable prognosis in patients with SCLC treated with platinum-based chemotherapy. UHRF1 plays an oncogenic role in SCLC by modulating YAP1. Therefore, UHRF1 could be used as a biomarker to predict the prognosis of SCLC patients and serve as a potential therapeutic target for SCLC patients.
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Affiliation(s)
- Jia Hou
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wenyuan Li
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shirong Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Deli Tan
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Kejia Lv
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yue Zhu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yuzhu Hou
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, ShaanXi, China
| | - Hui Guo
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Key Laboratory for Environment and Disease-related Genes of the Education Ministry, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Lili Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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5
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Mechanisms of DNA methylation and histone modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:51-92. [PMID: 37019597 DOI: 10.1016/bs.pmbts.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The field of genetics has expanded a lot in the past few decades due to the accessibility of human genome sequences, but still, the regulation of transcription cannot be explicated exclusively by the sequence of DNA of an individual. The coordination and crosstalk between chromatin factors which are conserved is indispensable for all living creatures. The regulation of gene expression has been dependent on the methylation of DNA, post-translational modifications of histones, effector proteins, chromatin remodeler enzymes that affect the chromatin structure and function, and other cellular activities such as DNA replication, DNA repair, proliferation and growth. The mutation and deletion of these factors can lead to human diseases. Various studies are being performed to identify and understand the gene regulatory mechanisms in the diseased state. The information from these high throughput screening studies is able to aid the treatment developments based on the epigenetics regulatory mechanisms. This book chapter will discourse on various modifications and their mechanisms that take place on histones and DNA that regulate the transcription of genes.
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6
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Wu SC, Kim A, Gu Y, Martinez DI, Zocchi L, Chen CC, Lopez J, Salcido K, Singh S, Wu J, Nael A, Benavente CA. UHRF1 overexpression promotes osteosarcoma metastasis through altered exosome production and AMPK/SEMA3E suppression. Oncogenesis 2022; 11:51. [PMID: 36068209 PMCID: PMC9448786 DOI: 10.1038/s41389-022-00430-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Loss-of-function mutations at the retinoblastoma (RB1) gene are associated with increased mortality, metastasis, and poor therapeutic outcome in several cancers, including osteosarcoma. However, the mechanism(s) through which RB1 loss worsens clinical outcome remains understudied. Ubiquitin-like with PHD and Ring Finger domains 1 (UHRF1) has been identified as a critical downstream effector of the RB/E2F signaling pathway that is overexpressed in various cancers. Here, we determined the role and regulatory mechanisms of UHRF1 in rendering osteosarcoma cells more aggressive. Higher UHRF1 expression correlated with malignancy in osteosarcoma cell lines, clinical samples, and genetically engineered mouse models. Gain- and loss-of-function assays revealed that UHRF1 has cell-intrinsic and extrinsic functions promoting cell proliferation, migration, invasion, angiogenesis, and metastasis. UHRF1 overexpression induced angiogenesis by suppressing AMPK activation and Semaphorin 3E (SEMA3E) expression. Further, UHRF1-mediated migration and metastasis resulted, at least in part, through altered expression of extracellular vesicles and their cargo, including urokinase-type plasminogen activator (uPA). Novel osteosarcoma genetically engineered mouse models confirmed that knocking out Uhrf1 considerably decreased metastasis and reversed the poorer survival associated with Rb1 loss. This presents a new mechanistic insight into RB1 loss-associated poor prognosis and novel oncogenic roles of UHRF1 in the regulation of angiogenesis and exosome secretion, both critical for osteosarcoma metastasis. This provides substantial support for targeting UHRF1 or its downstream effectors as novel therapeutic options to improve current treatment for osteosarcoma.
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Affiliation(s)
- Stephanie C Wu
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Ahhyun Kim
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Yijun Gu
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Daniel I Martinez
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Loredana Zocchi
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Claire C Chen
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Jocelyne Lopez
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Kelsey Salcido
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Sarah Singh
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA
| | - Ali Nael
- Department of Pathology, University of California, Irvine, CA, 92697, USA
- Department of Pathology, Children's Hospital of Orange County, Orange, CA, 92868, 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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7
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Zhou S, Dong J, Xiong M, Gan S, Wen Y, Zhang J, Wang X, Yuan S, Gui Y. UHRF1 interacts with snRNAs and regulates alternative splicing in mouse spermatogonial stem cells. Stem Cell Reports 2022; 17:1859-1873. [PMID: 35905740 PMCID: PMC9391524 DOI: 10.1016/j.stemcr.2022.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 12/22/2022] Open
Abstract
Life-long male fertility relies on exquisite homeostasis and the development of spermatogonial stem cells (SSCs); however, the underlying molecular genetic and epigenetic regulation in this equilibrium process remains unclear. Here, we document that UHRF1 interacts with snRNAs to regulate pre-mRNA alternative splicing in SSCs and is required for the homeostasis of SSCs in mice. Genetic deficiency of UHRF1 in mouse prospermatogonia results in gradual loss of spermatogonial stem cells, eventually leading to Sertoli-cell-only syndrome (SCOS) and male infertility. Comparative RNA-seq data provide evidence that Uhrf1 ablation dysregulates previously reported SSC maintenance- and differentiation-related genes. We further found that UHRF1 could act as an alternative RNA splicing regulator and interact with Tle3 transcripts to regulate its splicing event in spermatogonia. Collectively, our data reveal a multifunctional role for UHRF1 in regulating gene expression programs and alternative splicing during SSC homeostasis, which may provide clues for treating human male infertility.
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Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Juan Dong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengneng Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shiming Gan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yujiao Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jin Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Laboratory Animal Center, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518057, China.
| | - Yaoting Gui
- Guangdong Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, Guangdong 518036, China.
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8
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Lee C, Kim J. Genome maintenance in retinoblastoma: Implications for therapeutic vulnerabilities (Review). Oncol Lett 2022; 23:192. [PMID: 35527780 PMCID: PMC9073582 DOI: 10.3892/ol.2022.13312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 11/19/2022] Open
Abstract
Retinoblastoma (RB) is a pediatric ocular malignancy that is initiated mostly by biallelic inactivation of the RB transcriptional corepressor 1 (RB1) tumor suppressor gene in the developing retina. Unlike the prevailing prediction based on multiple studies involving RB1 gene disruption in experimental models, human RB tumors have been demonstrated to possess a relatively stable genome, characterized by a low mutation rate and a few recurrent chromosomal alterations related to somatic copy number changes. This suggests that RB may harbor heightened genome maintenance mechanisms to counteract or compensate for the risk of massive genome instability, which can potentially be driven by the early RB1 loss as a tumor-initiating event. Although the genome maintenance mechanisms might have been evolved to promote RB cell survival by preventing lethal genomic defects, emerging evidence suggests that the dependency of RB cells on these mechanisms also exposes their unique vulnerability to chemotherapy, particularly when the genome maintenance machineries are tumor cell-specific. This review summarizes the genome maintenance mechanisms identified in RB, including findings on the roles of chromatin regulators in DNA damage response/repair and protein factors involved in maintaining chromosome stability and promoting survival in RB. In addition, advantages and challenges for exploiting these therapeutic vulnerabilities in RB are discussed.
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Affiliation(s)
- Chunsik Lee
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Jong Kim
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
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9
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Saeki N, Inoue K, Ideta-Otsuka M, Watamori K, Mizuki S, Takenaka K, Igarashi K, Miura H, Takeda S, Imai Y. Epigenetic regulator UHRF1 suppressively orchestrates pro-inflammatory gene expression in rheumatoid arthritis. J Clin Invest 2022; 132:150533. [PMID: 35472067 PMCID: PMC9151705 DOI: 10.1172/jci150533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/19/2022] [Indexed: 11/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is characterized by chronic synovial inflammation with aberrant epigenetic alterations, eventually leading to joint destruction. However, the epigenetic regulatory mechanisms underlying RA pathogenesis remain largely unknown. Here we showed that Ubiquitin-like containing PHD and RING finger domains 1 (UHRF1) is a central epigenetic regulator that suppressively orchestrates multiple pathogeneses in RA. UHRF1 expression was remarkably up-regulated in synovial fibroblasts (SF) from arthritis model mice and RA patients. Mice with SF-specific Uhrf1 conditional knockout showed more severe arthritic phenotypes than littermate control. Uhrf1-deficient SF also exhibited enhanced apoptosis resistance and up-regulated expression of several cytokines including Ccl20. In RA patients, DAS28, CRP, and Th17 accumulation as well as apoptosis resistance were negatively correlated with UHRF1 expression in synovium. Finally, Ryuvidine administration that stabilizes UHRF1 ameliorated arthritis pathogeneses in a mouse model of RA. This study demonstrated that UHRF1 expressed in RA SF can contribute to negative feedback mechanisms that suppress multiple pathogenic events in arthritis, suggesting that targeting UHRF1 could be one of the therapeutic strategies for RA.
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Affiliation(s)
- Noritaka Saeki
- Division of Laboratory Animal Research, Ehime University, Toon, Japan
| | - Kazuki Inoue
- Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Shenzhen, China
| | - Maky Ideta-Otsuka
- Laboratory of Instrumental Analysis, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Kunihiko Watamori
- Department of Bone and Joint Surgery, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shinichi Mizuki
- The Center for Rheumatic Diseases, Matsuyama Red Cross Hospital, Matsuyama, Japan
| | - Katsuto Takenaka
- Department of Hematology, Clinical Immunology and Infectious Diseases, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Katsuhide Igarashi
- Laboratory of Biofunctional Science, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Hiromasa Miura
- Department of Bone and Joint Surgery, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shu Takeda
- Division of Endocrinology, Toranomon Hospital Endocrine Center, Tokyo, Japan
| | - Yuuki Imai
- Division of Laboratory Animal Research, Ehime University, Toon, Japan
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10
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UHRF1 establishes crosstalk between somatic and germ cells in male reproduction. Cell Death Dis 2022; 13:377. [PMID: 35440090 PMCID: PMC9018721 DOI: 10.1038/s41419-022-04837-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 11/08/2022]
Abstract
AbstractSertoli cells (SCs) support and nourish germ cells (GCs) through their crosstalk during spermatogenesis. However, the underlying epigenetic mechanism that ensures SCs’ functions in this process remains unclear. Here, we report that UHRF1, a critical epigenetic regulator, is mainly expressed in human and mouse pre-mature SCs, and is essential for establishing Sertoli-Germ cell crosstalk. SC-specific UHRF1 knockout mice exhibit complete sterility with Sertoli cell (SC) proliferation and differentiation aberrance, blood-testis barrier (BTB) disruption, and immature germ cell (GC) sloughing. RNA sequencing and Whole Genome Bisulfite Sequencing (WGBS) revealed that many extracellular matrix (ECM)-related genes (e.g., Timp1, Trf, and Spp1) appeared upregulated with the DNA hypomethylation status in UHRF1-deficient SCs. Strikingly, overexpression of Timp1, Trf, and Spp1 in SCs in vitro and in vivo could phenocopy the SC-specific UHRF1-deficient mice. Our data demonstrated that UHRF1 regulates the transcriptional program of ECM-related genes in SCs and establishes SC-GC crosstalk.
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11
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Xiong M, Zhou S, Feng S, Gui Y, Li J, Wu Y, Dong J, Yuan S. UHRF1 is indispensable for meiotic sex chromosome inactivation and interacts with the DNA damage response pathway in mice. Biol Reprod 2022; 107:168-182. [PMID: 35284939 DOI: 10.1093/biolre/ioac054] [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: 10/01/2021] [Revised: 01/04/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
During male meiosis, the constitutively unsynapsed XY chromosomes undergo meiotic sex chromosome inactivation (MSCI), and the DNA damage response (DDR) pathway is critical for MSCI establishment. Our previous study showed that UHRF1(ubiquitin-like, with PHD and ring finger domains 1) deletion led to meiotic arrest and male infertility; however, the underlying mechanisms of UHRF1 in the regulation of meiosis remain unclear. Here, we report that UHRF1 is required for MSCI and cooperates with the DDR pathway in male meiosis. UHRF1-deficient spermatocytes display aberrant pairing and synapsis of homologous chromosomes during the pachytene stage. In addition, UHRF1 deficiency leads to aberrant recruitment of ATR and FANCD2 on the sex chromosomes and disrupts the diffusion of ATR to the XY chromatin. Furthermore, we show that UHRF1 acts as a cofactor of BRCA1 to facilitate the recruitment of DDR factors onto sex chromosomes for MSCI establishment. Accordingly, deletion of UHRF1 leads to the failure of meiotic silencing on sex chromosomes, resulting in meiotic arrest. In addition to our previous findings, the present study reveals that UHRF1 participates in MSCI, ensuring the progression of male meiosis. This suggests a multifunctional role of UHRF1 in the male germline.
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Affiliation(s)
- Mengneng Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shenglei Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jinmei Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yanqing Wu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Juan Dong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518057, China.,Laboratory of Animal Center, Huazhong University of Science and Technology, Wuhan 430030, China
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12
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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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13
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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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14
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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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15
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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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16
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Hui B, Pan S, Che S, Sun Y, Yan Y, Guo J, Gong T, Ren J, Zhang X. Silencing UHRF1 Enhances Radiosensitivity of Esophageal Squamous Cell Carcinoma by Inhibiting the PI3K/Akt/mTOR Signaling Pathway. Cancer Manag Res 2021; 13:4841-4852. [PMID: 34188537 PMCID: PMC8232844 DOI: 10.2147/cmar.s311192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/29/2021] [Indexed: 12/24/2022] Open
Abstract
Purpose Resistance to radiotherapy results in a high treatment failure rate for locally advanced esophageal squamous cell carcinoma (ESCC). Ubiquitin-like with plant homeodomain and ring-finger domains 1 (UHRF1), is associated with poor prognosis in ESCC. The present study aims to characterize the effect of UHRF1 silencing on the radiosensitivity of ESCC and its potential mechanism. Methods Both in vitro and in vivo experiments were conducted to observe the effects of UHRF1 silencing on the radiosensitivity of ESCC. The effects of UHRF1 silencing on the apoptosis of ESCC cells were assessed by flow cytometry. The expression of apoptosis-related factors (caspase-3 and Bcl-2), PI3K/Akt/mTOR signaling pathway-related factors (PTEN, p-Akt and Akt, p-mTOR and mTOR), and DNMT1 were measured via Western blot, and the status of PTEN methylation was detected by methylation-specific PCR. Immunohistochemistry was used to detect the expressions of PTEN, p-AKT, and p-mTOR in xenograft tumor tissues. Results In vitro and in vivo experiments showed that UHRF1 knock-down inhibited ESCC cell growth and enhanced their radiosensitivity. shUHRF1 combined with radiation significantly increased ESCC cell apoptosis. Meanwhile, it activated the expression of caspase-3 and inhibited the expression of Bcl-2. shUHRF1 inhibited the expression of DNMT1 and reduced the methylation of PTEN, and then upregulated the expression of PTEN to inhibit the PI3K/Akt/mTOR signaling pathway. On the contrary, the PI3K/Akt/mTOR signaling pathway can be activated by upregulation of UHRF1. Conclusion Our findings provide a theoretical basis for UHRF1 as a target to improve the radiosensitivity of ESCC.
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Affiliation(s)
- Beina Hui
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710061, People's Republic of China
| | - Shupei Pan
- Department of Radiation Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710004, People's Republic of China
| | - Shaomin Che
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710061, People's Republic of China
| | - Yuchen Sun
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710061, People's Republic of China
| | - Yanli Yan
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710061, People's Republic of China
| | - Jia Guo
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710061, People's Republic of China
| | - Tuotuo Gong
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710061, People's Republic of China
| | - Juan Ren
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710061, People's Republic of China
| | - Xiaozhi Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710061, People's Republic of China
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17
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Magnani E, Macchi F, Madakashira BP, Zhang C, Alaydaroos F, Sadler KC. uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements. Front Immunol 2021; 12:627926. [PMID: 33854502 PMCID: PMC8039153 DOI: 10.3389/fimmu.2021.627926] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Activation of transposable elements (TEs) can cause cellular damage. Cytoplasmic nucleic acid sensing pathways evolved to detect pathogens, but can also serve to cull cells with inappropriate TE activation as TEs can be viral mimetics. Epigenetic silencing of TEs is mediated in part by DNA methylation, but it is not clear if TE activation or the immune system contribute to the cellular damage caused by loss of DNA methylation. Here, we provide mechanistic insight into the observation of an activated interferon response in the liver of zebrafish larvae with deletion in critical components of the DNA methylation machinery, uhrf1 and dnmt1. We focus on dissecting the relationship between DNA methylation, TE activation and induction of an immune response through cytoplasmic DNA and double stranded RNA sensing pathways and identify tnfa as a mediator of cell death in the liver of these mutants. Integrated RNAseq and methylome analysis identified LTR transposons as the most upregulated in these mutants and also the most methylated in control larvae, indicating a direct role of DNA methylation in suppressing this TE subclass. RNAseq analysis from these same samples revealed expression signatures of a type-I interferon response and of tnfa activation, mimicking the pattern of gene expression in virally infected cells. CRISPR/Cas9 mediated depletion of the cellular antiviral sensors sting and mavs reduced expression of interferon response genes and tnfa depletion dramatically reduced cell death in uhrf1 mutant livers. This suggests that the antiviral response induced by DNA hypomethylation and TE activation in the liver is mediated by the signaling pathways activated by both cytoplasmic double stranded RNA and DNA and that tnfa mediates cell death as a potential mechanism to eliminate these damaged cells.
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Affiliation(s)
- Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Fatima Alaydaroos
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kirsten C Sadler
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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18
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Tolmacheva EN, Vasilyev SA, Lebedev IN. Aneuploidy and DNA Methylation as Mirrored Features of Early Human Embryo Development. Genes (Basel) 2020; 11:E1084. [PMID: 32957536 PMCID: PMC7564410 DOI: 10.3390/genes11091084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 12/18/2022] Open
Abstract
Genome stability is an integral feature of all living organisms. Aneuploidy is the most common cause of fetal death in humans. The timing of bursts in increased aneuploidy frequency coincides with the waves of global epigenetic reprogramming in mammals. During gametogenesis and early embryogenesis, parental genomes undergo two waves of DNA methylation reprogramming. Failure of these processes can critically affect genome stability, including chromosome segregation during cell division. Abnormal methylation due to errors in the reprogramming process can potentially lead to aneuploidy. On the other hand, the presence of an entire additional chromosome, or chromosome loss, can affect the global genome methylation level. The associations of these two phenomena are well studied in the context of carcinogenesis, but here, we consider the relationship of DNA methylation and aneuploidy in early human and mammalian ontogenesis. In this review, we link these two phenomena and highlight the critical ontogenesis periods and genome regions that play a significant role in human reproduction and in the formation of pathological phenotypes in newborns with chromosomal aneuploidy.
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Affiliation(s)
- Ekaterina N. Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, 634050 Tomsk, Russia; (S.A.V.); (I.N.L.)
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19
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Ganz J, Melancon E, Wilson C, Amores A, Batzel P, Strader M, Braasch I, Diba P, Kuhlman JA, Postlethwait JH, Eisen JS. Epigenetic factors Dnmt1 and Uhrf1 coordinate intestinal development. Dev Biol 2019; 455:473-484. [PMID: 31394080 DOI: 10.1016/j.ydbio.2019.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/05/2019] [Accepted: 08/01/2019] [Indexed: 12/15/2022]
Abstract
Intestinal tract development is a coordinated process involving signaling among the progenitors and developing cells from all three germ layers. Development of endoderm-derived intestinal epithelium has been shown to depend on epigenetic modifications, but whether that is also the case for intestinal tract cell types from other germ layers remains unclear. We found that functional loss of a DNA methylation machinery component, ubiquitin-like protein containing PHD and RING finger domains 1 (uhrf1), leads to reduced numbers of ectoderm-derived enteric neurons and severe disruption of mesoderm-derived intestinal smooth muscle. Genetic chimeras revealed that Uhrf1 functions both cell-autonomously in enteric neuron precursors and cell-non-autonomously in surrounding intestinal cells, consistent with what is known about signaling interactions between these cell types that promote one another's development. Uhrf1 recruits the DNA methyltransferase Dnmt1 to unmethylated DNA during replication. Dnmt1 is also expressed in enteric neurons and smooth muscle progenitors. dnmt1 mutants have fewer enteric neurons and disrupted intestinal smooth muscle compared to wildtypes. Because dnmt1;uhrf1 double mutants have a similar phenotype to dnmt1 and uhrf1 single mutants, Dnmt1 and Uhrf1 must function together during enteric neuron and intestinal muscle development. This work shows that genes controlling epigenetic modifications are important to coordinate intestinal tract development, provides the first demonstration that these genes influence development of the ENS, and advances uhrf1 and dnmt1 as potential new Hirschsprung disease candidates.
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Affiliation(s)
- Julia Ganz
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Ellie Melancon
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Catherine Wilson
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Angel Amores
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Peter Batzel
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Marie Strader
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Ingo Braasch
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Parham Diba
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Julie A Kuhlman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - John H Postlethwait
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Judith S Eisen
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA.
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20
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Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance. Nucleic Acids Res 2019; 46:4405-4416. [PMID: 29506131 PMCID: PMC5961305 DOI: 10.1093/nar/gky151] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/21/2018] [Indexed: 12/30/2022] Open
Abstract
UHRF1 is a histone- and DNA-binding E3 ubiquitin ligase that functions with DNMT1 to maintain mammalian DNA methylation. UHRF1 facilitates DNMT1 recruitment to replicating chromatin through a coordinated mechanism involving histone and DNA recognition and histone ubiquitination. UHRF2 shares structural homology with UHRF1, but surprisingly lacks functional redundancy to facilitate DNA methylation maintenance. Molecular mechanisms uncoupling UHRF2 from DNA methylation maintenance are poorly defined. Through comprehensive and comparative biochemical analysis of recombinant human UHRF1 and UHRF2 reader and writer activities, we reveal conserved modes of histone PTM recognition but divergent DNA binding properties. While UHRF1 and UHRF2 diverge in their affinities toward hemi-methylated DNA, we surprisingly show that both hemi-methylated and hemi-hydroxymethylated DNA oligonucleotides stimulate UHRF2 ubiquitin ligase activity toward histone H3 peptide substrates. This is the first example of an E3 ligase allosterically regulated by DNA hydroxymethylation. However, UHRF2 is not a productive histone E3 ligase toward purified mononucleosomes, suggesting UHRF2 has an intra-domain architecture distinct from UHRF1 that is conformationally constrained when bound to chromatin. Collectively, our studies reveal that uncoupling of UHRF2 from the DNA methylation maintenance program is linked to differences in the molecular readout of chromatin signatures that connect UHRF1 to ubiquitination of histone H3.
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Affiliation(s)
- Robert M Vaughan
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Bradley M Dickson
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Evan M Cornett
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
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21
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Wang S, Zhang C, Hasson D, Desai A, SenBanerjee S, Magnani E, Ukomadu C, Lujambio A, Bernstein E, Sadler KC. Epigenetic Compensation Promotes Liver Regeneration. Dev Cell 2019; 50:43-56.e6. [PMID: 31231040 PMCID: PMC6615735 DOI: 10.1016/j.devcel.2019.05.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
Abstract
Two major functions of the epigenome are to regulate gene expression and to suppress transposons. It is unclear how these functions are balanced during physiological challenges requiring tissue regeneration, where exquisite coordination of gene expression is essential. Transcriptomic analysis of seven time points following partial hepatectomy identified the epigenetic regulator UHRF1, which is essential for DNA methylation, as dynamically expressed during liver regeneration in mice. UHRF1 deletion in hepatocytes (Uhrf1HepKO) caused genome-wide DNA hypomethylation but, surprisingly, had no measurable effect on gene or transposon expression or liver homeostasis. Partial hepatectomy of Uhrf1HepKO livers resulted in early and sustained activation of proregenerative genes and enhanced liver regeneration. This was attributed to redistribution of H3K27me3 from promoters to transposons, effectively silencing them and, consequently, alleviating repression of liver regeneration genes, priming them for expression in Uhrf1HepKO livers. Thus, epigenetic compensation safeguards the genome against transposon activation, indirectly affecting gene regulation.
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Affiliation(s)
- Shuang Wang
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anal Desai
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sucharita SenBanerjee
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; College of Arts and Sciences, Wentworth Institute of Technology, 504 Parker St., Boston, MA 02115, USA
| | - Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates
| | - Chinweike Ukomadu
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kirsten C Sadler
- Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Program in Biology, New York University Abu Dhabi, Abu Dhabi, P.O. Box 129188, United Arab Emirates.
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22
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UHRF genes regulate programmed interdigital tissue regression and chondrogenesis in the embryonic limb. Cell Death Dis 2019; 10:347. [PMID: 31024001 PMCID: PMC6484032 DOI: 10.1038/s41419-019-1575-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/26/2019] [Accepted: 04/04/2019] [Indexed: 12/12/2022]
Abstract
The primordium of the limb contains a number of progenitors far superior to those necessary to form the skeletal components of this appendage. During the course of development, precursors that do not follow the skeletogenic program are removed by cell senescence and apoptosis. The formation of the digits provides the most representative example of embryonic remodeling via cell degeneration. In the hand/foot regions of the embryonic vertebrate limb (autopod), the interdigital tissue and the zones of interphalangeal joint formation undergo massive degeneration that accounts for jointed and free digit morphology. Developmental senescence and caspase-dependent apoptosis are considered responsible for these remodeling processes. Our study uncovers a new upstream level of regulation of remodeling by the epigenetic regulators Uhrf1 and Uhrf2 genes. These genes are spatially and temporally expressed in the pre-apoptotic regions. UHRF1 and UHRF2 showed a nuclear localization associated with foci of methylated cytosine. Interestingly, nuclear labeling increased in cells progressing through the stages of degeneration prior to TUNEL positivity. Functional analysis in cultured limb skeletal progenitors via the overexpression of either UHRF1 or UHRF2 inhibited chondrogenesis and induced cell senescence and apoptosis accompanied with changes in global and regional DNA methylation. Uhrfs modulated canonical cell differentiation factors, such as Sox9 and Scleraxis, promoted apoptosis via up-regulation of Bak1, and induced cell senescence, by arresting progenitors at the S phase and upregulating the expression of p21. Expression of Uhrf genes in vivo was positively modulated by FGF signaling. In the micromass culture assay Uhrf1 was down-regulated as the progenitors lost stemness and differentiated into cartilage. Together, our findings emphasize the importance of tuning the balance between cell differentiation and cell stemness as a central step in the initiation of the so-called “embryonic programmed cell death” and suggest that the structural organization of the chromatin, via epigenetic modifications, may be a precocious and critical factor in these regulatory events.
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Cao Y, Li M, Liu F, Ni X, Wang S, Zhang H, Sui X, Huo R. Deletion of maternal UHRF1 severely reduces mouse oocyte quality and causes developmental defects in preimplantation embryos. FASEB J 2019; 33:8294-8305. [PMID: 30995416 DOI: 10.1096/fj.201801696rrrr] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ubiquitin-like, containing PHD and RING finger domains, 1 (UHRF1) protein recognizes DNA methylation and histone modification and plays a critical role in epigenetic regulation. Recently, UHRF1 was shown to have a role in DNA methylation in oocytes and early embryos. Here, we reveal that maternal UHRF1 determines the quality of mouse oocytes. We generated oocyte-specific Uhrf1-knockout mice and found that females were sterile, and few maternal UHRF1-null embryos developed into blastocysts. The UHRF1-null oocytes had an increased incidence of aneuploidy and DNA damage. In addition to defective DNA methylation, histone modification was affected during oogenesis, with UHRF1-null germinal vesicle and metaphase II-stage oocytes exhibiting reduced global histone H3 lysine 9 dimethylation levels and elevated acetylation of histone H4 lysine 12. Taken together, our results suggest that UHRF1 plays an important role in determining oocyte quality and affects epigenetic regulation of oocyte maturation as a maternal protein, which is crucial for embryo developmental potential. Further exploration of the biologic function and underlying mechanisms of maternal UHRF1 will enhance our understanding of the maternal control of the oocyte and early embryonic development.-Cao, Y., Li, M., Liu, F., Ni, X., Wang, S., Zhang, H., Sui, X., Huo, R. Deletion of maternal UHRF1 severely reduces mouse oocyte quality and causes developmental defects in preimplantation embryos.
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Affiliation(s)
- Yumeng Cao
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Mingrui Li
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Fei Liu
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - XiaoBei Ni
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Shuai Wang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Hao Zhang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Xuesong Sui
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Ran Huo
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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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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25
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Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. EPIGENETICS AND REGENERATION 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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26
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Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a. Nat Commun 2018; 9:2583. [PMID: 29968706 PMCID: PMC6030064 DOI: 10.1038/s41467-018-04818-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 05/23/2018] [Indexed: 11/18/2022] Open
Abstract
Embryonic stem cells (ESCs) maintain pluripotency through unique epigenetic states. When ESCs commit to a specific lineage, epigenetic changes in histones and DNA accompany the transition to specialized cell types. Investigating how epigenetic regulation controls lineage specification is critical in order to generate the required cell types for clinical applications. Uhrf1 is a widely known hemi-methylated DNA-binding protein, playing a role in DNA methylation through the recruitment of Dnmt1 and in heterochromatin formation alongside G9a, Trim28, and HDACs. Although Uhrf1 is not essential in ESC self-renewal, it remains elusive how Uhrf1 regulates cell specification. Here we report that Uhrf1 forms a complex with the active trithorax group, the Setd1a/COMPASS complex, to maintain bivalent histone marks, particularly those associated with neuroectoderm and mesoderm specification. Overall, our data demonstrate that Uhrf1 safeguards proper differentiation via bivalent histone modifications. Uhrf1 is a known regulator of heterochromatin and DNA methylation in embryonic stem cells (ESCs). Here, the authors demonstrate that Uhrf1 acts together with the Set1/COMPASS complex regulator of active transcription to promote H3K4 methylation at bivalent loci and Uhrf1 loss results in disruption of differentiation.
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Np95/Uhrf1 regulates tumor suppressor gene expression of neural stem/precursor cells, contributing to neurogenesis in the adult mouse brain. Neurosci Res 2018; 143:31-43. [PMID: 29859850 DOI: 10.1016/j.neures.2018.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 01/30/2023]
Abstract
Adult neurogenesis is a process of generating new neurons from neural stem/precursor cells (NS/PCs) in restricted adult brain regions throughout life. It is now generally known that adult neurogenesis in the hippocampal dentate gyrus (DG) and subventricular zone participates in various higher brain functions, such as learning and memory formation, olfactory discrimination and repair after brain injury. However, the mechanisms underlying adult neurogenesis remain to be fully understood. Here, we show that Nuclear protein 95 KDa (Np95, also known as UHRF1 or ICBP90), which is an essential protein for maintaining DNA methylation during cell division, is involved in multiple processes of adult neurogenesis. Specific ablation of Np95 in adult NS/PCs (aNS/PCs) led to a decrease in their proliferation and an impairment of neuronal differentiation and to suppression of neuronal maturation associated with the impairment of dendritic formation in the hippocampal DG. We also found that deficiency of Np95 in NS/PCs increased the expression of tumor suppressor genes p16 and p53, and confirmed that expression of these genes in NS/PCs recapitulates the phenotype of Np95-deficient NS/PCs. Taken together, our findings suggest that Np95 plays an essential role in proliferation and differentiation of aNS/PCs through the regulation of tumor suppressor gene expression in adult neurogenesis.
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The Extract of Leonurus sibiricus Transgenic Roots with AtPAP1 Transcriptional Factor Induces Apoptosis via DNA Damage and Down Regulation of Selected Epigenetic Factors in Human Cancer Cells. Neurochem Res 2018; 43:1363-1370. [PMID: 29786770 PMCID: PMC6006195 DOI: 10.1007/s11064-018-2551-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/10/2018] [Accepted: 05/13/2018] [Indexed: 12/21/2022]
Abstract
The aim of this study was to determine the anticancer potential of Leonurus sibiricus extract derived from in vitro transgenic roots transformed by Agrobacetrium rhizogenes with AtPAP1 transcriptional factor, and that of transformed roots without construct, on grade IV human glioma cells and the U87MG cell line, and attempt to characterize the mechanism involved in this process. The anticancer effect induced by the tested extracts was associated with DNA damage, PARP cleavage/increased H2A.X histone levels and UHRF-1/DNMT1 down-regulation of mRNA levels. Additionally, we demonstrated differences in the content of compounds in the tested extracts by HPLC analysis with ATPAP1 construct and without. Both the tested extracts showed anticancer properties and the better results were observed for AtPAP1 with transcriptional factor root extract; this effect could be ascribed to the presence of higher condensed phenolic acids such as neochlorogenic acid, chlorogenic acids, ferulic acid, caffeic acid and p-coumaric acid. Further studies with AtPAP1 (with the transcriptional factor from Arabidopisi thaliana) root extract which showed better activities in combination with anticancer drugs are needed.
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29
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UHRF1 depletion sensitizes retinoblastoma cells to chemotherapeutic drugs via downregulation of XRCC4. Cell Death Dis 2018; 9:164. [PMID: 29415984 PMCID: PMC5833858 DOI: 10.1038/s41419-017-0203-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/19/2022]
Abstract
UHRF1 (ubiquitin-like with PHD and ring finger domains 1) is highly expressed in various human cancers including retinoblastoma, and associated with tumor-promoting effects such as inhibition of apoptosis and high proliferation. However, the molecular mechanisms underlying tumor-promoting functions of UHRF1 in retinoblastoma still remain elusive. Here, we show that stable knockdown of UHRF1 renders retinoblastoma cells sensitized to conventional chemotherapeutic drugs such as etoposide and camptothecin, resulting in enhanced DNA damage and apoptotic cell death. We found that UHRF1-depleted retinoblastoma cells can recognize DNA damages normally but have markedly low expression of XRCC4 (X-ray repair cross complementing 4) among the components of nonhomologous end-joining (NHEJ) repair complex. Conversely, overexpression of UHRF1 increased the XRCC4 expression and stable knockdown of XRCC4 sensitized retinoblastoma cells to etoposide treatment, suggesting that XRCC4 is a key mediator for the drug sensitivity upon UHRF1 depletion in retinoblastoma cells. Consistent with the findings, chromatin association of DNA ligase IV in response to acute DNA damage was found to be significantly reduced in UHRF1-depleted retinoblastoma cells and functional complementation for XRCC4 in UHRF1-depleted cells attenuated the drug sensitivity, demonstrating that XRCC4 downregulation in UHRF1-depleted cells impaired DNA repair and consequently induced robust apoptosis upon genotoxic drug treatment. In human primary retinoblastoma, high expression of UHRF1 and XRCC4 could be detected, and elevated XRCC4 expression correlated with reduced apoptosis markers, implying that UHRF1-mediated XRCC4 upregulation under pathophysiological conditions triggered by RB1 gene inactivation may confer protection against endogenous DNA damages that arise during retinoblastoma development. Taken together, these results present a new mechanistic insight into how UHRF1 mediates its tumor-promoting functions in retinoblastoma, and also provide a basis for UHRF1 targeting to improve the efficacy of current chemotherapy for retinoblastoma treatment.
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30
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Gao L, Tan XF, Zhang S, Wu T, Zhang ZM, Ai HW, Song J. An Intramolecular Interaction of UHRF1 Reveals Dual Control for Its Histone Association. Structure 2018; 26:304-311.e3. [PMID: 29395786 DOI: 10.1016/j.str.2017.12.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/17/2017] [Accepted: 12/27/2017] [Indexed: 12/24/2022]
Abstract
UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) is one of the essential components of mammalian DNA methylation machinery. Chromatin association of UHRF1 is controlled via an interplay between its intramolecular interaction and dual recognition of histone H3 trimethylated at lysine 9 (H3K9me3) and hemimethylated DNA. Here, we report the crystal structure of the N-terminal tandem Tudor domain (TTD) of UHRF1 in complex with the C-terminal polybasic region (PBR). Structural analysis reveals that PBR binding leads to displacement of the TTD-plant homeodomain (PHD) linker, as well as blockage of the H3K9me3-engaging cage, both of which contribute to a chromatin-occluded UHRF1 conformation. Disruption of the TTD-PBR interaction, which is facilitated by the binding of UHRF1 to hemimethylated DNA or regulatory protein USP7, shifts the UHRF1 conformation toward an open state, allowing for efficient H3K9me3 binding. Together, this study provides structural basis for the allosteric regulation of UHRF1.
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Affiliation(s)
- Linfeng Gao
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Xiao-Feng Tan
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Shen Zhang
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Tianchen Wu
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA
| | - Zhi-Min Zhang
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Hui-Wang Ai
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA; Department of Chemistry, University of California, Riverside, CA 92521, USA; Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, and Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Jikui Song
- Environmental Toxicology Graduate Program, University of California, Riverside, CA 92521, USA; Department of Biochemistry, University of California, Riverside, CA 92521, USA.
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Ubiquitome Analysis Reveals PCNA-Associated Factor 15 (PAF15) as a Specific Ubiquitination Target of UHRF1 in Embryonic Stem Cells. J Mol Biol 2017; 429:3814-3824. [DOI: 10.1016/j.jmb.2017.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/26/2017] [Accepted: 10/12/2017] [Indexed: 12/30/2022]
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32
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Zhang ZY, Zhu B, Zhao XW, Zhan YB, Bao JJ, Zhou JQ, Zhang FJ, Yu B, Liu J, Wang YM, Bai YH, Hong J, Liu XZ. Regulation of UHRF1 by microRNA-378 modulates medulloblastoma cell proliferation and apoptosis. Oncol Rep 2017; 38:3078-3084. [PMID: 28901497 DOI: 10.3892/or.2017.5939] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/05/2017] [Indexed: 11/05/2022] Open
Abstract
A previous study revealed that ubiquitin-like with PHD and RING finger domains 1 (UHRF1) promoted cell proliferation and was a potential biomarker in medulloblastoma (MB). In the present study, we reported that miR-378 inhibited the expression of UHRF1 to affect the proliferation of MB through competitive binding to the same region of its 3'-UTR. We found that the expression of miR-378 was significantly downregulated in MB tissues and inversely correlated with the expression of UHRF1. Western blot analysis revealed that overexpression of miR-378 led to the suppression of UHRF1. Moreover, a dual-luciferase assay demonstrated that miR-378 negatively regulated the activity of target gene UHRF1 by binding to its 3'-UTR. An in vitro assay revealed that overexpression of miR-378 suppressed MB cell proliferation and promoted cell apoptosis. Ectopic expression of UHRF1 rescued miR-378-suppressed cell proliferation and miR-378-promoted cell apoptosis. Collectively, the present study demonstrated that miR-378 could inhibit the proliferation of MB by downregulation of UHRF1 and act as a potential therapeutic target against MB.
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Affiliation(s)
- Zhen-Yu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Bin Zhu
- Queen Mary Institute, Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Xin-Wei Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Yun-Bo Zhan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Jian-Ji Bao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Jin-Qiao Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Feng-Jiang Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Bin Yu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Jun Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Yan-Min Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Ya-Hui Bai
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Jin Hong
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Xian-Zhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
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33
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Globular adiponectin inhibits leptin-stimulated esophageal adenocarcinoma cell proliferation via adiponectin receptor 2-mediated suppression of UHRF1. Mol Cell Biochem 2017; 431:103-112. [PMID: 28285359 DOI: 10.1007/s11010-017-2980-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/24/2017] [Indexed: 12/20/2022]
Abstract
Esophageal adenocarcinoma (EAC) is one of the most common malignancies in the world which is associated the increased prevalence of obesity. In the context of obesity, leptin can directly contribute to progression of EAC. Adiponectin inhibits leptin-induced oncogenic signaling in EAC cells. However, the exact molecular mechanisms linking obesity, adipokines, and EAC remain far from completely understood. In the present study, we tested the role of ubiquitin-like with PHD and ring finger domains 1 (UHRF1) in adiponectin-induced protective effects against leptin-induced EAC cell proliferation. We found that globular adiponectin (gAD) significantly inhibited leptin-induced increase of cell proliferation and decrease of apoptosis in OE 19 cells. Moreover, leptin-induced increase of UHRF1 expression was suppressed by gAD. Compared with normal controls, UHRF1 expression was markedly increased in EAC tissues and cell lines. Silence of UHRF1 increased the expression of cleaved caspase 3 and 9 and Bax, reduced the expression of Bcl-2, promoted apoptosis, and inhibited cell proliferation in OE 19 cells. Overexpression of UHRF1 significantly blocked gAD-induced decrease of cell proliferation and increase of apoptosis in leptin-treated cells. Silence of adiponectin receptor 1/2 (AdipoR1/2) could inhibit gAD-induced decrease of cell proliferation and increase of apoptosis in leptin-treated cells. Silence of AdipoR2, but not AdipoR1, suppressed gAD-induced decrease of UHRF1 expression in leptin-treated cells. The results indicated that gAD inhibited the prooncogenic effects of leptin via AdipoR2-mediated suppression of UHRF1. Our study provides novel insights into the role of UHRF1 in the development of EAC and the mechanism of antitumor effect of gAD.
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Ding G, Chen P, Zhang H, Huang X, Zang Y, Li J, Li J, Wong J. Regulation of Ubiquitin-like with Plant Homeodomain and RING Finger Domain 1 (UHRF1) Protein Stability by Heat Shock Protein 90 Chaperone Machinery. J Biol Chem 2016; 291:20125-35. [PMID: 27489107 DOI: 10.1074/jbc.m116.727214] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Indexed: 01/07/2023] Open
Abstract
As a protein critical for DNA maintenance methylation and cell proliferation, UHRF1 is frequently highly expressed in various human cancers and is considered as a drug target for cancer therapy. In a high throughput screening for small molecules that induce UHRF1 protein degradation, we have identified the HSP90 inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG). We present evidence that UHRF1 interacts with HSP90 chaperone complex and is a novel HSP90 client protein. Pharmacological inhibition of HSP90 with 17-AAG or 17-dimethylaminoethylamino-17-demethoxygeldanamycin results in UHRF1 ubiquitination and proteasome-dependent degradation. Interestingly, this HSP90 inhibitor-induced UHRF1 degradation is independent of CHIP and CUL5, two previously identified ubiquitin E3 ligases for HSP90 client proteins. In addition, this degradation is dependent neither on the intrinsic E3 ligase of UHRF1 nor on the E3 ligase SCF(β-TRCP) that has been implicated in regulation of UHRF1 stability. We also provide evidence that HSP90 inhibitors may suppress cancer cell proliferation in part through its induced UHRF1 degradation. Taken together, our results identify UHRF1 as a novel HSP90 client protein and shed light on the regulation of UHRF1 stability and function.
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Affiliation(s)
- Guangjin Ding
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241
| | - Peilin Chen
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241
| | - Hui Zhang
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241
| | - Xiaojie Huang
- the National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, and
| | - Yi Zang
- the National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, and
| | - Jiwen Li
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241
| | - Jia Li
- the National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, and
| | - Jiemin Wong
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, the Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China
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35
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Zhang ZY, Cai JJ, Hong J, Li KKW, Ping Z, Wang Y, Ng HK, Yao Y, Mao Y. Clinicopathological analysis of UHRF1 expression in medulloblastoma tissues and its regulation on tumor cell proliferation. Med Oncol 2016; 33:99. [PMID: 27449774 DOI: 10.1007/s12032-016-0799-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Studies have showed the involvement of ubiquitin-like with PHD and RING finger domains 1 (UHRF1) in tumorigenesis and progression. This study focused on the relationships between UHRF1 and medulloblastoma (MB). Immunostaining and western blotting demonstrated differential expression of UHRF1 in MB tissues and no UHRF1 expression in normal cerebellum tissues. Univariate survival analysis revealed MB patients with high UHRF1 expression had significantly shorter OS and PFS than patients with low UHRF1 (OS p = 0.009, PFS p = 0.003). Multivariate analysis illustrated that UHRF1 expression level is an independent prognostic factor influencing the OS and PFS (OS p = 0.038, PFS p = 0.014). UHRF1 expression levels were significantly different among molecular subgroups of MB (p = 0.003). Down-regulation of UHRF1 by RNAi inhibited proliferation and clonogenic ability of MB cell lines with cell cycle arrest in G1/G2-phase. Meanwhile, cells transfected with lenti-shUHRF1 showed increased p16 expression and location shift of CDK4 in MB cells. These findings indicate UHRF1 may promote cell proliferation and be a potential biomarker that can be used as a prognostic parameter and a therapeutic target for MB.
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Affiliation(s)
- Zhen-Yu Zhang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Wulumuqi Zhong Road 12, Shanghai, 200040, China
- Department of Neurosurgery, First Affiliated Hospital of Zhengzhou University, Jianshe Dong Road 1, Zhengzhou, 450001, Henan, China
| | - Jia-Jun Cai
- Department of Neurosurgery, Huashan Hospital, Fudan University, Wulumuqi Zhong Road 12, Shanghai, 200040, China
| | - Jin Hong
- Department of Cardiology, First Affiliated Hospital of Zhengzhou University, Jianshe Dong Road 1, Zhengzhou, 450001, Henan, China
| | - Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, 30-32 Ngan Shing Street, Shatin, N.T., Hong Kong, China
| | - Zhou Ping
- Department of Neurosurgery, Huashan Hospital, Fudan University, Wulumuqi Zhong Road 12, Shanghai, 200040, China
| | - Yin Wang
- Department of Neuropathology, Huashan Hospital, Fudan University, Wulumuqi Zhong Road 12, Shanghai, 200040, China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, 30-32 Ngan Shing Street, Shatin, N.T., Hong Kong, China
| | - Yu Yao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Wulumuqi Zhong Road 12, Shanghai, 200040, China.
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Wulumuqi Zhong Road 12, Shanghai, 200040, China.
- State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
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36
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UHRF1 suppression promotes cell differentiation and reduces inflammatory reaction in anaplastic thyroid cancer. Oncotarget 2016; 9:31945-31957. [PMID: 30174788 PMCID: PMC6112835 DOI: 10.18632/oncotarget.10674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 06/02/2016] [Indexed: 01/07/2023] Open
Abstract
Anaplastic thyroid cancer (ATC), an undifferentiated subtype of thyroid cancer, is one of the most malignant endocrine cancer with low survival rate, and resistant to chemotherapy and radiation therapy. Here we found that UHRF1 was highly expressed in human ATC compared with normal tissue and papillary thyroid cancer (PTC). Knockdown of UHRF1 inhibited proliferation of ATC in vitro and in vivo. Consistently, overexpression of UHRF1 promoted the proliferation of thyroid cancer cells. Moreover, UHRF1 suppression induced differentiation of three-dimensional (3D) cultured ATC cells and down-regulated the expression of dedifferentiation marker (CD97). The stem cell markers (Sox2, Oct4 and Nanog) were suppressed simultaneously. In addition, UHRF1 knockdown reduced the transcription of cytokines (IL-8, TGF-α and TNF-α), which might relieve the inflammatory reaction in ATC patients. This study demonstrated a role of UHRF1 in ATC proliferation, dedifferentiation and inflammatory reaction, presenting UHRF1 as a potential target in ATC therapy.
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Hashimoto S, Anai H, Hanada K. Mechanisms of interstrand DNA crosslink repair and human disorders. Genes Environ 2016; 38:9. [PMID: 27350828 PMCID: PMC4918140 DOI: 10.1186/s41021-016-0037-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/11/2016] [Indexed: 12/22/2022] Open
Abstract
Interstrand DNA crosslinks (ICLs) are the link between Watson-Crick strands of DNAs with the covalent bond and prevent separation of DNA strands. Since the ICL lesion affects both strands of the DNA, the ICL repair is not simple. So far, nucleotide excision repair (NER), structure-specific endonucleases, translesion DNA synthesis (TLS), homologous recombination (HR), and factors responsible for Fanconi anemia (FA) are identified to be involved in ICL repair. Since the presence of ICL lesions causes severe defects in transcription and DNA replication, mutations in these DNA repair pathways give rise to a various hereditary disorders. NER plays an important role for the ICL recognition and removal in quiescent cells, and defects of NER causes congential progeria syndrome, such as xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy. On the other hand, the ICL repair in S phase requires more complicated orchestration of multiple factors, including structure-specific endonucleases, and TLS, and HR. Disturbed this ICL repair orchestration in S phase causes genome instability resulting a cancer prone disease, Fanconi anemia. So far more than 30 factors in ICL repair have already identified. Recently, a new factor, UHRF1, was discovered as a sensor of ICLs. In addition to this, numbers of nucleases that are involved in the first incision, also called unhooking, of ICL lesions have also been identified. Here we summarize the recent studies of ICL associated disorders and repair mechanism, with emphasis in the first incision of ICLs.
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Affiliation(s)
- Satoru Hashimoto
- Department of Clinical Pharmacology and Therapeutics, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan
| | - Hirofumi Anai
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan
| | - Katsuhiro Hanada
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan
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Kent B, Magnani E, Walsh MJ, Sadler KC. UHRF1 regulation of Dnmt1 is required for pre-gastrula zebrafish development. Dev Biol 2016; 412:99-113. [PMID: 26851214 DOI: 10.1016/j.ydbio.2016.01.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 12/16/2022]
Abstract
Landmark epigenetic events underlie early embryonic development, yet how epigenetic modifiers are regulated to achieve rapid epigenome re-patterning is not known. Uhrf1 and DNA methyltransferase 1 (Dnmt1) are known to largely mediate maintenance DNA methylation and Uhrf1 is also required for both Dnmt1 localization and stability. Here, we investigate how these two key epigenetic modifiers regulate early zebrafish development and characterize the developmental consequences of disrupting their homeostatic relationship. Unlike Uhrf1 knockdown, which causes developmental arrest and death prior to gastrulation, overexpression of human UHRF1 (WT-UHRF1) caused asymmetric epiboly, inefficient gastrulation and multi-systemic defects. UHRF1 phosphorylation was previously demonstrated as essential for zebrafish embryogenesis, and we found that penetrance of the asymmetric epiboly phenotype was significantly increased in embryos injected with mRNA encoding non-phosphorylatable UHRF1 (UHRF1(S661A)). Surprisingly, both WT-UHRF1 and UHRF1(S661A) overexpression caused DNA hypomethylation. However, since other approaches that caused an equivalent degree of DNA hypomethylation did not cause the asymmetric epiboly phenotype, we conclude that bulk DNA methylation is not the primary mechanism. Instead, UHRF1(S661A) overexpression resulted in accumulation of Dnmt1 protein and the overexpression of both WT and a catalytically inactive Dnmt1 phenocopied the assymetric epiboly phenotype. Dnmt1 knockdown suppressed the phenotype caused by UHRF1(S661A) overexpression, and Uhrf1 knockdown suppressed the effect of Dnmt1 overexpression. Therefore, we conclude that the interaction between these two proteins is the mechanism underlying the gastrulation defects. This indicates that Dnmt1 stability requires UHRF1 phosphorylation and that crosstalk between the proteins is essential for the function of these two important epigenetic regulators during gastrulation.
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Affiliation(s)
- Brandon Kent
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Elena Magnani
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Martin J Walsh
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States
| | - Kirsten C Sadler
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States; Department of Medicine/Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, Box 1020, 1 Gustave L. Levy Place, New York, NY 10029, United States.
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Zhang H, Liu H, Chen Y, Yang X, Wang P, Liu T, Deng M, Qin B, Correia C, Lee S, Kim J, Sparks M, Nair AA, Evans DL, Kalari KR, Zhang P, Wang L, You Z, Kaufmann SH, Lou Z, Pei H. A cell cycle-dependent BRCA1-UHRF1 cascade regulates DNA double-strand break repair pathway choice. Nat Commun 2016; 7:10201. [PMID: 26727879 PMCID: PMC4728409 DOI: 10.1038/ncomms10201] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023] Open
Abstract
BRCA1 is an important mediator of the DNA damage response, which promotes homologous recombination (HR) and antagonizes 53BP1-dependent non-homologous end joining in S/G2 phase. But how this is achieved remains unclear. Here, we report that the E3 ubiquitin ligase UHRF1 (Ubiquitin-like, with PHD and RING finger domains 1) directly participates in the interplay between BRCA1 and 53BP1. Mechanistically, UHRF1 is recruited to DNA double-strand breaks (DSBs) by BRCA1 in S phase, which requires the BRCT domain of BRCA1 and phosphorylated Ser674 of UHRF1. Subsequently, UHRF1 mediates K63-linked polyubiquitination of RIF1, and results in its dissociation from 53BP1 and DSBs thereby facilitating HR initiation. Thus, UHRF1 is a key regulator of DSB repair choice, which is separate from its role in heterochromatin formation and epigenetic regulator. BRCA1 is a key regulator of DNA double-strand break repair, functioning to promote homologous recombination and repress non-homologous end-joining. Here the authors show that the ubiquitin ligase UHRF1 is recruited to breaks by BRCA1, where it targets RIF1 and thereby facilitates recombination.
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Affiliation(s)
- Haoxing Zhang
- School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hailong Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yali Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xu Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Panfei Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Tongzheng Liu
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Cristina Correia
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Seungbaek Lee
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jungjin Kim
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Melanie Sparks
- Department of Cell Biology and Physiology, Washington University, St Louis, Missouri 63130, USA
| | - Asha A Nair
- BSI-Genetics &Bioinformatics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Debra L Evans
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R Kalari
- BSI-Genetics &Bioinformatics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Pumin Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Liewei Wang
- Molecular Pharmacology and Experimental therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University, St Louis, Missouri 63130, USA
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China.,Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA.,Molecular Pharmacology and Experimental therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Huadong Pei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 100850, China
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40
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Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:123-150. [PMID: 27826837 DOI: 10.1007/978-3-319-43624-1_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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 levels and patterns are associated with various human diseases, including cancer and developmental disorders. DNA methylation is mediated by three active DNA methyltransferases (Dnmts), namely, Dnmt1, Dnmt3a, and Dnmt3b, in mammals. Over the last two 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 X-chromosome inactivation.
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Affiliation(s)
- Jiameng Dan
- 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, 1808 Park Road 1C, Smithville, TX, 78957, 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, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA.
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41
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Piazzi M, Williamson A, Lee CF, Pearson S, Lacaud G, Kouskoff V, McCubrey JA, Cocco L, Whetton AD. Quantitative phosphoproteome analysis of embryonic stem cell differentiation toward blood. Oncotarget 2015; 6:10924-39. [PMID: 25890499 PMCID: PMC4484429 DOI: 10.18632/oncotarget.3454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/24/2015] [Indexed: 11/25/2022] Open
Abstract
Murine embryonic stem (ES) cells can differentiate in vitro into three germ layers (endodermic, mesodermic, ectodermic). Studies on the differentiation of these cells to specific early differentiation stages has been aided by an ES cell line carrying the Green Fluorescent Protein (GFP) targeted to the Brachyury (Bry) locus which marks mesoderm commitment. Furthermore, expression of the Vascular Endothelial Growth Factor receptor 2 (Flk1) along with Bry defines hemangioblast commitment. Isobaric-tag for relative and absolute quantification (iTRAQ(TM)) and phosphopeptide enrichment coupled to liquid chromatography separation and mass spectrometry allow the study of phosphorylation changes occurring at different stages of ES cell development using Bry and Flk1 expression respectively. We identified and relatively quantified 37 phosphoentities which are modulated during mesoderm-induced ES cells differentiation, comparing epiblast-like, early mesoderm and hemangioblast-enriched cells. Among the proteins differentially phosphorylated toward mesoderm differentiation were: the epigenetic regulator Dnmt3b, the protein kinase GSK3b, the chromatin remodeling factor Smarcc1, the transcription factor Utf1; as well as protein specifically related to stem cell differentiation, as Eomes, Hmga2, Ints1 and Rif1. As most key factors regulating early hematopoietic development have also been implicated in various types of leukemia, understanding the post-translational modifications driving their regulation during normal development could result in a better comprehension of their roles during abnormal hematopoiesis in leukemia.
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Affiliation(s)
- Manuela Piazzi
- Cell Signaling Laboratory, Department of Biomedical Science (DIBINEM), University of Bologna, Italy
| | - Andrew Williamson
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Chia-Fang Lee
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Stella Pearson
- Stem Cell Research Group, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Georges Lacaud
- Stem Cell Biology Group Paterson Institute for Cancer Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Valerie Kouskoff
- Stem Cell Research Group, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - James A. McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Lucio Cocco
- Cell Signaling Laboratory, Department of Biomedical Science (DIBINEM), University of Bologna, Italy
| | - Anthony D. Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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Tian Y, Paramasivam M, Ghosal G, Chen D, Shen X, Huang Y, Akhter S, Legerski R, Chen J, Seidman MM, Qin J, Li L. UHRF1 contributes to DNA damage repair as a lesion recognition factor and nuclease scaffold. Cell Rep 2015; 10:1957-66. [PMID: 25818288 DOI: 10.1016/j.celrep.2015.03.038] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 03/02/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
We identified ubiquitin-like with PHD and RING finger domain 1 (UHRF1) as a binding factor for DNA interstrand crosslink (ICL) lesions through affinity purification of ICL-recognition activities. UHRF1 is recruited to DNA lesions in vivo and binds directly to ICL-containing DNA. UHRF1-deficient cells display increased sensitivity to a variety of DNA damages. We found that loss of UHRF1 led to retarded lesion processing and reduced recruitment of ICL repair nucleases to the site of DNA damage. UHRF1 interacts physically with both ERCC1 and MUS81, two nucleases involved in the repair of ICL lesions. Depletion of both UHRF1 and components of the Fanconi anemia (FA) pathway resulted in increased DNA damage sensitivity compared to defect of each mechanism alone. These results suggest that UHRF1 promotes recruitment of lesion-processing activities via its affinity to recognize DNA damage and functions as a nuclease recruitment scaffold in parallel to the FA pathway.
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Affiliation(s)
- Yanyan Tian
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Manikandan Paramasivam
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gargi Ghosal
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ding Chen
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi Shen
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yaling Huang
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shamima Akhter
- Department of Genetics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Randy Legerski
- Department of Genetics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jun Qin
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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UHRF1 is a sensor for DNA interstrand crosslinks and recruits FANCD2 to initiate the Fanconi anemia pathway. Cell Rep 2015; 10:1947-56. [PMID: 25801034 PMCID: PMC4386029 DOI: 10.1016/j.celrep.2015.02.053] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 02/12/2015] [Accepted: 02/23/2015] [Indexed: 12/12/2022] Open
Abstract
The Fanconi anemia (FA) pathway is critical for the cellular response to toxic DNA interstrand crosslinks (ICLs). Using a biochemical purification strategy, we identified UHRF1 as a protein that specifically interacts with ICLs in vitro and in vivo. Reduction of cellular levels of UHRF1 by RNAi attenuates the FA pathway and sensitizes cells to mitomycin C. Knockdown cells display a drastic reduction in FANCD2 foci formation. Using live-cell imaging, we observe that UHRF1 is rapidly recruited to chromatin in response to DNA crosslinking agents and that this recruitment both precedes and is required for the recruitment of FANCD2 to ICLs. Based on these results, we describe a mechanism of ICL sensing and propose that UHRF1 is a critical factor that binds to ICLs. In turn, this binding is necessary for the subsequent recruitment of FANCD2, which allows the DNA repair process to initiate. UHRF1 is a sensor for DNA interstrand crosslinks (ICLs) UHRF1 is recruited to ICLs within seconds of their appearance in the genome Recruitment of UHRF1 is required for proper recruitment of FANCD2 to ICLs UHRF1 is an integral part of the Fanconi anemia DNA repair pathway
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Jacob V, Chernyavskaya Y, Chen X, Tan PS, Kent B, Hoshida Y, Sadler KC. DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos. Development 2015; 142:510-21. [PMID: 25564650 DOI: 10.1242/dev.115980] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) recruits DNMT1 to hemimethylated DNA during replication and is essential for maintaining DNA methylation. uhrf1 mutant zebrafish have global DNA hypomethylation and display embryonic defects, including a small liver, and they die as larvae. We make the surprising finding that, despite their reduced organ size, uhrf1 mutants express high levels of genes controlling S-phase and have many more cells undergoing DNA replication, as measured by BrdU incorporation. In contrast to wild-type hepatocytes, which are continually dividing during hepatic outgrowth and thus dilute the BrdU label, uhrf1 mutant hepatocytes retain BrdU throughout outgrowth, reflecting cell cycle arrest. Pulse-chase-pulse experiments with BrdU and EdU, and DNA content analysis indicate that uhrf1 mutant cells undergo DNA re-replication and that apoptosis is the fate of many of the re-replicating and arrested hepatocytes. Importantly, the DNA re-replication phenotype and hepatic outgrowth failure are preceded by global loss of DNA methylation. Moreover, uhrf1 mutants are phenocopied by mutation of dnmt1, and Dnmt1 knockdown in uhrf1 mutants enhances their small liver phenotype. Together, these data indicate that unscheduled DNA replication and failed cell cycle progression leading to apoptosis are the mechanisms by which DNA hypomethylation prevents organ expansion in uhrf1 mutants. We propose that cell cycle arrest leading to apoptosis is a strategy that restricts propagation of epigenetically damaged cells during embryogenesis.
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Affiliation(s)
- Vinitha Jacob
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Yelena Chernyavskaya
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Xintong Chen
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Poh Seng Tan
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Division of Gastroenterology and Hepatology, University Medicine Cluster, National University Health System, Singapore
| | - Brandon Kent
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Yujin Hoshida
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
| | - Kirsten C Sadler
- Department of Medicine, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1020, New York, NY 10029, USA
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45
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Murao N, Matsuda T, Noguchi H, Koseki H, Namihira M, Nakashima K. Characterization of Np95 expression in mouse brain from embryo to adult: A novel marker for proliferating neural stem/precursor cells. NEUROGENESIS 2014; 1:e976026. [PMID: 27504471 PMCID: PMC4973607 DOI: 10.4161/23262133.2014.976026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/31/2014] [Accepted: 10/08/2014] [Indexed: 01/12/2023]
Abstract
Nuclear protein 95 KDa (Np95, also known as UHRF1 or ICBP90) plays an important role in maintaining DNA methylation of newly synthesized DNA strands by recruiting DNA methyltransferase 1 (DNMT1) during cell division. In addition, Np95 participates in chromatin remodeling by interacting with histone modification enzymes such as histone deacetylases. However, its expression pattern and function in the brain have not been analyzed extensively. We here investigated the expression pattern of Np95 in the mouse brain, from developmental to adult stages. In the fetal brain, Np95 is abundantly expressed at the midgestational stage, when a large number of neural stem/precursor cells (NS/PCs) exist. Interestingly, Np95 is expressed specifically in NS/PCs but not in differentiated cells such as neurons or glial cells. Furthermore, we demonstrate that Np95 is preferentially expressed in type 2a cells, which are highly proliferative NS/PCs in the dentate gyrus of the adult hippocampus. Moreover, the number of Np95-expressing cells increases in response to kainic acid administration or to voluntary running, which are known to enhance the proliferation of adult NS/PCs. These results suggest that Np95 participates in the process of proliferation and differentiation of NS/PCs, and that it should be a useful novel marker for proliferating NS/PCs, facilitating the analysis of the complex behavior of NS/PCs in the brain.
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Affiliation(s)
- Naoya Murao
- Department of Stem Cell Biology and Medicine; Graduate School of Medical Sciences; Kyushu University; Fukuoka, Japan; Laboratory of Gene Regulation Research; Graduate School of Biological Sciences; Nara Institute of Science and Technology; Nara, Japan
| | - Taito Matsuda
- Department of Stem Cell Biology and Medicine; Graduate School of Medical Sciences; Kyushu University ; Fukuoka, Japan
| | - Hirofumi Noguchi
- Department of Stem Cell Biology and Medicine; Graduate School of Medical Sciences; Kyushu University; Fukuoka, Japan; Laboratory of Gene Regulation Research; Graduate School of Biological Sciences; Nara Institute of Science and Technology; Nara, Japan
| | - Haruhiko Koseki
- Developmental Genetics; RIKEN Research Center for Allergy and Immunology ; Kanagawa, Japan
| | - Masakazu Namihira
- Molecular Neurophysiology Research Group; Biomedical Research Institute; National Institute of Advanced Industrial Science and Technology ; Ibaraki, Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine; Graduate School of Medical Sciences; Kyushu University ; Fukuoka, Japan
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46
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De Vos M, El Ramy R, Quénet D, Wolf P, Spada F, Magroun N, Babbio F, Schreiber V, Leonhardt H, Bonapace IM, Dantzer F. Poly(ADP-ribose) polymerase 1 (PARP1) associates with E3 ubiquitin-protein ligase UHRF1 and modulates UHRF1 biological functions. J Biol Chem 2014; 289:16223-38. [PMID: 24782312 DOI: 10.1074/jbc.m113.527424] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1, also known as ARTD1) is an abundant nuclear enzyme that plays important roles in DNA repair, gene transcription, and differentiation through the modulation of chromatin structure and function. In this work we identify a physical and functional poly(ADP-ribose)-mediated interaction of PARP1 with the E3 ubiquitin ligase UHRF1 (also known as NP95, ICBP90) that influences two UHRF1-regulated cellular processes. On the one hand, we uncovered a cooperative interplay between PARP1 and UHRF1 in the accumulation of the heterochromatin repressive mark H4K20me3. The absence of PARP1 led to reduced accumulation of H4K20me3 onto pericentric heterochromatin that coincided with abnormally enhanced transcription. The loss of H4K20me3 was rescued by the additional depletion of UHRF1. In contrast, although PARP1 also seemed to facilitate the association of UHRF1 with DNMT1, its absence did not impair the loading of DNMT1 onto heterochromatin or the methylation of pericentric regions, possibly owing to a compensating interaction of DNMT1 with PCNA. On the other hand, we showed that PARP1 controls the UHRF1-mediated ubiquitination of DNMT1 to timely regulate its abundance during S and G2 phase. Together, this report identifies PARP1 as a novel modulator of two UHRF1-regulated heterochromatin-associated events: the accumulation of H4K20me3 and the clearance of DNMT1.
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Affiliation(s)
- Mike De Vos
- From the Poly(ADP-ribosyl)ation and Genome Integrity Group, Equipe Labellisée Ligue Nationale Contre le Cancer, Laboratoire d'Excellence Medalis, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Boulevard Sebastien Brant, BP10413, 67412 Illkirch, France
| | - Rosy El Ramy
- From the Poly(ADP-ribosyl)ation and Genome Integrity Group, Equipe Labellisée Ligue Nationale Contre le Cancer, Laboratoire d'Excellence Medalis, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Boulevard Sebastien Brant, BP10413, 67412 Illkirch, France
| | - Delphine Quénet
- From the Poly(ADP-ribosyl)ation and Genome Integrity Group, Equipe Labellisée Ligue Nationale Contre le Cancer, Laboratoire d'Excellence Medalis, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Boulevard Sebastien Brant, BP10413, 67412 Illkirch, France
| | - Patricia Wolf
- the Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany, and
| | - Fabio Spada
- the Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany, and
| | - Najat Magroun
- From the Poly(ADP-ribosyl)ation and Genome Integrity Group, Equipe Labellisée Ligue Nationale Contre le Cancer, Laboratoire d'Excellence Medalis, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Boulevard Sebastien Brant, BP10413, 67412 Illkirch, France
| | - Federica Babbio
- the Department of Structural and Functional Biology, University of Insubria, Via Alberto da Giussano 12, 21052 Busto Arsizio, Italy
| | - Valérie Schreiber
- From the Poly(ADP-ribosyl)ation and Genome Integrity Group, Equipe Labellisée Ligue Nationale Contre le Cancer, Laboratoire d'Excellence Medalis, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Boulevard Sebastien Brant, BP10413, 67412 Illkirch, France
| | - Heinrich Leonhardt
- the Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany, and
| | - Ian Marc Bonapace
- the Department of Structural and Functional Biology, University of Insubria, Via Alberto da Giussano 12, 21052 Busto Arsizio, Italy
| | - Françoise Dantzer
- From the Poly(ADP-ribosyl)ation and Genome Integrity Group, Equipe Labellisée Ligue Nationale Contre le Cancer, Laboratoire d'Excellence Medalis, Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg, UMR7242, Centre Nationale de la Recherche Scientifique/Université de Strasbourg, Boulevard Sebastien Brant, BP10413, 67412 Illkirch, France,
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Luo T, Cui S, Bian C, Yu X. Uhrf2 is important for DNA damage response in vascular smooth muscle cells. Biochem Biophys Res Commun 2013; 441:65-70. [PMID: 24134842 DOI: 10.1016/j.bbrc.2013.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 10/05/2013] [Indexed: 10/26/2022]
Abstract
Emerging evidence shows that Uhrf1 plays an important role in DNA damage response for maintaining genomic stability. Interestingly, Uhrf1 has a paralog Uhrf2 in mammals. Uhrf1 and Uhrf2 share similar domain architectures. However, the role of Uhrf2 in DNA damage response has not been studied yet. During the analysis of the expression level of Uhrf2 in different tissues, we found that Uhrf2 is highly expressed in aorta and aortic vascular smooth muscle cells. Thus, we studied the role of Uhrf2 in DNA damage response in aortic vascular smooth muscle cells. Using laser microirradiation, we found that like Uhrf1, Uhrf2 was recruited to the sites of DNA damage. We dissected the functional domains of Uhrf2 and found that the TTD, PHD and SRA domains are important for the relocation of Uhrf2 to the sites of DNA damage. Moreover, depletion of Uhrf2 suppressed DNA damage-induced H2AX phosphorylation and DNA damage repair. Taken together, our results demonstrate the function of Uhrf2 in DNA damage response.
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Affiliation(s)
- Tao Luo
- Vascular Surgery Department of Xuan Wu Hospital, Institute of Vascular Surgery, Capital Medical University, Beijing, China
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48
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Taylor EM, Bonsu NM, Price RJ, Lindsay HD. Depletion of Uhrf1 inhibits chromosomal DNA replication in Xenopus egg extracts. Nucleic Acids Res 2013; 41:7725-37. [PMID: 23788677 PMCID: PMC3763540 DOI: 10.1093/nar/gkt549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 05/22/2013] [Accepted: 05/25/2013] [Indexed: 12/31/2022] Open
Abstract
UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) has a well-established role in epigenetic regulation through the recognition of various histone marks and interaction with chromatin-modifying proteins. However, its function in regulating cell cycle progression remains poorly understood and has been largely attributed to a role in transcriptional regulation. In this study we have used Xenopus laevis egg extracts to analyse Uhrf1 function in DNA replication in the absence of transcriptional influences. We demonstrate that removal of Uhrf1 inhibits chromosomal replication in this system. We further show that this requirement for Uhrf1, or an associated factor, occurs at an early stage of DNA replication and that the consequences of Uhrf1 depletion are not solely due to its role in loading Dnmt1 onto newly replicated DNA. We describe the pattern of Uhrf1 chromatin association before the initiation of DNA replication and show that this reflects functional requirements both before and after origin licensing. Our data demonstrate that the removal of Xenopus Uhrf1 influences the chromatin association of key replication proteins and reveal Uhrf1 as an important new factor required for metazoan DNA replication.
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Affiliation(s)
- Elaine M. Taylor
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Nicola M. Bonsu
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - R. Jordan Price
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Howard D. Lindsay
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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49
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Yang C, Wang Y, Zhang F, Sun G, Li C, Jing S, Liu Q, Cheng Y. Inhibiting UHRF1 expression enhances radiosensitivity in human esophageal squamous cell carcinoma. Mol Biol Rep 2013; 40:5225-35. [PMID: 23943380 DOI: 10.1007/s11033-013-2559-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 04/29/2013] [Indexed: 12/15/2022]
Abstract
Radiotherapy is an effective treatment for some esophageal cancers, but the molecular mechanisms of radiosensitivity remain unknown. Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) is a novel nuclear protein which is overexpressed in various cancers but not yet examined in esophageal squamous cell carcinoma (ESCC). The correlation between UHRF1 and the radioresistance in ESCC is still unclear. In the present study, the expression of UHRF1 was examined by immunohistochemistry in specimens of ESCC patients treated with radiotherapy. The results showed that UHRF1 was significantly overexpressed in ESCC specimens. Overexpression of UHRF1 correlated significantly with advanced T-stage, positive lymph node metastasis and poor differentiation. In addition, UHRF1 was associated with radiotherapy response, in which overexpression of UHRF1 was observed more frequently in the radioresistant group than in the effective group. At the molecular level, inhibition of UHRF1 by lentivirus-mediated shRNA targeting UHRF1 increased the radiosensitivity and apoptosis, while decreased radiation-induced G2/M phase arrest in TE-1 cells. Moreover, inhibition of UHRF1 resulted in higher residual γH2AX expression after irradiation, but not initial γH2AX. Further study showed that inhibition of UHRF1 down-regulated the endogenous expressions of DNA repair protein Ku70 and Ku80 in TE-1 cells, and significantly inhibited the increase of these proteins after irradiation. Above all, our data suggested that UHRF1 might play an important role in radioresistance of ESCC, and inhibition of UHRF1 can increase the radiosensitivity of TE-1 cells by altering cell cycle progression, enhancing apoptosis, and decreasing DNA damage repair capacity.
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Affiliation(s)
- Congrong Yang
- Department of Radiation Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
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50
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Lange UC, Siebert S, Wossidlo M, Weiss T, Ziegler-Birling C, Walter J, Torres-Padilla ME, Daujat S, Schneider R. Dissecting the role of H3K64me3 in mouse pericentromeric heterochromatin. Nat Commun 2013; 4:2233. [DOI: 10.1038/ncomms3233] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/03/2013] [Indexed: 12/17/2022] Open
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