51
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Endogenous reverse transcriptase and RNase H-mediated antiviral mechanism in embryonic stem cells. Cell Res 2021; 31:998-1010. [PMID: 34158624 PMCID: PMC8217788 DOI: 10.1038/s41422-021-00524-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleic acid-based systems play important roles in antiviral defense, including CRISPR/Cas that adopts RNA-guided DNA cleavage to prevent DNA phage infection and RNA interference (RNAi) that employs RNA-guided RNA cleavage to defend against RNA virus infection. Here, we report a novel type of nucleic acid-based antiviral system that exists in mouse embryonic stem cells (mESCs), which suppresses RNA virus infection by DNA-mediated RNA cleavage. We found that the viral RNA of encephalomyocarditis virus can be reverse transcribed into complementary DNA (vcDNA) by the reverse transcriptase (RTase) encoded by endogenous retrovirus-like elements in mESCs. The vcDNA is negative-sense single-stranded and forms DNA/RNA hybrid with viral RNA. The viral RNA in the heteroduplex is subsequently destroyed by cellular RNase H1, leading to robust suppression of viral growth. Furthermore, either inhibition of the RTase activity or depletion of endogenous RNase H1 results in the promotion of virus proliferation. Altogether, our results provide intriguing insights into the antiviral mechanism of mESCs and the antiviral function of endogenized retroviruses and cellular RNase H. Such a natural nucleic acid-based antiviral mechanism in mESCs is referred to as ERASE (endogenous RTase/RNase H-mediated antiviral system), which is an addition to the previously known nucleic acid-based antiviral mechanisms including CRISPR/Cas in bacteria and RNAi in plants and invertebrates.
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52
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Young GR, Ferron AKW, Panova V, Eksmond U, Oliver PL, Kassiotis G, Stoye JP. Gv1, a Zinc Finger Gene Controlling Endogenous MLV Expression. Mol Biol Evol 2021; 38:2468-2474. [PMID: 33560369 PMCID: PMC8136514 DOI: 10.1093/molbev/msab039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The genomes of inbred mice harbor around 50 endogenous murine leukemia virus (MLV) loci, although the specific complement varies greatly between strains. The Gv1 locus is known to control the transcription of endogenous MLVs and to be the dominant determinant of cell-surface presentation of MLV envelope, the GIX antigen. Here, we identify a single Krüppel-associated box zinc finger protein (ZFP) gene, Zfp998, as Gv1 and show it to be necessary and sufficient to determine the GIX+ phenotype. By long-read sequencing of bacterial artificial chromosome clones from 129 mice, the prototypic GIX+ strain, we reveal the source of sufficiency and deficiency as splice-acceptor variations and highlight the varying origins of the chromosomal region encompassing Gv1. Zfp998 becomes the second identified ZFP gene responsible for epigenetic suppression of endogenous MLVs in mice and further highlights the prominent role of this gene family in control of endogenous retroviruses.
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Affiliation(s)
- George R Young
- Retrovirus-host Interactions Laboratory, The Francis Crick Institute, London, UK
| | - Aaron K W Ferron
- Retrovirus-host Interactions Laboratory, The Francis Crick Institute, London, UK
| | - Veera Panova
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - Urszula Eksmond
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | | | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
| | - Jonathan P Stoye
- Retrovirus-host Interactions Laboratory, The Francis Crick Institute, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
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53
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Sun Z, Yu H, Zhao J, Tan T, Pan H, Zhu Y, Chen L, Zhang C, Zhang L, Lei A, Xu Y, Bi X, Huang X, Gao B, Wang L, Correia C, Chen M, Sun Q, Feng Y, Shen L, Wu H, Wang J, Shen X, Daley GQ, Li H, Zhang J. LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells. Protein Cell 2021; 13:490-512. [PMID: 34331666 PMCID: PMC9226220 DOI: 10.1007/s13238-021-00864-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/15/2021] [Indexed: 01/21/2023] Open
Abstract
LIN28 is an RNA binding protein with important roles in early embryo development, stem cell differentiation/reprogramming, tumorigenesis and metabolism. Previous studies have focused mainly on its role in the cytosol where it interacts with Let-7 microRNA precursors or mRNAs, and few have addressed LIN28's role within the nucleus. Here, we show that LIN28 displays dynamic temporal and spatial expression during murine embryo development. Maternal LIN28 expression drops upon exit from the 2-cell stage, and zygotic LIN28 protein is induced at the forming nucleolus during 4-cell to blastocyst stage development, to become dominantly expressed in the cytosol after implantation. In cultured pluripotent stem cells (PSCs), loss of LIN28 led to nucleolar stress and activation of a 2-cell/4-cell-like transcriptional program characterized by the expression of endogenous retrovirus genes. Mechanistically, LIN28 binds to small nucleolar RNAs and rRNA to maintain nucleolar integrity, and its loss leads to nucleolar phase separation defects, ribosomal stress and activation of P53 which in turn binds to and activates 2C transcription factor Dux. LIN28 also resides in a complex containing the nucleolar factor Nucleolin (NCL) and the transcriptional repressor TRIM28, and LIN28 loss leads to reduced occupancy of the NCL/TRIM28 complex on the Dux and rDNA loci, and thus de-repressed Dux and reduced rRNA expression. Lin28 knockout cells with nucleolar stress are more likely to assume a slowly cycling, translationally inert and anabolically inactive state, which is a part of previously unappreciated 2C-like transcriptional program. These findings elucidate novel roles for nucleolar LIN28 in PSCs, and a new mechanism linking 2C program and nucleolar functions in PSCs and early embryo development.
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Affiliation(s)
- Zhen Sun
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hua Yu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jing Zhao
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Tianyu Tan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongru Pan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuqing Zhu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Lang Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Cheng Zhang
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Li Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Anhua Lei
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yuyan Xu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xianju Bi
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100085, China
| | - Xin Huang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bo Gao
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Cristina Correia
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiming Sun
- Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yu Feng
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Li Shen
- Institute of Life Science, Zhejiang University, Hangzhou, 310058, China
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jianlong Wang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, 100085, China
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Boston Children's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hu Li
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences and the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, 310058, China.
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54
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Fu H, Zhang W, Li N, Yang J, Ye X, Tian C, Lu X, Liu L. Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells. Genome Biol 2021; 22:201. [PMID: 34243810 PMCID: PMC8268579 DOI: 10.1186/s13059-021-02417-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/24/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Naïve and primed pluripotent stem cells (PSCs) represent two different pluripotent states. Primed PSCs following in vitro culture exhibit lower developmental potency as evidenced by failure in germline chimera assays, unlike mouse naïve PSCs. However, the molecular mechanisms underlying the lower developmental competency of primed PSCs remain elusive. RESULTS We examine the regulation of telomere maintenance, retrotransposon activity, and genomic stability of primed PSCs and compare them with naïve PSCs. Surprisingly, primed PSCs only minimally maintain telomeres and show fragile telomeres, associated with declined DNA recombination and repair activity, in contrast to naïve PSCs that robustly elongate telomeres. Also, we identify LINE1 family integrant L1Md_T as naïve-specific retrotransposon and ERVK family integrant IAPEz to define primed PSCs, and their transcription is differentially regulated by heterochromatic histones and Dnmt3b. Notably, genomic instability of primed PSCs is increased, in association with aberrant retrotransposon activity. CONCLUSIONS Our data suggest that fragile telomere, retrotransposon-associated genomic instability, and declined DNA recombination repair, together with reduced function of cell cycle and mitochondria, increased apoptosis, and differentiation properties may link to compromised developmental potency of primed PSCs, noticeably distinguishable from naïve PSCs.
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Affiliation(s)
- Haifeng Fu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Pharmacy, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaoying Ye
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenglei Tian
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
- College of Pharmacy, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China.
- The Key Laboratory of Bioactive Materials Ministry of Education, Nankai University, Tianjin, China.
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55
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Onishi-Seebacher M, Erikson G, Sawitzki Z, Ryan D, Greve G, Lübbert M, Jenuwein T. Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia. BMC Med Genomics 2021; 14:166. [PMID: 34174884 PMCID: PMC8234671 DOI: 10.1186/s12920-021-01003-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 06/07/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Repeat elements constitute a large proportion of the human genome and recent evidence indicates that repeat element expression has functional roles in both physiological and pathological states. Specifically for cancer, transcription of endogenous retrotransposons is often suppressed to attenuate an anti-tumor immune response, whereas aberrant expression of heterochromatin-derived satellite RNA has been identified as a tumor driver. These insights demonstrate separate functions for the dysregulation of distinct repeat subclasses in either the attenuation or progression of human solid tumors. For hematopoietic malignancies, such as Acute Myeloid Leukemia (AML), only very few studies on the expression/dysregulation of repeat elements were done. METHODS To study the expression of repeat elements in AML, we performed total-RNA sequencing of healthy CD34 + cells and of leukemic blast cells from primary AML patient material. We also developed an integrative bioinformatic approach that can quantify the expression of repeat transcripts from all repeat subclasses (SINE/ALU, LINE, ERV and satellites) in relation to the expression of gene and other non-repeat transcripts (i.e. R/G ratio). This novel approach can be used as an instructive signature for repeat element expression and has been extended to the analysis of poly(A)-RNA sequencing datasets from Blueprint and TCGA consortia that together comprise 120 AML patient samples. RESULTS We identified that repeat element expression is generally down-regulated during hematopoietic differentiation and that relative changes in repeat to gene expression can stratify risk prediction of AML patients and correlate with overall survival probabilities. A high R/G ratio identifies AML patient subgroups with a favorable prognosis, whereas a low R/G ratio is prevalent in AML patient subgroups with a poor prognosis. CONCLUSIONS We developed an integrative bioinformatic approach that defines a general model for the analysis of repeat element dysregulation in physiological and pathological development. We find that changes in repeat to gene expression (i.e. R/G ratios) correlate with hematopoietic differentiation and can sub-stratify AML patients into low-risk and high-risk subgroups. Thus, the definition of a R/G ratio can serve as a valuable biomarker for AML and could also provide insights into differential patient response to epigenetic drug treatment.
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Affiliation(s)
- M Onishi-Seebacher
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Novartis Institute for Biomedical Research (NIBR), Basel, Switzerland
| | - G Erikson
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Z Sawitzki
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, International Max Planck Research School for Molecular and Cellular Biology (IMPRS-MCB) and University of Freiburg, Freiburg, Germany
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - D Ryan
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - G Greve
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - M Lübbert
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany
| | - T Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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56
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Bayat M, Asemani Y, Mohammadi MR, Sanaei M, Namvarpour M, Eftekhari R. An overview of some potential immunotherapeutic options against COVID-19. Int Immunopharmacol 2021; 95:107516. [PMID: 33765610 PMCID: PMC7908848 DOI: 10.1016/j.intimp.2021.107516] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023]
Abstract
After the advent of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) in the late 2019, the resulting severe and pernicious syndrome (COVID-19) immediately was deployed all around the world. To date, despite relentless efforts to control the disease by drug repurposing, there is no approved specific therapy for COVID-19. Given the role of innate and acquired immune components in the control and elimination of viral infections and inflammatory mutilations during SARS-CoV2 pathogenesis, immunotherapeutic strategies appear to be beneficent. Passive immunotherapies such as convalescent plasma, which has received much attention especially in severe cases, as well as suppressing inflammatory cytokines, interferon administration, inhibition of kinases and complement cascade, virus neutralization with key engineered products, cell-based therapies, immunomodulators and anti-inflammatory drugs are among the key immunotherapeutic approaches to deal with COVID-19, which is discussed in this review. Also, details of leading COVID-19 vaccine candidates as the most potent immunotherapy have been provided. However, despite salient improvements, there is still a lack of completely assured vaccines for universal application. Therefore, adopting proper immunotherapies according to the cytokine pattern and involved immune responses, alongside engineered biologics specially ACE2-Fc to curb SARS-CoV2 infection until achieving a tailored vaccine is probably the best strategy to better manage this pandemic. Therefore, gaining knowledge about the mechanism of action, potential targets, as well as the effectiveness of immune-based approaches to confront COVID-19 in the form of a well-ordered review study is highly momentous.
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Affiliation(s)
- Maryam Bayat
- Department of Immunology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yahya Asemani
- Department of Immunology, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Corresponding author at: Department of Immunology, Medical School, Shahid Beheshti University of Medical Sciences, P.O. Box: 1985717443, Tehran, Iran
| | - Mohammad Reza Mohammadi
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahsa Sanaei
- Department of Environmental, Polymer and Organic Chemistry, School of Chemistry, Damghan University, Damghan, Iran
| | - Mozhdeh Namvarpour
- Department of Immunology, Shahid Sadoughi University of Medical Science and services, Yazd, Iran
| | - Reyhaneh Eftekhari
- Department of Microbiology, Faculty of Biology, Semnan University, Semnan, Iran
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57
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Gnan S, Flyamer IM, Klein KN, Castelli E, Rapp A, Maiser A, Chen N, Weber P, Enervald E, Cardoso MC, Bickmore WA, Gilbert DM, Buonomo SCB. Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction. Nat Commun 2021; 12:2910. [PMID: 34006872 PMCID: PMC8131703 DOI: 10.1038/s41467-021-22899-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing programme and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. The role of RIF1 in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing programme and nuclear architecture.
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Affiliation(s)
- Stefano Gnan
- grid.418924.20000 0004 0627 3632Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy ,grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK ,grid.462584.90000 0004 0367 1475Present Address: Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Ilya M. Flyamer
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kyle N. Klein
- grid.255986.50000 0004 0472 0419Department of Biological Science, Florida State University, Tallahassee, FL USA
| | - Eleonora Castelli
- grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Alexander Rapp
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Andreas Maiser
- grid.5252.00000 0004 1936 973XDepartment of Biology II, LMU Munich, Munich, Germany
| | - Naiming Chen
- grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK
| | - Patrick Weber
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Elin Enervald
- grid.418924.20000 0004 0627 3632Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy ,grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK ,grid.10548.380000 0004 1936 9377Present Address: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - M. Cristina Cardoso
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Wendy A. Bickmore
- grid.4305.20000 0004 1936 7988MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David M. Gilbert
- grid.255986.50000 0004 0472 0419Department of Biological Science, Florida State University, Tallahassee, FL USA
| | - Sara C. B. Buonomo
- grid.418924.20000 0004 0627 3632Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL Rome), Monterotondo, Italy ,grid.4305.20000 0004 1936 7988Institute of Cell Biology, School of Biological Sciences University of Edinburgh, Edinburgh, UK
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58
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Ma X, Chen T, Peng Z, Wang Z, Liu J, Yang T, Wu L, Liu G, Zhou M, Tong M, Guan Y, Zhang X, Lin Y, Tang X, Li L, Tang Z, Pan T, Zhang H. Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies. EMBO J 2021; 40:e106632. [PMID: 33739466 PMCID: PMC8126954 DOI: 10.15252/embj.2020106632] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 01/08/2023] Open
Abstract
HIV-1 latency is a major obstacle to achieving a functional cure for AIDS. Reactivation of HIV-1-infected cells followed by their elimination via immune surveillance is one proposed strategy for eradicating the viral reservoir. However, current latency-reversing agents (LRAs) show high toxicity and low efficiency, and new targets are needed to develop more promising LRAs. Here, we found that the histone chaperone CAF-1 (chromatin assembly factor 1) is enriched on the HIV-1 long terminal repeat (LTR) and forms nuclear bodies with liquid-liquid phase separation (LLPS) properties. CAF-1 recruits epigenetic modifiers and histone chaperones to the nuclear bodies to establish and maintain HIV-1 latency in different latency models and primary CD4+ T cells. Three disordered regions of the CHAF1A subunit are important for phase-separated CAF-1 nuclear body formation and play a key role in maintaining HIV-1 latency. Disruption of phase-separated CAF-1 bodies could be a potential strategy to reactivate latent HIV-1.
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Affiliation(s)
- Xiancai Ma
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Chen
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhilin Peng
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ziwen Wang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jun Liu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Yang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Liyang Wu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Guangyan Liu
- College of Basic Medical SciencesShenyang Medical CollegeShenyangLiaoningChina
| | - Mo Zhou
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Muye Tong
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yuanjun Guan
- Core Laboratory Platform for Medical ScienceZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xu Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yingtong Lin
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xiaoping Tang
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Linghua Li
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Zhonghui Tang
- Department of BioinformaticsZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ting Pan
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Hui Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
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Theurillat I, Hendriks IA, Cossec JC, Andrieux A, Nielsen ML, Dejean A. Extensive SUMO Modification of Repressive Chromatin Factors Distinguishes Pluripotent from Somatic Cells. Cell Rep 2021; 32:108146. [PMID: 32937131 PMCID: PMC7495044 DOI: 10.1016/j.celrep.2020.108146] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/22/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022] Open
Abstract
Post-translational modification by SUMO is a key regulator of cell identity. In mouse embryonic fibroblasts (MEFs), SUMO impedes reprogramming to pluripotency, while in embryonic stem cells (ESCs), it represses the emergence of totipotent-like cells, suggesting that SUMO targets distinct substrates to preserve somatic and pluripotent states. Using MS-based proteomics, we show that the composition of endogenous SUMOylomes differs dramatically between MEFs and ESCs. In MEFs, SUMO2/3 targets proteins associated with canonical SUMO functions, such as splicing, and transcriptional regulators driving somatic enhancer selection. In contrast, in ESCs, SUMO2/3 primarily modifies highly interconnected repressive chromatin complexes, thereby preventing chromatin opening and transitioning to totipotent-like states. We also characterize several SUMO-modified pluripotency factors and show that SUMOylation of Dppa2 and Dppa4 impedes the conversion to 2-cell-embryo-like states. Altogether, we propose that rewiring the repertoire of SUMO target networks is a major driver of cell fate decision during embryonic development. Endogenous SUMO2/3 proteomics in ESCs and MEFs uncovers drastic SUMOylome rewiring In ESCs, SUMO2/3 targets densely interconnected repressive chromatin proteins In MEFs, SUMO2/3 targets key determinants of fibroblastic cell identity SUMOylation of Dppa2/4 prevents conversion of ESCs to the 2C-like state
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Affiliation(s)
- Ilan Theurillat
- Nuclear Organization and Oncogenesis Unit, Institut Pasteur, Équipe Labellisée Ligue Nationale Contre le Cancer, 75015 Paris, France; INSERM, U993, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jack-Christophe Cossec
- Nuclear Organization and Oncogenesis Unit, Institut Pasteur, Équipe Labellisée Ligue Nationale Contre le Cancer, 75015 Paris, France; INSERM, U993, 75015 Paris, France
| | - Alexandra Andrieux
- Nuclear Organization and Oncogenesis Unit, Institut Pasteur, Équipe Labellisée Ligue Nationale Contre le Cancer, 75015 Paris, France; INSERM, U993, 75015 Paris, France
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anne Dejean
- Nuclear Organization and Oncogenesis Unit, Institut Pasteur, Équipe Labellisée Ligue Nationale Contre le Cancer, 75015 Paris, France; INSERM, U993, 75015 Paris, France.
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60
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DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation. Nat Commun 2021; 12:2490. [PMID: 33941775 PMCID: PMC8093215 DOI: 10.1038/s41467-021-22665-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation and trimethylated histone H4 Lysine 20 (H4K20me3) constitute two important heterochromatin-enriched marks that frequently cooperate in silencing repetitive elements of the mammalian genome. However, it remains elusive how these two chromatin modifications crosstalk. Here, we report that DNA methyltransferase 1 (DNMT1) specifically ‘recognizes’ H4K20me3 via its first bromo-adjacent-homology domain (DNMT1BAH1). Engagement of DNMT1BAH1-H4K20me3 ensures heterochromatin targeting of DNMT1 and DNA methylation at LINE-1 retrotransposons, and cooperates with the previously reported readout of histone H3 tail modifications (i.e., H3K9me3 and H3 ubiquitylation) by the RFTS domain to allosterically regulate DNMT1’s activity. Interplay between RFTS and BAH1 domains of DNMT1 profoundly impacts DNA methylation at both global and focal levels and genomic resistance to radiation-induced damage. Together, our study establishes a direct link between H4K20me3 and DNA methylation, providing a mechanism in which multivalent recognition of repressive histone modifications by DNMT1 ensures appropriate DNA methylation patterning and genomic stability. How histone modifications crosstalk with DNA methylation to regulate epigenomic patterning and genome stability in mammals remains elusive. Here, the authors show that DNA methyltransferase DNMT1 is a reader for histone H4K20 trimethylation via its BAH1 domain, which leads to optimal maintenance of DNA methylation at repetitive LINE-1 elements.
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61
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Yang F, Huang X, Zang R, Chen J, Fidalgo M, Sanchez-Priego C, Yang J, Caichen A, Ma F, Macfarlan T, Wang H, Gao S, Zhou H, Wang J. DUX-miR-344-ZMYM2-Mediated Activation of MERVL LTRs Induces a Totipotent 2C-like State. Cell Stem Cell 2021; 26:234-250.e7. [PMID: 32032525 DOI: 10.1016/j.stem.2020.01.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 07/31/2019] [Accepted: 12/09/2019] [Indexed: 01/13/2023]
Abstract
Mouse embryonic stem cells (ESCs) sporadically express preimplantation two-cell-stage (2C) transcripts, including MERVL endogenous retrovirus and Zscan4 cluster genes. Such 2C-like cells (2CLCs) can contribute to both embryonic and extraembryonic tissues when reintroduced into early embryos, although the molecular mechanism underlying such an expanded 2CLC potency remains elusive. We examine global nucleosome occupancy and gene expression in 2CLCs and identified miR-344 as the noncoding molecule that positively controls 2CLC potency. We find that activation of endogenous MERVL or miR-344-2 alone is sufficient to induce 2CLCs with activation of 2C genes and an expanded potency. Mechanistically, miR-344 is activated by DUX and post-transcriptionally represses ZMYM2 and its partner LSD1, and ZMYM2 recruits LSD1/HDAC corepressor complex to MERVL LTR for transcriptional repression. Consistently, zygotic depletion of Zmym2 compromises the totipotency-to-pluripotency transition during early development. Our studies establish the previously unappreciated DUX-miR-344-Zmym2/Lsd1 axis that controls MERVL for expanded stem cell potency.
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Affiliation(s)
- Fan Yang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xin Huang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruge Zang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Frontier Science Center for Stem Cell Research, Ministry of Education of China, Tongji University, Shanghai 200092, China
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Frontier Science Center for Stem Cell Research, Ministry of Education of China, Tongji University, Shanghai 200092, China
| | - Miguel Fidalgo
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela 15782, Spain
| | - Carlos Sanchez-Priego
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jihong Yang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Caichen
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fanglin Ma
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Todd Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Huayan Wang
- Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Frontier Science Center for Stem Cell Research, Ministry of Education of China, Tongji University, Shanghai 200092, China.
| | - Hongwei Zhou
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jianlong Wang
- The Black Family Stem Cell Institute and Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Chung JY, Thone MN, Kwon YJ. COVID-19 vaccines: The status and perspectives in delivery points of view. Adv Drug Deliv Rev 2021; 170:1-25. [PMID: 33359141 PMCID: PMC7759095 DOI: 10.1016/j.addr.2020.12.011] [Citation(s) in RCA: 217] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/29/2022]
Abstract
Due to the high prevalence and long incubation periods often without symptoms, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected millions of individuals globally, causing the coronavirus disease 2019 (COVID-19) pandemic. Even with the recent approval of the anti-viral drug, remdesivir, and Emergency Use Authorization of monoclonal antibodies against S protein, bamlanivimab and casirimab/imdevimab, efficient and safe COVID-19 vaccines are still desperately demanded not only to prevent its spread but also to restore social and economic activities via generating mass immunization. Recent Emergency Use Authorization of Pfizer and BioNTech’s mRNA vaccine may provide a pathway forward, but monitoring of long-term immunity is still required, and diverse candidates are still under development. As the knowledge of SARS-CoV-2 pathogenesis and interactions with the immune system continues to evolve, a variety of drug candidates are under investigation and in clinical trials. Potential vaccines and therapeutics against COVID-19 include repurposed drugs, monoclonal antibodies, antiviral and antigenic proteins, peptides, and genetically engineered viruses. This paper reviews the virology and immunology of SARS-CoV-2, alternative therapies for COVID-19 to vaccination, principles and design considerations in COVID-19 vaccine development, and the promises and roles of vaccine carriers in addressing the unique immunopathological challenges presented by the disease.
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63
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Wang Z, Wu R, Nie Q, Bouchonville KJ, Diasio RB, Offer SM. Chromatin assembly factor 1 suppresses epigenetic reprogramming toward adaptive drug resistance. JOURNAL OF THE NATIONAL CANCER CENTER 2021; 1:15-22. [PMID: 39036786 PMCID: PMC11256593 DOI: 10.1016/j.jncc.2020.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022] Open
Abstract
The long-term effectiveness of targeted cancer therapies is limited by the development of resistance. Although epigenetic reprogramming has been implicated in resistance, the mechanisms remain elusive. Herein, we demonstrate that increased chromatin accessibility is involved in adaptive BRAF inhibitor (BRAFi)-resistance in melanoma cells. We observed loss of chromatin assembly factor 1 (CAF-1) and its related histone H3 lysine 9 trimethylation (H3K9me3) with adaptive BRAFi resistance. We further showed that depletion of CAF-1 provides chromatin plasticity for effective reprogramming by AP1 components to promote BRAFi resistance. Our data suggest that therapeutic approaches to restore H3K9me3 levels may compensate for the loss of CAF-1 and, in turn, suppress resistance to BRAF inhibitors.
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Affiliation(s)
- Zhiquan Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Rentian Wu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Nie
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Kelly J. Bouchonville
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Robert B. Diasio
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Mayo Clinic Cancer Center, Rochester, MN 55905, USA
| | - Steven M. Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic College of Medicine, Rochester, MN 55905, USA
- Mayo Clinic Cancer Center, Rochester, MN 55905, USA
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64
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Sun L, Fu X, Ma G, Hutchins AP. Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions. Front Cell Dev Biol 2021; 9:637309. [PMID: 33681220 PMCID: PMC7930395 DOI: 10.3389/fcell.2021.637309] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
A major event in embryonic development is the rearrangement of epigenetic information as the somatic genome is reprogrammed for a new round of organismal development. Epigenetic data are held in chemical modifications on DNA and histones, and there are dramatic and dynamic changes in these marks during embryogenesis. However, the mechanisms behind this intricate process and how it is regulating and responding to embryonic development remain unclear. As embryos develop from totipotency to pluripotency, they pass through several distinct stages that can be captured permanently or transiently in vitro. Pluripotent naïve cells resemble the early epiblast, primed cells resemble the late epiblast, and blastomere-like cells have been isolated, although fully totipotent cells remain elusive. Experiments using these in vitro model systems have led to insights into chromatin changes in embryonic development, which has informed exploration of pre-implantation embryos. Intriguingly, human and mouse cells rely on different signaling and epigenetic pathways, and it remains a mystery why this variation exists. In this review, we will summarize the chromatin rearrangements in early embryonic development, drawing from genomic data from in vitro cell lines, and human and mouse embryos.
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Affiliation(s)
| | | | | | - Andrew P. Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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65
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Boulanger M, Chakraborty M, Tempé D, Piechaczyk M, Bossis G. SUMO and Transcriptional Regulation: The Lessons of Large-Scale Proteomic, Modifomic and Genomic Studies. Molecules 2021; 26:molecules26040828. [PMID: 33562565 PMCID: PMC7915335 DOI: 10.3390/molecules26040828] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
One major role of the eukaryotic peptidic post-translational modifier SUMO in the cell is transcriptional control. This occurs via modification of virtually all classes of transcriptional actors, which include transcription factors, transcriptional coregulators, diverse chromatin components, as well as Pol I-, Pol II- and Pol III transcriptional machineries and their regulators. For many years, the role of SUMOylation has essentially been studied on individual proteins, or small groups of proteins, principally dealing with Pol II-mediated transcription. This provided only a fragmentary view of how SUMOylation controls transcription. The recent advent of large-scale proteomic, modifomic and genomic studies has however considerably refined our perception of the part played by SUMO in gene expression control. We review here these developments and the new concepts they are at the origin of, together with the limitations of our knowledge. How they illuminate the SUMO-dependent transcriptional mechanisms that have been characterized thus far and how they impact our view of SUMO-dependent chromatin organization are also considered.
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Affiliation(s)
- Mathias Boulanger
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Mehuli Chakraborty
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Denis Tempé
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marc Piechaczyk
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
| | - Guillaume Bossis
- Institut de Génétique Moléculaire de Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France; (M.B.); (M.C.); (D.T.)
- Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Correspondence: (M.P.); (G.B.)
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66
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Nsd2 Represses Endogenous Retrovirus MERVL in Embryonic Stem Cells. Stem Cells Int 2021; 2021:6663960. [PMID: 33531910 PMCID: PMC7834818 DOI: 10.1155/2021/6663960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
The facilitates chromatin transcription (FACT) complex is a histone H2A/H2B chaperone, which represses endogenous retroviruses (ERVs) and transcription of ERV-chimeric transcripts. It binds to both transcription start site and gene body region. Here, we investigated the downstream targets of FACT complex to identify the potential regulators of MERVL, which is a key 2-cell marker gene. H3K36me2 profile was positively correlated with that of FACT component Ssrp1. Among H3K36me2 deposition enzymes, Nsd2 was downregulated after the loss of Ssrp1. Furthermore, we demonstrated that Nsd2 repressed the expression of ERVs without affecting the expression of pluripotency genes. The expression of MERVL and 2-cell genes was partially rescued by Nsd2 overexpression. The enrichment of H3K36me2 decreased on MERVL-chimeric gene in ESCs without Ssrp1. Our study discovers that Nsd2 is a repressor of MERVL, and FACT partially represses MERVL expression by regulating the expression of Nsd2 and its downstream H3K36me2.
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Czerwinska P, Jaworska AM, Wlodarczyk NA, Mackiewicz AA. Melanoma Stem Cell-Like Phenotype and Significant Suppression of Immune Response within a Tumor Are Regulated by TRIM28 Protein. Cancers (Basel) 2020; 12:E2998. [PMID: 33076560 PMCID: PMC7650661 DOI: 10.3390/cancers12102998] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022] Open
Abstract
TRIM28 emerged as a guard of the intrinsic "state of cell differentiation", facilitating self-renewal of pluripotent stem cells. Recent reports imply TRIM28 engagement in cancer stem cell (CSC) maintenance, although the exact mechanism remains unresolved. TRIM28 high expression is associated with worse melanoma patient outcomes. Here, we investigated the association between TRIM28 level and melanoma stemness, and aligned it with the antitumor immune response to find the mechanism of "stemness high/immune low" melanoma phenotype acquisition. Based on the SKCM TCGA data, the TRIM28 expression profile, clinicopathological features, expression of correlated genes, and the level of stemness and immune scores were analyzed in patient samples. The biological function for differentially expressed genes was annotated with GSEA. Results were validated with additional datasets from R2: Genomics Analysis and Visualization Platform and in vitro with a panel of seven melanoma cell lines. All statistical analyses were accomplished using GraphPad Prism 8. TRIM28HIGH-expressing melanoma patients are characterized by worse outcomes and significantly different gene expression profiles than the TRIM28NORM cohort. TRIM28 high level related to higher melanoma stemness as measured with several distinct scores and TRIM28HIGH-expressing melanoma cell lines possess the greater potential of melanosphere formation. Moreover, TRIM28HIGH melanoma tumors were significantly depleted with infiltrating immune cells, especially cytotoxic T cells, helper T cells, and B cells. Furthermore, TRIM28 emerged as a good predictor of "stemness high/immune low" melanoma phenotype. Our data indicate that TRIM28 might facilitate this phenotype by direct repression of interferon signaling. TRIM28 emerged as a direct link between stem cell-like phenotype and attenuated antitumor immune response in melanoma, although further studies are needed to evaluate the direct mechanism of TRIM28-mediated stem-like phenotype acquisition.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (A.M.J.); (N.A.W.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Anna Maria Jaworska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (A.M.J.); (N.A.W.)
| | - Nikola Agata Wlodarczyk
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (A.M.J.); (N.A.W.)
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 15 Garbary St., 61-866 Poznan, Poland; (A.M.J.); (N.A.W.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
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68
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Olson A, Basukala B, Lee S, Gagne M, Wong WW, Henderson AJ. Targeted Chromatinization and Repression of HIV-1 Provirus Transcription with Repurposed CRISPR/Cas9. Viruses 2020; 12:E1154. [PMID: 33053801 PMCID: PMC7600714 DOI: 10.3390/v12101154] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
The major barrier to HIV-1 cure is the persistence of latent provirus, which is not eradicated by antiretroviral therapy. The "shock and kill" approach entails stimulating viral production with latency-reversing agents followed by the killing of cells actively producing the virus by immune clearance. However, this approach does not induce all intact proviruses, leaving a residual reservoir. CRISPR/Cas9 has been utilized to excise integrated Human Immunodeficiency Virus (HIV) DNA from infected cells in an RNA-guided, sequence-specific manner. Here, we seek to epigenetically silence the proviral DNA by introducing nuclease-deficient disabled Cas9 (dCas9) coupled with a transcriptional repressor domain derived from Kruppel-associated box (KRAB). We show that specific guide RNAs (gRNAs) and dCas9-KRAB repress HIV-1 transcription and reactivation of latent HIV-1 provirus. This repression is correlated with chromatin changes, including decreased H3 histone acetylation and increased histone H3 lysine 9 trimethylation, histone marks that are associated with transcriptional repression. dCas9-KRAB-mediated inhibition of HIV-1 transcription suggests that CRISPR can be engineered as a tool for block-and-lock strategies.
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Affiliation(s)
- Alex Olson
- Department of Medicine and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; (A.O.); (M.G.)
| | - Binita Basukala
- Department of Biology, Boston University, Boston, MA 02215, USA;
| | - Seunghee Lee
- Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA; (S.L.); (W.W.W.)
| | - Matthew Gagne
- Department of Medicine and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; (A.O.); (M.G.)
| | - Wilson W. Wong
- Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA; (S.L.); (W.W.W.)
| | - Andrew J. Henderson
- Department of Medicine and Microbiology, Boston University School of Medicine, Boston, MA 02118, USA; (A.O.); (M.G.)
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Chen F, Zhang W, Xie D, Gao T, Dong Z, Lu X. Histone chaperone FACT represses retrotransposon MERVL and MERVL-derived cryptic promoters. Nucleic Acids Res 2020; 48:10211-10225. [PMID: 32894293 PMCID: PMC7544220 DOI: 10.1093/nar/gkaa732] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Endogenous retroviruses (ERVs) were usually silenced by various histone modifications on histone H3 variants and respective histone chaperones in embryonic stem cells (ESCs). However, it is still unknown whether chaperones of other histones could repress ERVs. Here, we show that H2A/H2B histone chaperone FACT plays a critical role in silencing ERVs and ERV-derived cryptic promoters in ESCs. Loss of FACT component Ssrp1 activated MERVL whereas the re-introduction of Ssrp1 rescued the phenotype. Additionally, Ssrp1 interacted with MERVL and suppressed cryptic transcription of MERVL-fused genes. Remarkably, Ssrp1 interacted with and recruited H2B deubiquitinase Usp7 to Ssrp1 target genes. Suppression of Usp7 caused similar phenotypes as loss of Ssrp1. Furthermore, Usp7 acted by deubiquitinating H2Bub and thereby repressed the expression of MERVL-fused genes. Taken together, our study uncovers a unique mechanism by which FACT complex silences ERVs and ERV-derived cryptic promoters in ESCs.
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Affiliation(s)
- Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Dan Xie
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Tingting Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Zhiqiang Dong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Life Sciences, Nankai University, Tianjin 300307, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
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70
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Trim24 and Trim33 Play a Role in Epigenetic Silencing of Retroviruses in Embryonic Stem Cells. Viruses 2020; 12:v12091015. [PMID: 32932986 PMCID: PMC7551373 DOI: 10.3390/v12091015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Embryonic stem cells (ESC) have the ability to epigenetically silence endogenous and exogenous retroviral sequences. Trim28 plays an important role in establishing this silencing, but less is known about the role other Trim proteins play. The Tif1 family is a sub-group of the Trim family, which possess histone binding ability in addition to the distinctive RING domain. Here, we have examined the interaction between three Tif1 family members, namely Trim24, Trim28 and Trim33, and their function in retroviral silencing. We identify a complex formed in ESC, comprised of these three proteins. We further show that when Trim33 is depleted, the complex collapses and silencing efficiency of both endogenous and exogenous sequences is reduced. Similar transcriptional activation takes place when Trim24 is depleted. Analysis of the H3K9me3 chromatin modification showed a decrease in this repressive mark, following both Trim24 and Trim33 depletion. As Trim28 is an identified binding partner of the H3K9 methyltransferase ESET, this further supports the involvement of Trim28 in the complex. The results presented here suggest that a complex of Tif1 family members, each of which possesses different specificity and efficiency, contributes to the silencing of retroviral sequences in ESC.
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71
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TRIM28 functions as the SUMO E3 ligase for PCNA in prevention of transcription induced DNA breaks. Proc Natl Acad Sci U S A 2020; 117:23588-23596. [PMID: 32900933 DOI: 10.1073/pnas.2004122117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In human cells, the DNA replication factor proliferating cell nuclear antigen (PCNA) can be conjugated to either the small ubiquitinlike modifier SUMO1 or SUMO2, but only SUMO2-conjugated PCNA is induced by transcription to facilitate resolution of transcription-replication conflict (TRC). To date, the SUMO E3 ligase that provides substrate specificity for SUMO2-PCNA conjugation in response to TRC remains unknown. Using a proteomic approach, we identified TRIM28 as the E3 ligase that catalyzes SUMO2-PCNA conjugation. In vitro, TRIM28, together with the RNA polymerase II (RNAPII)-interacting protein RECQ5, promotes SUMO2-PCNA conjugation but inhibits SUMO1-PCNA formation. This activity requires a PCNA-interacting protein (PIP) motif located within the bromodomain of TRIM28. In cells, TRIM28 interaction with PCNA on human chromatin is dependent on both transcription and RECQ5, and SUMO2-PCNA level correlates with TRIM28 expression. As a consequence, TRIM28 depletion led to RNAPII accumulation at TRC sites, and expression of a TRIM28 PIP mutant failed to suppress TRC-induced DNA breaks.
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72
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Xing QR, El Farran CA, Gautam P, Chuah YS, Warrier T, Toh CXD, Kang NY, Sugii S, Chang YT, Xu J, Collins JJ, Daley GQ, Li H, Zhang LF, Loh YH. Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing. SCIENCE ADVANCES 2020; 6:eaba1190. [PMID: 32917699 PMCID: PMC7486102 DOI: 10.1126/sciadv.aba1190] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/30/2020] [Indexed: 05/16/2023]
Abstract
Cellular reprogramming suffers from low efficiency especially for the human cells. To deconstruct the heterogeneity and unravel the mechanisms for successful reprogramming, we adopted single-cell RNA sequencing (scRNA-Seq) and single-cell assay for transposase-accessible chromatin (scATAC-Seq) to profile reprogramming cells across various time points. Our analysis revealed that reprogramming cells proceed in an asynchronous trajectory and diversify into heterogeneous subpopulations. We identified fluorescent probes and surface markers to enrich for the early reprogrammed human cells. Furthermore, combinatory usage of the surface markers enabled the fine segregation of the early-intermediate cells with diverse reprogramming propensities. scATAC-Seq analysis further uncovered the genomic partitions and transcription factors responsible for the regulatory phasing of reprogramming process. Binary choice between a FOSL1 and a TEAD4-centric regulatory network determines the outcome of a successful reprogramming. Together, our study illuminates the multitude of diverse routes transversed by individual reprogramming cells and presents an integrative roadmap for identifying the mechanistic part list of the reprogramming machinery.
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Affiliation(s)
- Q R Xing
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chadi A El Farran
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Pradeep Gautam
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Yu Song Chuah
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Tushar Warrier
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Cheng-Xu Delon Toh
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Nam-Young Kang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, Singapore 138667, Singapore
- Department of Creative IT Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Shigeki Sugii
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore 138669, Singapore
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Young-Tae Chang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, A*STAR, Singapore 138667, Singapore
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang 37673, Republic of Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - James J Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Division of Pediatric Hematology and Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
- Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.
| | - Li-Feng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Yuin-Han Loh
- Epigenetics and Cell Fates Laboratory, Programme in Stem Cell, Regenerative Medicine and Aging, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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73
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Affiliation(s)
- Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA, USA.
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74
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Geis FK, Goff SP. Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview. Viruses 2020; 12:v12080884. [PMID: 32823517 PMCID: PMC7472088 DOI: 10.3390/v12080884] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution. ERVs can provide new regulatory gene elements or novel binding sites for transcription factors, and ERV gene products can even be repurposed for the benefit of the host.
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Affiliation(s)
- Franziska K. Geis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Stephen P. Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
- Correspondence: ; Tel.: +1-212-305-3794
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75
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Li Z, Hua X, Serra-Cardona A, Xu X, Gan S, Zhou H, Yang WS, Chen CL, Xu RM, Zhang Z. DNA polymerase α interacts with H3-H4 and facilitates the transfer of parental histones to lagging strands. SCIENCE ADVANCES 2020; 6:eabb5820. [PMID: 32923642 PMCID: PMC7449674 DOI: 10.1126/sciadv.abb5820] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/14/2020] [Indexed: 05/03/2023]
Abstract
How parental histones, the carriers of epigenetic modifications, are deposited onto replicating DNA remains poorly understood. Here, we describe the eSPAN method (enrichment and sequencing of protein-associated nascent DNA) in mouse embryonic stem (ES) cells and use it to detect histone deposition onto replicating DNA strands with a relatively small number of cells. We show that DNA polymerase α (Pol α), which synthesizes short primers for DNA synthesis, binds histone H3-H4 preferentially. A Pol α mutant defective in histone binding in vitro impairs the transfer of parental H3-H4 to lagging strands in both yeast and mouse ES cells. Last, dysregulation of both coding genes and noncoding endogenous retroviruses is detected in mutant ES cells defective in parental histone transfer. Together, we report an efficient eSPAN method for analysis of DNA replication-linked processes in mouse ES cells and reveal the mechanism of Pol α in parental histone transfer.
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Affiliation(s)
- Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xiaowei Xu
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Songlin Gan
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zhou
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Wen-Si Yang
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-long Chen
- Curie Institute, PSL Research University, CNRS UMR 3244, F-75005, Paris, France
- Sorbonne University, F-75005 Paris, France
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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76
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Zhong J, Tang J, Ye C, Dong L. The immunology of COVID-19: is immune modulation an option for treatment? THE LANCET. RHEUMATOLOGY 2020; 2:e428-e436. [PMID: 32835246 PMCID: PMC7239618 DOI: 10.1016/s2665-9913(20)30120-x] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In December, 2019, an outbreak of COVID-19 emerged in Wuhan, China and quickly spread globally. As of May 7, 2020, there were 3 672 238 confirmed infections and 254 045 deaths attributed to COVID-19. Evidence has shown that there are asymptomatic carriers of COVID-19 who can transmit the disease to others. The virus incubation time shows a wide range (0-24 days) and the virus displays a high infectivity. It is therefore urgent to develop an effective therapy to treat patients with COVID-19 and to control the spread of the causative agent, severe respiratory syndrome coronavirus 2. Repurposing of approved drugs is widely adopted to fight newly emerged diseases such as COVID-19, as these drugs have known pharmacokinetic and safety profiles. As pathological examination has confirmed the involvement of immune hyperactivation and acute respiratory distress syndrome in fatal cases of COVID-19, several disease-modifying anti-rheumatic drugs (DMARDS), such as hydroxychloroquine and tocilizumab, have been proposed as potential therapies for the treatment of COVID-19. In this Review, we discuss the immunological aspects of COVID-19 and the potential implication of DMARDs in treating this disease.
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Affiliation(s)
- Jixin Zhong
- Department of Rheumatology and Immunology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jungen Tang
- Department of Rheumatology and Immunology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Cong Ye
- Department of Rheumatology and Immunology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lingli Dong
- Department of Rheumatology and Immunology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, China
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77
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Cheng L, Zhang X, Wang Y, Gan H, Xu X, Lv X, Hua X, Que J, Ordog T, Zhang Z. Chromatin Assembly Factor 1 (CAF-1) facilitates the establishment of facultative heterochromatin during pluripotency exit. Nucleic Acids Res 2020; 47:11114-11131. [PMID: 31586391 PMCID: PMC6868363 DOI: 10.1093/nar/gkz858] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 11/24/2022] Open
Abstract
Establishment and subsequent maintenance of distinct chromatin domains during embryonic stem cell (ESC) differentiation are crucial for lineage specification and cell fate determination. Here we show that the histone chaperone Chromatin Assembly Factor 1 (CAF-1), which is recruited to DNA replication forks through its interaction with proliferating cell nuclear antigen (PCNA) for nucleosome assembly, participates in the establishment of H3K27me3-mediated silencing during differentiation. Deletion of CAF-1 p150 subunit impairs the silencing of many genes including Oct4, Sox2 and Nanog as well as the establishment of H3K27me3 at these gene promoters during ESC differentiation. Mutations of PCNA residues involved in recruiting CAF-1 to the chromatin also result in defects in differentiation in vitro and impair early embryonic development as p150 deletion. Together, these results reveal that the CAF-1-PCNA nucleosome assembly pathway plays an important role in the establishment of H3K27me3-mediated silencing during cell fate determination.
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Affiliation(s)
- Liang Cheng
- Biochemistry and Molecular Biology Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55902, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Xu Zhang
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Yan Wang
- Biochemistry and Molecular Biology Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55902, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Haiyun Gan
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xiaowei Xu
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xiangdong Lv
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Jianwen Que
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
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78
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Fukuda K, Shinkai Y. SETDB1-Mediated Silencing of Retroelements. Viruses 2020; 12:E596. [PMID: 32486217 PMCID: PMC7354471 DOI: 10.3390/v12060596] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) is a protein lysine methyltransferase and methylates histone H3 at lysine 9 (H3K9). Among other H3K9 methyltransferases, SETDB1 and SETDB1-mediated H3K9 trimethylation (H3K9me3) play pivotal roles for silencing of endogenous and exogenous retroelements, thus contributing to genome stability against retroelement transposition. Furthermore, SETDB1 is highly upregulated in various tumor cells. In this article, we describe recent advances about how SETDB1 activity is regulated, how SETDB1 represses various types of retroelements such as L1 and class I, II, and III endogenous retroviruses (ERVs) in concert with other epigenetic factors such as KAP1 and the HUSH complex and how SETDB1-mediated H3K9 methylation can be maintained during replication.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Japan
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79
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Singh PB, Newman AG. On the relations of phase separation and Hi-C maps to epigenetics. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191976. [PMID: 32257349 PMCID: PMC7062049 DOI: 10.1098/rsos.191976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
The relationship between compartmentalization of the genome and epigenetics is long and hoary. In 1928, Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller's discovery of position-effect variegation in 1930 went on to show that heterochromatin is a cytologically visible state of heritable (epigenetic) gene repression. Current insights into compartmentalization have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalization seen in Hi-C maps is owing to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5 Mb) heterochromatin-like domains and smaller (less than 100 kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes contributes to polymer-polymer phase separation that packages epigenetically heritable chromatin states during interphase. Contacts mediated by HP1 'bridging' are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic subcompartment that emerges from contacts between large KRAB-ZNF heterochromatin-like domains. Further, mutational analyses have revealed a finer, innate, compartmentalization in Hi-C experiments that probably reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres-where the HP1-H3K9me2/3 interaction represents the most evolutionarily conserved paradigm-could drive and generate the fundamental compartmentalization of the interphase nucleus. This has implications for the mechanism(s) that maintains cellular identity, be it a terminally differentiated fibroblast or a pluripotent embryonic stem cell.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, 5/1 Kerei, Zhanibek Khandar Street, Nur-Sultan Z05K4F4, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Street 2, Novosibirsk 630090, Russian Federation
| | - Andrew G. Newman
- Institute of Cell and Neurobiology, Charité—Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
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80
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Tian Q, Wang XF, Xie SM, Yin Y, Zhou LQ. H3.3 impedes zygotic transcriptional program activated by Dux. Biochem Biophys Res Commun 2020; 522:422-427. [DOI: 10.1016/j.bbrc.2019.11.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
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81
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The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation. Mol Cell 2019; 77:571-585.e4. [PMID: 31901448 DOI: 10.1016/j.molcel.2019.09.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/11/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
Сhromatin is critical for genome compaction and gene expression. On a coarse scale, the genome is divided into euchromatin, which harbors the majority of genes and is enriched in active chromatin marks, and heterochromatin, which is gene-poor but repeat-rich. The conserved molecular hallmark of heterochromatin is the H3K9me3 modification, which is associated with gene silencing. We found that in Drosophila, deposition of most of the H3K9me3 mark depends on SUMO and the SUMO ligase Su(var)2-10, which recruits the histone methyltransferase complex SetDB1/Wde. In addition to repressing repeats, H3K9me3 influences expression of both hetero- and euchromatic host genes. High H3K9me3 levels in heterochromatin are required to suppress spurious transcription and ensure proper gene expression. In euchromatin, a set of conserved genes is repressed by Su(var)2-10/SetDB1-induced H3K9 trimethylation, ensuring tissue-specific gene expression. Several components of heterochromatin are themselves repressed by this pathway, providing a negative feedback mechanism to ensure chromatin homeostasis.
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82
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Zhang W, Chen F, Chen R, Xie D, Yang J, Zhao X, Guo R, Zhang Y, Shen Y, Göke J, Liu L, Lu X. Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes. Nucleic Acids Res 2019; 47:8485-8501. [PMID: 31304534 PMCID: PMC7145578 DOI: 10.1093/nar/gkz594] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 01/09/2023] Open
Abstract
Endogenous retroviruses (ERVs) contribute to ∼10 percent of the mouse genome. They are often silenced in differentiated somatic cells but differentially expressed at various embryonic developmental stages. A minority of mouse embryonic stem cells (ESCs), like 2-cell cleavage embryos, highly express ERV MERVL. However, the role of ERVs and mechanism of their activation in these cells are still poorly understood. In this study, we investigated the regulation and function of the stage-specific expressed ERVs, with a particular focus on the totipotency marker MT2/MERVL. We show that the transcription factor Zscan4c functions as an activator of MT2/MERVL and 2-cell/4-cell embryo genes. Zinc finger domains of Zscan4c play an important role in this process. In addition, Zscan4c interacts with MT2 and regulates MT2-nearby 2-cell/4-cell genes through promoting enhancer activity of MT2. Furthermore, MT2 activation is accompanied by enhanced H3K4me1, H3K27ac, and H3K14ac deposition on MT2. Zscan4c also interacts with GBAF chromatin remodelling complex through SCAN domain to further activate MT2 enhancer activity. Taken together, we delineate a previously unrecognized regulatory axis that Zscan4c interacts with and activates MT2/MERVL loci and their nearby genes through epigenetic regulation.
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Affiliation(s)
- Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Ruiqing Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Dan Xie
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Jiao Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Renpeng Guo
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Yongwang Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Yang Shen
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Life Sciences, Nankai University, Tianjin 300071, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China.,College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
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83
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Brumbaugh J, Di Stefano B, Hochedlinger K. Reprogramming: identifying the mechanisms that safeguard cell identity. Development 2019; 146:146/23/dev182170. [PMID: 31792064 DOI: 10.1242/dev.182170] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development and homeostasis rely upon concerted regulatory pathways to establish the specialized cell types needed for tissue function. Once a cell type is specified, the processes that restrict and maintain cell fate are equally important in ensuring tissue integrity. Over the past decade, several approaches to experimentally reprogram cell fate have emerged. Importantly, efforts to improve and understand these approaches have uncovered novel molecular determinants that reinforce lineage commitment and help resist cell fate changes. In this Review, we summarize recent studies that have provided insights into the various chromatin factors, post-transcriptional processes and features of genomic organization that safeguard cell identity in the context of reprogramming to pluripotency. We also highlight how these factors function in other experimental, physiological and pathological cell fate transitions, including direct lineage conversion, pluripotency-to-totipotency reversion and cancer.
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Affiliation(s)
- Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA .,Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
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84
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Velychko S, Adachi K, Kim KP, Hou Y, MacCarthy CM, Wu G, Schöler HR. Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs. Cell Stem Cell 2019; 25:737-753.e4. [PMID: 31708402 PMCID: PMC6900749 DOI: 10.1016/j.stem.2019.10.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/23/2019] [Accepted: 10/04/2019] [Indexed: 02/01/2023]
Abstract
Oct4 is widely considered the most important among the four Yamanaka reprogramming factors. Here, we show that the combination of Sox2, Klf4, and cMyc (SKM) suffices for reprogramming mouse somatic cells to induced pluripotent stem cells (iPSCs). Simultaneous induction of Sox2 and cMyc in fibroblasts triggers immediate retroviral silencing, which explains the discrepancy with previous studies that attempted but failed to generate iPSCs without Oct4 using retroviral vectors. SKM induction could partially activate the pluripotency network, even in Oct4-knockout fibroblasts. Importantly, reprogramming in the absence of exogenous Oct4 results in greatly improved developmental potential of iPSCs, determined by their ability to give rise to all-iPSC mice in the tetraploid complementation assay. Our data suggest that overexpression of Oct4 during reprogramming leads to off-target gene activation during reprogramming and epigenetic aberrations in resulting iPSCs and thereby bear major implications for further development and application of iPSC technology. SKM can induce pluripotency in somatic cells in the absence of exogenous Oct4 SM coexpression activates the retroviral silencing machinery in somatic cells Oct4 overexpression drives massive off-target gene activation during reprogramming OSKM, but not SKM, iPSCs show abnormal imprinting and differentiation patterns
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Affiliation(s)
- Sergiy Velychko
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Kenjiro Adachi
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Kee-Pyo Kim
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Yanlin Hou
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Caitlin M MacCarthy
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Guangming Wu
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, 6 Luoxuan Avenue, Haizhu District, 510320 Guangzhou, PRC.
| | - Hans R Schöler
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany; Medical Faculty, University of Münster, Domagkstrasse 3, 48449 Münster, Germany.
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85
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Bui PL, Nishimura K, Seminario Mondejar G, Kumar A, Aizawa S, Murano K, Nagata K, Hayashi Y, Fukuda A, Onuma Y, Ito Y, Nakanishi M, Hisatake K. Template Activating Factor-I α Regulates Retroviral Silencing during Reprogramming. Cell Rep 2019; 29:1909-1922.e5. [DOI: 10.1016/j.celrep.2019.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/02/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023] Open
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86
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Ninova M, Fejes Tóth K, Aravin AA. The control of gene expression and cell identity by H3K9 trimethylation. Development 2019; 146:dev181180. [PMID: 31540910 PMCID: PMC6803365 DOI: 10.1242/dev.181180] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Histone 3 lysine 9 trimethylation (H3K9me3) is a conserved histone modification that is best known for its role in constitutive heterochromatin formation and the repression of repetitive DNA elements. More recently, it has become evident that H3K9me3 is also deposited at certain loci in a tissue-specific manner and plays important roles in regulating cell identity. Notably, H3K9me3 can repress genes encoding silencing factors, pointing to a fundamental principle of repressive chromatin auto-regulation. Interestingly, recent studies have shown that H3K9me3 deposition requires protein SUMOylation in different contexts, suggesting that the SUMO pathway functions as an important module in gene silencing and heterochromatin formation. In this Review, we discuss the role of H3K9me3 in gene regulation in various systems and the molecular mechanisms that guide the silencing machinery to target loci.
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Affiliation(s)
- Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 East California Boulevard, Pasadena, CA 91125, USA
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87
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Yilmaz V, Strati K. Regulating cellular plasticity to persist: a way for tumor viruses to triumph. Curr Opin Virol 2019; 39:1-7. [PMID: 31302443 DOI: 10.1016/j.coviro.2019.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Vural Yilmaz
- University of Cyprus, Department of Biological Sciences, 1 University Avenue, 2109, Nicosia, Cyprus
| | - Katerina Strati
- University of Cyprus, Department of Biological Sciences, 1 University Avenue, 2109, Nicosia, Cyprus.
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88
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Campbell AE, Belleville AE, Resnick R, Shadle SC, Tapscott SJ. Facioscapulohumeral dystrophy: activating an early embryonic transcriptional program in human skeletal muscle. Hum Mol Genet 2019; 27:R153-R162. [PMID: 29718206 DOI: 10.1093/hmg/ddy162] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 04/27/2018] [Indexed: 12/12/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is the third most prevalent muscular dystrophy. A progressive disease, it presents clinically as weakness and wasting of the face, shoulder and upper arm muscles, with later involvement of the trunk and lower extremities. FSHD develops through complex genetic and epigenetic events that converge on a common mechanism of toxicity with mis-expression of the transcription factor double homeobox 4 (DUX4). There is currently no treatment available for FSHD. However, the consensus that ectopic DUX4 expression in skeletal muscle is the root cause of FSHD pathophysiology has allowed research efforts to turn toward cultivating a deeper understanding of DUX4 biology and the pathways that underlie FSHD muscle pathology, and to translational studies aimed at developing targeted therapeutics using ever more sophisticated cell and animal-based models of FSHD. This review summarizes recent advances in our understanding of FSHD, including the regulation and activity of DUX4 in its normal developmental roles as well as its pathological contexts. We highlight how these advances raise new questions and challenges for the field as it moves into the next decade of FSHD research.
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Affiliation(s)
- Amy E Campbell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrea E Belleville
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rebecca Resnick
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Sean C Shadle
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
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89
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Yan YL, Zhang C, Hao J, Wang XL, Ming J, Mi L, Na J, Hu X, Wang Y. DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program. PLoS Biol 2019; 17:e3000324. [PMID: 31226106 PMCID: PMC6608977 DOI: 10.1371/journal.pbio.3000324] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 07/03/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022] Open
Abstract
The molecular mechanism controlling the zygotic genome activation (ZGA) in mammals remains poorly understood. The 2-cell (2C)-like cells spontaneously emerging from cultures of mouse embryonic stem cells (ESCs) share some key transcriptional and epigenetic programs with 2C-stage embryos. By studying the transition of ESCs into 2C-like cells, we identified developmental pluripotency associated 2 and 4 (Dppa2/4) as important regulators controlling zygotic transcriptional program through directly up-regulating the expression of double homeobox (Dux). In addition, we found that DPPA2 protein is sumoylated and its activity is negatively regulated by small ubiquitin-like modifier (Sumo) E3 ligase protein inhibitor of activated STAT 4 (PIAS4). PIAS4 is down-regulated during ZGA process and during transitioning of ESCs into 2C-like cells. Depleting Pias4 or overexpressing Dppa2/4 is sufficient to activate 2C-like transcriptional program, whereas depleting Dppa2/4 or forced expression of Pias4 or Sumo2-Dppa2 inhibits 2C-like transcriptional program. Furthermore, ectopic expression of Pias4 or Sumo2-Dppa2 impairs early mouse embryo development. In summary, our study identifies key molecular rivals consisting of transcription factors and a Sumo2 E3 ligase that regulate zygotic transcriptional program upstream of Dux.
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Affiliation(s)
- Yao-Long Yan
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chao Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jing Hao
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xue-Lian Wang
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jia Ming
- School of Medicine, Tsinghua University, Beijing, China
| | - Li Mi
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Na
- School of Medicine, Tsinghua University, Beijing, China
| | - Xinli Hu
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yangming Wang
- Institute of Molecular Medicine, Peking University, Beijing, China
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90
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Nicetto D, Zaret KS. Role of H3K9me3 heterochromatin in cell identity establishment and maintenance. Curr Opin Genet Dev 2019; 55:1-10. [PMID: 31103921 DOI: 10.1016/j.gde.2019.04.013] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/18/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023]
Abstract
Compacted, transcriptionally repressed chromatin, referred to as heterochromatin, represents a major fraction of the higher eukaryotic genome and exerts pivotal functions of silencing repetitive elements, maintenance of genome stability, and control of gene expression. Among the different histone post-translational modifications (PTMs) associated with heterochromatin, tri-methylation of lysine 9 on histone H3 (H3K9me3) is gaining increased attention. Besides its known role in repressing repetitive elements and non-coding portions of the genome, recent observations indicate H3K9me3 as an important player in silencing lineage-inappropriate genes. The ability of H3K9me3 to influence cell identity challenges the original concept of H3K9me3-marked heterochromatin as mainly a constitutive type of chromatin and provides a further level of understanding of how to modulate cell fate control. Here, we summarize the role of H3K9me3 marked heterochromatin and its dynamics in establishing and maintaining cellular identity.
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Affiliation(s)
- Dario Nicetto
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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91
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Cancer stemness, intratumoral heterogeneity, and immune response across cancers. Proc Natl Acad Sci U S A 2019; 116:9020-9029. [PMID: 30996127 DOI: 10.1073/pnas.1818210116] [Citation(s) in RCA: 321] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Regulatory programs that control the function of stem cells are active in cancer and confer properties that promote progression and therapy resistance. However, the impact of a stem cell-like tumor phenotype ("stemness") on the immunological properties of cancer has not been systematically explored. Using gene-expression-based metrics, we evaluated the association of stemness with immune cell infiltration and genomic, transcriptomic, and clinical parameters across 21 solid cancers. We found pervasive negative associations between cancer stemness and anticancer immunity. This occurred despite high stemness cancers exhibiting increased mutation load, cancer-testis antigen expression, and intratumoral heterogeneity. Stemness was also strongly associated with cell-intrinsic suppression of endogenous retroviruses and type I IFN signaling, and increased expression of multiple therapeutically accessible immunosuppressive pathways. Thus, stemness is not only a fundamental process in cancer progression but may provide a mechanistic link between antigenicity, intratumoral heterogeneity, and immune suppression across cancers.
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92
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Ng C, Aichinger M, Nguyen T, Au C, Najar T, Wu L, Mesa KR, Liao W, Quivy JP, Hubert B, Almouzni G, Zuber J, Littman DR. The histone chaperone CAF-1 cooperates with the DNA methyltransferases to maintain Cd4 silencing in cytotoxic T cells. Genes Dev 2019; 33:669-683. [PMID: 30975723 PMCID: PMC6546056 DOI: 10.1101/gad.322024.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/22/2019] [Indexed: 12/12/2022]
Abstract
In this study, Ng et al. investigated the maintenance of silent gene states and how the Cd4 gene is stably repressed in CD8+ T cells. Using CRISPR and shRNA screening, they identified the histone chaperone CAF-1 as a critical component for Cd4 repression and propose that the heritable silencing of the Cd4 gene in CD8+ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone-modifying enzymes. The transcriptional repression of alternative lineage genes is critical for cell fate commitment. Mechanisms by which locus-specific gene silencing is initiated and heritably maintained during cell division are not clearly understood. To study the maintenance of silent gene states, we investigated how the Cd4 gene is stably repressed in CD8+ T cells. Through CRISPR and shRNA screening, we identified the histone chaperone CAF-1 as a critical component for Cd4 repression. We found that the large subunit of CAF-1, Chaf1a, requires the N-terminal KER domain to associate with the histone deacetylases HDAC1/2 and the histone demethylase LSD1, enzymes that also participate in Cd4 silencing. When CAF-1 was lacking, Cd4 derepression was markedly enhanced in the absence of the de novo DNA methyltransferase Dnmt3a but not the maintenance DNA methyltransferase Dnmt1. In contrast to Dnmt1, Dnmt3a deficiency did not significantly alter levels of DNA methylation at the Cd4 locus. Instead, Dnmt3a deficiency sensitized CD8+ T cells to Cd4 derepression mediated by compromised functions of histone-modifying factors, including the enzymes associated with CAF-1. Thus, we propose that the heritable silencing of the Cd4 gene in CD8+ T cells exploits cooperative functions among the DNA methyltransferases, CAF-1, and histone-modifying enzymes.
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Affiliation(s)
- Charles Ng
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Martin Aichinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Tung Nguyen
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Christy Au
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Tariq Najar
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Lin Wu
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Kai R Mesa
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Will Liao
- New York Genome Center, New York, New York 10013, USA
| | - Jean-Pierre Quivy
- UMR3664, Centre National de la Recherche Scientifique, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, PSL Research University, F-75005 Paris, France
| | | | - Genevieve Almouzni
- UMR3664, Centre National de la Recherche Scientifique, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, PSL Research University, F-75005 Paris, France
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dan R Littman
- The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, New York, New York 10016, USA
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93
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SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells. Nat Commun 2019; 10:1335. [PMID: 30902974 PMCID: PMC6430823 DOI: 10.1038/s41467-019-09078-0] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Endogenous retroviruses (ERVs) can confer benefits to their host but present a threat to genome integrity if not regulated correctly. Here we identify the SWI/SNF-like remodeler SMARCAD1 as a key factor in the control of ERVs in embryonic stem cells. SMARCAD1 is enriched at ERV subfamilies class I and II, particularly at active intracisternal A-type particles (IAPs), where it preserves repressive histone methylation marks. Depletion of SMARCAD1 results in de-repression of IAPs and adjacent genes. Recruitment of SMARCAD1 to ERVs is dependent on KAP1, a central component of the silencing machinery. SMARCAD1 and KAP1 occupancy at ERVs is co-dependent and requires the ATPase function of SMARCAD1. Our findings uncover a role for the enzymatic activity of SMARCAD1 in cooperating with KAP1 to silence ERVs. This reveals ATP-dependent chromatin remodeling as an integral step in retrotransposon regulation in stem cells and advances our understanding of the mechanisms driving heterochromatin establishment. Tight regulation of retrotransposons such as endogenous retroviruses (ERVs) is essential for genome and transcriptome integrity. Here, the authors show that the ATPase function of the chromatin remodeler SMARCAD1 facilitates the binding of KAP1 to ERVs and is required for their repression in embryonic stem cells.
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94
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Delaney CE, Methot SP, Guidi M, Katic I, Gasser SM, Padeken J. Heterochromatic foci and transcriptional repression by an unstructured MET-2/SETDB1 co-factor LIN-65. J Cell Biol 2019; 218:820-838. [PMID: 30737265 PMCID: PMC6400574 DOI: 10.1083/jcb.201811038] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
Delaney et al. show that the unstructured domain cofactor LIN-65 is essential for the stable formation of heterochromatic foci. It stably interacts with the H3K9 methyltransferase MET-2/SETDB1 and modulates MET-2 nuclear localization, activity, and H3K9me-mediated silencing in C. elegans. The segregation of the genome into accessible euchromatin and histone H3K9-methylated heterochromatin helps silence repetitive elements and tissue-specific genes. In Caenorhabditis elegans, MET-2, the homologue of mammalian SETDB1, catalyzes H3K9me1 and me2, yet like SETDB1, its regulation is enigmatic. Contrary to the cytosolic enrichment of overexpressed MET-2, we show that endogenous MET-2 is nuclear throughout development, forming perinuclear foci in a cell cycle–dependent manner. Mass spectrometry identified two cofactors that bind MET-2: LIN-65, a highly unstructured protein, and ARLE-14, a conserved GTPase effector. All three factors colocalize in heterochromatic foci. Ablation of lin-65, but not arle-14, mislocalizes and destabilizes MET-2, resulting in decreased H3K9 dimethylation, dispersion of heterochromatic foci, and derepression of MET-2 targets. Mutation of met-2 or lin-65 also disrupts the perinuclear anchoring of genomic heterochromatin. Loss of LIN-65, like that of MET-2, compromises temperature stress resistance and germline integrity, which are both linked to promiscuous repeat transcription and gene expression.
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Affiliation(s)
- Colin E Delaney
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stephen P Methot
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Micol Guidi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Iskra Katic
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland .,University of Basel, Faculty of Natural Sciences, Basel, Switzerland
| | - Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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95
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Yang B, Xu X, Russell L, Sullenberger MT, Yanowitz JL, Maine EM. A DNA repair protein and histone methyltransferase interact to promote genome stability in the Caenorhabditis elegans germ line. PLoS Genet 2019; 15:e1007992. [PMID: 30794539 PMCID: PMC6402707 DOI: 10.1371/journal.pgen.1007992] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 03/06/2019] [Accepted: 01/28/2019] [Indexed: 12/29/2022] Open
Abstract
Histone modifications regulate gene expression and chromosomal events, yet how histone-modifying enzymes are targeted is poorly understood. Here we report that a conserved DNA repair protein, SMRC-1, associates with MET-2, the C. elegans histone methyltransferase responsible for H3K9me1 and me2 deposition. We used molecular, genetic, and biochemical methods to investigate the biological role of SMRC-1 and to explore its relationship with MET-2. SMRC-1, like its mammalian ortholog SMARCAL1, provides protection from DNA replication stress. SMRC-1 limits accumulation of DNA damage and promotes germline and embryonic viability. MET-2 and SMRC-1 localize to mitotic and meiotic germline nuclei, and SMRC-1 promotes an increase in MET-2 abundance in mitotic germline nuclei upon replication stress. In the absence of SMRC-1, germline H3K9me2 generally decreases after multiple generations at high culture temperature. Genetic data are consistent with MET-2 and SMRC-1 functioning together to limit replication stress in the germ line and in parallel to promote other germline processes. We hypothesize that loss of SMRC-1 activity causes chronic replication stress, in part because of insufficient recruitment of MET-2 to nuclei.
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Affiliation(s)
- Bing Yang
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Xia Xu
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Logan Russell
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | | | - Judith L. Yanowitz
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Eleanor M. Maine
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
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96
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Wu X, Kwong AC, Rice CM. Antiviral resistance of stem cells. Curr Opin Immunol 2019; 56:50-59. [PMID: 30352329 PMCID: PMC6462420 DOI: 10.1016/j.coi.2018.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/27/2018] [Accepted: 10/02/2018] [Indexed: 01/07/2023]
Abstract
Stem cells are important for growth and regeneration given their ability to self-renew and differentiate into mature cells. Resistance to certain viral infections has been established as a phenotype of stem cells, a protection in line with their important physiological function. Antiviral resistance is critical to all cells, but it is differentially regulated between stem cells and differentiated cells. Stem cells utilize antiviral RNA interference, interferon-independent repression of endogenous retroviruses and intrinsic expression of antiviral interferon-stimulated genes. Differentiated cells often rely on the interferon-associated protein-based response to induce a local antiviral state. This review outlines the antiviral resistance mechanisms of stem cells and discusses some ideas as to why stem cells and differentiated cells may have evolved to utilize distinct mechanisms.
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Affiliation(s)
- Xianfang Wu
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, United States
| | - Andrew C Kwong
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, United States; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, United States.
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97
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Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nat Commun 2019; 10:34. [PMID: 30604769 PMCID: PMC6318327 DOI: 10.1038/s41467-018-08006-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/11/2018] [Indexed: 01/18/2023] Open
Abstract
The majority of mammalian genomes are devoted to transposable elements (TEs). Whilst TEs are increasingly recognized for their important biological functions, they are a potential danger to genomic stability and are carefully regulated by the epigenetic system. However, the full complexity of this regulatory system is not understood. Here, using mouse embryonic stem cells, we show that TEs are suppressed by heterochromatic marks like H3K9me3, and are also labelled by all major types of chromatin modification in complex patterns, including bivalent activatory and repressive marks. We identified 29 epigenetic modifiers that significantly deregulated at least one type of TE. The loss of Setdb1, Ncor2, Rnf2, Kat5, Prmt5, Uhrf1, and Rrp8 caused widespread changes in TE expression and chromatin accessibility. These effects were context-specific, with different chromatin modifiers regulating the expression and chromatin accessibility of specific subsets of TEs. Our work reveals the complex patterns of epigenetic regulation of TEs. Transposable elements (TEs) fulfill essential but poorly understood roles in genome organization and gene expression control. Here the authors show that the regulation of TEs occurs through overlapping epigenetic mechanisms that control the expression and chromatin signatures at TEs.
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98
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Veazey RS, Lackner AA. Nonhuman Primate Models and Understanding the Pathogenesis of HIV Infection and AIDS. ILAR J 2018; 58:160-171. [PMID: 29228218 DOI: 10.1093/ilar/ilx032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/04/2017] [Indexed: 12/16/2022] Open
Abstract
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals. Research in NHP has led to "dogma changing" discoveries in immunology, infectious disease, and even our own genetics. We now know that many of our genes are retroviral remnants, or developed in response to archaic HIV-like retroviral infections. Early studies involving blood from HIV patients and in experiments in cultured tissues contributed to confusion regarding the cause of AIDS and impeded progress in the development of effective interventions. Research on the many retroviruses of different NHP species have broadened our understanding of human immunology and perhaps even our origins and evolution as a species. In combination with recent advances in molecular biology and computational analytics, research in NHPs has unique potential for discoveries that will directly lead to new cures for old human and animal diseases, including HIV/AIDS.
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Affiliation(s)
- Ronald S Veazey
- Division of Comparative Pathology, Tulane National Primate Research Center, Tulane University School of Medicine.,Department of Pathology and Laboratory Medicine, Tulane University School of Medicine
| | - Andrew A Lackner
- Tulane National Primate Research Center, Tulane University School of Medicine.,Department of Microbiology and Pathology and Laboratory Medicine, Tulane University School of Medicine
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99
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Volk A, Liang K, Suraneni P, Li X, Zhao J, Bulic M, Marshall S, Pulakanti K, Malinge S, Taub J, Ge Y, Rao S, Bartom E, Shilatifard A, Crispino JD. A CHAF1B-Dependent Molecular Switch in Hematopoiesis and Leukemia Pathogenesis. Cancer Cell 2018; 34:707-723.e7. [PMID: 30423293 PMCID: PMC6235627 DOI: 10.1016/j.ccell.2018.10.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 07/08/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022]
Abstract
CHAF1B is the p60 subunit of the chromatin assembly factor (CAF1) complex, which is responsible for assembly of histones H3.1/H4 heterodimers at the replication fork during S phase. Here we report that CHAF1B is required for normal hematopoiesis while its overexpression promotes leukemia. CHAF1B has a pro-leukemia effect by binding chromatin at discrete sites and interfering with occupancy of transcription factors that promote myeloid differentiation, such as CEBPA. Reducing Chaf1b activity by either heterozygous deletion or overexpression of a CAF1 dominant negative allele is sufficient to suppress leukemogenesis in vivo without impairing normal hematopoiesis.
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Affiliation(s)
- Andrew Volk
- Division of Hematology/Oncology, Northwestern University, 303 East Superior Street, 5-123, Chicago, IL 60611, USA
| | - Kaiwei Liang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Praveen Suraneni
- Division of Hematology/Oncology, Northwestern University, 303 East Superior Street, 5-123, Chicago, IL 60611, USA
| | - Xinyu Li
- School of Life Sciences, Jilin University, Changchun, China
| | - Jianyun Zhao
- School of Life Sciences, Jilin University, Changchun, China
| | - Marinka Bulic
- Division of Hematology/Oncology, Northwestern University, 303 East Superior Street, 5-123, Chicago, IL 60611, USA
| | - Stacy Marshall
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | | | | | - Jeffrey Taub
- Department of Oncology and Molecular Therapeutics Program of the Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Yubin Ge
- Department of Oncology and Molecular Therapeutics Program of the Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Sridhar Rao
- Blood Research Institute, Milwaukee, WI 53226, USA
| | - Elizabeth Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, 303 East Superior Street, 5-123, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA.
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100
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Tatsumi D, Hayashi Y, Endo M, Kobayashi H, Yoshioka T, Kiso K, Kanno S, Nakai Y, Maeda I, Mochizuki K, Tachibana M, Koseki H, Okuda A, Yasui A, Kono T, Matsui Y. DNMTs and SETDB1 function as co-repressors in MAX-mediated repression of germ cell-related genes in mouse embryonic stem cells. PLoS One 2018; 13:e0205969. [PMID: 30403691 PMCID: PMC6221296 DOI: 10.1371/journal.pone.0205969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 09/28/2018] [Indexed: 11/19/2022] Open
Abstract
In embryonic stem cells (ESCs), the expression of development-related genes, including germ cell-related genes, is globally repressed. The transcription factor MAX represses germ cell-related gene expression in ESCs via PCGF6-polycomb repressive complex 1 (PRC1), which consists of several epigenetic factors. However, we predicted that MAX represses germ cell-related gene expression through several additional mechanisms because PCGF6-PRC1 regulates the expression of only a subset of genes repressed by MAX. Here, we report that MAX associated with DNA methyltransferases (DNMTs) and the histone methyltransferase SETDB1 cooperatively control germ cell-related gene expression in ESCs. Both DNA methylation and histone H3 lysine 9 tri-methylation of the promoter regions of several germ cell-related genes were not affected by knockout of the PRC1 components, indicating that the MAX-DNMT and MAX-SETDB1 pathways are independent of the PCGF6-PRC1 pathway. Our findings provide insights into our understanding of MAX-based repressive mechanisms of germ cell-related genes in ESCs.
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Affiliation(s)
- Daiki Tatsumi
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Yohei Hayashi
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chuo-ku, Tokyo, Japan
| | - Mai Endo
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Takumi Yoshioka
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Kohei Kiso
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Shinichiro Kanno
- Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Yuji Nakai
- Institute for Food Sciences, Hirosaki University, Hirosaki, Aomori, Japan
| | - Ikuma Maeda
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
| | - Kentaro Mochizuki
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- Center for Environmental Conservation and Research Safety, Tohoku University, Sendai, Miyagi, Japan
| | - Makoto Tachibana
- Department of Enzyme Chemistry, Institute for Enzyme Research, Tokushima University, Shinkura-cho, Tokushima, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Core Research for Evolutional Science and Technology, Yokohama, Kanagawa, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Akira Yasui
- Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
- The Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Chuo-ku, Tokyo, Japan
- Center for Regulatory Epigenome and Diseases, Tohoku University School of Medicine, Sendai, Miyagi, Japan
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