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Lefkowitz RB, Miller CM, Martinez-Caballero JD, Ramos I. Epigenetic Control of Innate Immunity: Consequences of Acute Respiratory Virus Infection. Viruses 2024; 16:197. [PMID: 38399974 PMCID: PMC10893272 DOI: 10.3390/v16020197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Infections caused by acute respiratory viruses induce a systemic innate immune response, which can be measured by the increased levels of expression of inflammatory genes in immune cells. There is growing evidence that these acute viral infections, alongside transient transcriptomic responses, induce epigenetic remodeling as part of the immune response, such as DNA methylation and histone modifications, which might persist after the infection is cleared. In this article, we first review the primary mechanisms of epigenetic remodeling in the context of innate immunity and inflammation, which are crucial for the regulation of the immune response to viral infections. Next, we delve into the existing knowledge concerning the impact of respiratory virus infections on the epigenome, focusing on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Influenza A Virus (IAV), and Respiratory Syncytial Virus (RSV). Finally, we offer perspectives on the potential consequences of virus-induced epigenetic remodeling and open questions in the field that are currently under investigation.
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Affiliation(s)
- Rivka Bella Lefkowitz
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
| | - Clare M. Miller
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan David Martinez-Caballero
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (R.B.L.); (C.M.M.)
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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2
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A novel SNF2 ATPase complex in Trypanosoma brucei with a role in H2A.Z-mediated chromatin remodelling. PLoS Pathog 2022; 18:e1010514. [PMID: 35675371 PMCID: PMC9236257 DOI: 10.1371/journal.ppat.1010514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/27/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
A cascade of histone acetylation events with subsequent incorporation of a histone H2A variant plays an essential part in transcription regulation in various model organisms. A key player in this cascade is the chromatin remodelling complex SWR1, which replaces the canonical histone H2A with its variant H2A.Z. Transcriptional regulation of polycistronic transcription units in the unicellular parasite Trypanosoma brucei has been shown to be highly dependent on acetylation of H2A.Z, which is mediated by the histone-acetyltransferase HAT2. The chromatin remodelling complex which mediates H2A.Z incorporation is not known and an SWR1 orthologue in trypanosomes has not yet been reported. In this study, we identified and characterised an SWR1-like remodeller complex in T. brucei that is responsible for Pol II-dependent transcriptional regulation. Bioinformatic analysis of potential SNF2 DEAD/Box helicases, the key component of SWR1 complexes, identified a 1211 amino acids-long protein that exhibits key structural characteristics of the SWR1 subfamily. Systematic protein-protein interaction analysis revealed the existence of a novel complex exhibiting key features of an SWR1-like chromatin remodeller. RNAi-mediated depletion of the ATPase subunit of this complex resulted in a significant reduction of H2A.Z incorporation at transcription start sites and a subsequent decrease of steady-state mRNA levels. Furthermore, depletion of SWR1 and RNA-polymerase II (Pol II) caused massive chromatin condensation. The potential function of several proteins associated with the SWR1-like complex and with HAT2, the key factor of H2A.Z incorporation, is discussed. Trypanosoma brucei is the causative agent of African trypanosomiasis (sleeping sickness) in humans and nagana in cattle. Its unusual genomic organisation featuring large polycistronic units requires a general mechanism of transcription initiation, because individual gene promoters are mostly absent. Despite the fact that the histone variant H2A.Z has previously been identified as a key player of transcription regulation, the complex responsible for correct H2A.Z incorporation at transcription start sites (TSS) remains elusive. In other eukaryotes, SWR1, a SNF2 ATPase-associated chromatin remodelling complex, is responsible for correct incorporation of this histone variant. This study identified a SWR1-like complex in T. brucei. Depletion of the SNF2 ATPase resulted in a reduction of H2A.Z incorporation at the TSS and decreased steady-state mRNA levels accompanied by chromatin condensation. In addition to the SWR1-like complex, we also identified a trypanosome-specific HAT2 complex that includes the histone acetyltransferases HAT2, a key player in the H2A.Z incorporation process. This complex has a trypanosome-specific composition that is different from the NuA4/TIP60 complex in Saccharomyces cerevisiae.
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Challa K, Schmid CD, Kitagawa S, Cheblal A, Iesmantavicius V, Seeber A, Amitai A, Seebacher J, Hauer MH, Shimada K, Gasser SM. Damage-induced chromatome dynamics link Ubiquitin ligase and proteasome recruitment to histone loss and efficient DNA repair. Mol Cell 2021; 81:811-829.e6. [PMID: 33529595 DOI: 10.1016/j.molcel.2020.12.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
Eukaryotic cells package their genomes around histone octamers. In response to DNA damage, checkpoint activation in yeast induces core histone degradation resulting in 20%-40% reduction in nucleosome occupancy. To gain insight into this process, we developed a new approach to analyze the chromatin-associated proteome comprehensively before and after damage. This revealed extensive changes in protein composition after Zeocin-induced damage. First, core histones and the H1 homolog Hho1 were partially lost from chromatin along with replication, transcription, and chromatin remodeling machineries, while ubiquitin ligases and the proteasome were recruited. We found that the checkpoint- and INO80C-dependent recruitment of five ubiquitin-conjugating factors (Rad6, Bre1, Pep5, Ufd4, and Rsp5) contributes to core and linker histone depletion, reducing chromatin compaction and enhancing DNA locus mobility. Importantly, loss of Rad6/Bre1, Ufd4/TRIP12, and Pep5/VPS11 compromise DNA strand invasion kinetics during homology-driven repair. Thus we provide a comprehensive overview of a functionally relevant genome-wide chromatin response to DNA damage.
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Affiliation(s)
- Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Christoph D Schmid
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Saho Kitagawa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba 468-1, Aoba-ku, Sendai, 981-8545, Japan
| | - Anaïs Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Andrew Seeber
- Center for Advanced Imaging, Northwest Building, 52 Oxford St., Harvard University, Cambridge, MA 02138, USA
| | - Assaf Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Michael H Hauer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
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4
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Roles and mechanisms of BAP1 deubiquitinase in tumor suppression. Cell Death Differ 2021; 28:606-625. [PMID: 33462414 DOI: 10.1038/s41418-020-00709-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
The BAP1 gene has emerged as a major tumor suppressor mutated with various frequencies in numerous human malignancies, including uveal melanoma, malignant pleural mesothelioma, clear cell renal cell carcinoma, intrahepatic cholangiocarcinoma, hepatocellular carcinoma, and thymic epithelial tumors. BAP1 mutations are also observed at low frequency in other malignancies including breast, colorectal, pancreatic, and bladder cancers. BAP1 germline mutations are associated with high incidence of mesothelioma, uveal melanoma, and other cancers, defining the "BAP1 cancer syndrome." Interestingly, germline BAP1 mutations constitute an important paradigm for gene-environment interactions, as loss of BAP1 predisposes to carcinogen-induced tumorigenesis. Inactivating mutations of BAP1 are also identified in sporadic cancers, denoting the importance of this gene for normal tissue homeostasis and tumor suppression, although some oncogenic properties have also been attributed to BAP1. BAP1 belongs to the deubiquitinase superfamily of enzymes, which are responsible for the maturation and turnover of ubiquitin as well as the reversal of substrate ubiquitination, thus regulating ubiquitin signaling. BAP1 is predominantly nuclear and interacts with several chromatin-associated factors, assembling multi-protein complexes with mutually exclusive partners. BAP1 exerts its function through highly regulated deubiquitination of its substrates. As such, BAP1 orchestrates chromatin-associated processes including gene expression, DNA replication, and DNA repair. BAP1 also exerts cytoplasmic functions, notably in regulating Ca2+ signaling at the endoplasmic reticulum. This DUB is also subjected to multiple post-translational modifications, notably phosphorylation and ubiquitination, indicating that several signaling pathways tightly regulate its function. Recent progress indicated that BAP1 plays essential roles in multiple cellular processes including cell proliferation and differentiation, cell metabolism, as well as cell survival and death. In this review, we summarize the biological and molecular functions of BAP1 and explain how the inactivation of this DUB might cause human cancers. We also highlight some of the unresolved questions and suggest potential new directions.
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Horváth ÁI, Gyimesi M, Várkuti BH, Képiró M, Szegvári G, Lőrincz I, Hegyi G, Kovács M, Málnási-Csizmadia A. Effect of allosteric inhibition of non-muscle myosin 2 on its intracellular diffusion. Sci Rep 2020; 10:13341. [PMID: 32769996 PMCID: PMC7415145 DOI: 10.1038/s41598-020-69853-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 07/03/2020] [Indexed: 12/12/2022] Open
Abstract
Subcellular dynamics of non-muscle myosin 2 (NM2) is crucial for a broad-array of cellular functions. To unveil mechanisms of NM2 pharmacological control, we determined how the dynamics of NM2 diffusion is affected by NM2′s allosteric inhibitors, i.e. blebbistatin derivatives, as compared to Y-27632 inhibiting ROCK, NM2′s upstream regulator. We found that NM2 diffusion is markedly faster in central fibers than in peripheral stress fibers. Y-27632 accelerated NM2 diffusion in both peripheral and central fibers, whereas in peripheral fibers blebbistatin derivatives slightly accelerated NM2 diffusion at low, but markedly slowed it at high inhibitor concentrations. In contrast, rapid NM2 diffusion in central fibers was unaffected by direct NM2 inhibition. Using our optopharmacological tool, Molecular Tattoo, sub-effective concentrations of a photo-crosslinkable blebbistatin derivative were increased to effective levels in a small, irradiated area of peripheral fibers. These findings suggest that direct allosteric inhibition affects the diffusion profile of NM2 in a markedly different manner compared to the disruption of the upstream control of NM2. The pharmacological action of myosin inhibitors is channeled through autonomous molecular processes and might be affected by the load acting on the NM2 proteins.
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Affiliation(s)
- Ádám I Horváth
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary
| | - Máté Gyimesi
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary
| | - Boglárka H Várkuti
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary
| | - Miklós Képiró
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary
| | - Gábor Szegvári
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary
| | - István Lőrincz
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary
| | - György Hegyi
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary
| | - Mihály Kovács
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary.
| | - András Málnási-Csizmadia
- MTA-ELTE Motor Pharmacology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117, Budapest, Hungary.
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Jain S, Maini J, Narang A, Maiti S, Brahmachari V. The regulatory function of dIno80 correlates with its DNA binding activity. Gene 2020; 732:144368. [PMID: 31954859 DOI: 10.1016/j.gene.2020.144368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 01/06/2023]
Abstract
The INO80 complex, including the Ino80 protein, forms a highly conserved canonical complex that remodels chromatin in the context of multiple cellular functions. The Drosophila homologue, dIno80, is involved in homeotic gene regulation during development as a canonical Pho-dIno80 complex. Previously, we found that dIno80 regulates homeotic genes by interacting with epigenetic regulators, such as polycomb and trithorax, suggesting the occurrence of non-canonical Ino80 complexes. Here using spectroscopic methods and gel retardation assays, we identified a set of consensus DNA sequences that DNA binding domain of dIno80 (DBINO) interacts with having differential affinity and high specificity. Testing these sequences in reporter assays, showed that this interaction can positively regulate transcription. These results suggest that, dIno80 has a sequence preference for interaction with DNA leading to transcriptional changes.
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Affiliation(s)
- Shruti Jain
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
| | - Jayant Maini
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Ankita Narang
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Souvik Maiti
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110025, India
| | - Vani Brahmachari
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
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7
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Kang H, Zhang C, An Z, Shen WH, Zhu Y. AtINO80 and AtARP5 physically interact and play common as well as distinct roles in regulating plant growth and development. THE NEW PHYTOLOGIST 2019; 223:336-353. [PMID: 30843208 DOI: 10.1111/nph.15780] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 03/01/2019] [Indexed: 06/09/2023]
Abstract
The proper modulation of chromatin structure is dependent on the activities of chromatin-remodeling factors and their interplays. Here, we show that the Arabidopsis chromatin-remodeler AtINO80 interacts with the actin-related protein AtARP5 and can form a larger protein complex. Genetic analysis demonstrated that AtARP5 acts in concert with AtINO80 during plant cellular proliferation and replication stress response. At the same time, AtARP5 is not required for AtINO80-mediated control of flowering time and related transcriptional regulation, and their chromatin distribution patterns on regions of flowering-repressor genes FLC/MAF4/MAF5 are also different. An in vitro DNase I digestion assay revealed that the AtINO80N-terminus can weakly bind DNA, an interaction that is significantly inhibited by H2A.Z/H2B addition. AtARP6, a specific subunit of SWR1-C that mediates the H2A.Z exchange, was found to have a previously unexpected inhibitory role in the local chromatin enrichment of AtINO80. Further genetic analyses revealed the functional interplay between AtINO80 and AtARP6 and their critical roles in embryogenesis and post-embryonic organ development, as well as the synergy of AtARP5 and AtARP6 in maintaining genomic stability. Our findings provide insights into the common and distinct roles of AtINO80 and AtARP5 in diverse aspects of plant development.
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Affiliation(s)
- Huijia Kang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chi Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zengxuan An
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- CNRS, IBMP UPR 2357, Université de Strasbourg, Strasbourg, F-67000, France
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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8
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Hu J, Liu J, Chen A, Lyu J, Ai G, Zeng Q, Sun Y, Chen C, Wang J, Qiu J, Wu Y, Cheng J, Shi X, Song L. Ino80 promotes cervical cancer tumorigenesis by activating Nanog expression. Oncotarget 2018; 7:72250-72262. [PMID: 27750218 PMCID: PMC5342159 DOI: 10.18632/oncotarget.12667] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/10/2016] [Indexed: 02/03/2023] Open
Abstract
Ino80 ATPase is an integral component of the INO80 ATP-dependent chromatin-remodeling complex, which regulates transcription, DNA repair and replication. We found that Ino80 was highly expressed in cervical cancer cell lines and tumor samples. Ino80 knockdown inhibited cervical cancer cell proliferation, induced G0/G1 phase cell cycle arrest in vitro and suppressed tumor growth in vivo. However, Ino80 knockdown did not affect cell apoptosis, migration or invasion in vitro. Ino80 overexpression promoted proliferation in the H8 immortalized cervical epithelial cell line, which has low endogenous Ino80 expression as compared to cervical cancer cell lines. Ino80 bound to the Nanog transcription start site (TSS) and enhanced its expression in cervical cancer cells. Nanog overexpression in Ino80 knockdown cell lines promoted cell proliferation. This study demonstrated for the first time that Ino80 was upregulated in cervical cancer and promoted cell proliferation and tumorigenesis. Our findings suggest that Ino80 may be a potential therapeutic target for the treatment of cervical cancer.
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Affiliation(s)
- Jing Hu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Liu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Aozheng Chen
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jia Lyu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guihai Ai
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiongjing Zeng
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Sun
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chunxia Chen
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinbo Wang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jin Qiu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Wu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiajing Cheng
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiujuan Shi
- Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liwen Song
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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Wong TN, Miller CA, Jotte MRM, Bagegni N, Baty JD, Schmidt AP, Cashen AF, Duncavage EJ, Helton NM, Fiala M, Fulton RS, Heath SE, Janke M, Luber K, Westervelt P, Vij R, DiPersio JF, Welch JS, Graubert TA, Walter MJ, Ley TJ, Link DC. Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential. Nat Commun 2018; 9:455. [PMID: 29386642 PMCID: PMC5792556 DOI: 10.1038/s41467-018-02858-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/04/2018] [Indexed: 01/22/2023] Open
Abstract
Hematopoietic clones harboring specific mutations may expand over time. However, it remains unclear how different cellular stressors influence this expansion. Here we characterize clonal hematopoiesis after two different cellular stressors: cytotoxic therapy and hematopoietic transplantation. Cytotoxic therapy results in the expansion of clones carrying mutations in DNA damage response genes, including TP53 and PPM1D. Analyses of sorted populations show that these clones are typically multilineage and myeloid-biased. Following autologous transplantation, most clones persist with stable chimerism. However, DNMT3A mutant clones often expand, while PPM1D mutant clones often decrease in size. To assess the leukemic potential of these expanded clones, we genotyped 134 t-AML/t-MDS samples. Mutations in non-TP53 DNA damage response genes are infrequent in t-AML/t-MDS despite several being commonly identified after cytotoxic therapy. These data suggest that different hematopoietic stressors promote the expansion of distinct long-lived clones, carrying specific mutations, whose leukemic potential depends partially on the mutations they harbor. Cellular stressors can impact clonal hematopoiesis. Here, the authors explore the impact of cytotoxic therapy and hematopoietic transplantation on clonal expansion, suggesting different stressors can promote expansion of distinct long-lived clones.
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Affiliation(s)
- Terrence N Wong
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christopher A Miller
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Matthew R M Jotte
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nusayba Bagegni
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jack D Baty
- Division of Biostatistics, Washington University, St. Louis, MO, 63110, USA
| | - Amy P Schmidt
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Amanda F Cashen
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Nichole M Helton
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mark Fiala
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sharon E Heath
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Megan Janke
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kierstin Luber
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Peter Westervelt
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Ravi Vij
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - John F DiPersio
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - John S Welch
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | | | - Matthew J Walter
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Timothy J Ley
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Daniel C Link
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA. .,Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
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10
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Zhou B, Wang L, Zhang S, Bennett BD, He F, Zhang Y, Xiong C, Han L, Diao L, Li P, Fargo DC, Cox AD, Hu G. INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma. Genes Dev 2017; 30:1440-53. [PMID: 27340176 PMCID: PMC4926866 DOI: 10.1101/gad.277178.115] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/23/2016] [Indexed: 01/01/2023]
Abstract
Here, Zhou et al. investigated how oncogenic superenhancers (SE), which are found near oncogenes and control cancer gene expression, are regulated. The results demonstrate an essential role for INO80-dependent chromatin remodeling in SE function by showing that INO80 is required for SE-mediated oncogenic transcription and tumor growth in melanoma. Superenhancers (SEs) are large genomic regions with a high density of enhancer marks. In cancer, SEs are found near oncogenes and dictate cancer gene expression. However, how oncogenic SEs are regulated remains poorly understood. Here, we show that INO80, a chromatin remodeling complex, is required for SE-mediated oncogenic transcription and tumor growth in melanoma. The expression of Ino80, the SWI/SNF ATPase, is elevated in melanoma cells and patient melanomas compared with normal melanocytes and benign nevi. Furthermore, Ino80 silencing selectively inhibits melanoma cell proliferation, anchorage-independent growth, tumorigenesis, and tumor maintenance in mouse xenografts. Mechanistically, Ino80 occupies >90% of SEs, and its occupancy is dependent on transcription factors such as MITF and Sox9. Ino80 binding reduces nucleosome occupancy and facilitates Mediator recruitment, thus promoting oncogenic transcription. Consistently, genes co-occupied by Ino80 and Med1 are selectively expressed in melanomas compared with melanocytes. Together, our results reveal an essential role of INO80-dependent chromatin remodeling in SE function and suggest a novel strategy for disrupting SEs in cancer treatment.
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Affiliation(s)
- Bingying Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Li Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Shu Zhang
- Department of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Brian D Bennett
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Fan He
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yan Zhang
- Family Planning Research Institute, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Chengliang Xiong
- Family Planning Research Institute, Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Pishun Li
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Adrienne D Cox
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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11
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Sheng W, Chen Y, Gong Y, Dong T, Zhang B, Gao W. miR-148a inhibits self-renewal of thyroid cancer stem cells via repressing INO80 expression. Oncol Rep 2016; 36:3387-3396. [PMID: 27779717 DOI: 10.3892/or.2016.5203] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/23/2016] [Indexed: 11/06/2022] Open
Abstract
Anaplastic thyroid carcinoma (ATC) is aggressive and lethal with extrathyroidal invasion, distant metastasis, and resistance to conventional therapies. Cancer stem cells (CSCs) are proposed to be responsible for high recurrence rate in ATC. MicroRNAs (miRNAs) have recently been found as an important class of cellular regulators of ATC carcinogenesis. Identification of CSC-related miRNAs and targets is therefore a priority for the development of new therapeutic paradigms. Patient-derived ATC cells were cultured in conditional media on poly-hema-treated dish. ATC CSCs were isolated and enriched through as a series of steps including initial isolation of sphere-forming CSC population, subsequent amplification of this CSC population in a xenograft model treated with cisplatin, and purification of CSCs from xenograft tumors followed by final enrichment using sphere-forming assays. Expression of CSC markers was measured by flow cytometry, immunofluorescence staining, qPCR and western blot analyses. Expression of miRNAs in ATC-CSCs was profiled by microarray analysis. Proliferation and differentiation rates were determined based on the size of spheres formed in vitro and tumors formed in vivo. We successfully isolated and enriched an ATC-CSC population. We identified 17 miRNAs differentially expressed in primary ATC cells vs. ATC-CSCs, among which miRNA-148a was significantly downregulated in ATC-CSCs. Overexpression of miRNA148a in ATC-CSCs induced cell cycle arrest and loss of stem cell characteristics. In addition, we identified INO80 as a target gene of miR-148a. The expression of INO80 was upregulated in ATC-CSCs and downregulated upon miRNA-148 overexpression. Overexpression of miRNA-148a and knockdown of INO80 acted synergistically to decrease the expression of stem cell marker genes as well as to attenuate stem cell-specific properties including the ability to form tumors. This study identified novel contrasting roles for miR-148a and INO80 in the regulation of the stemness of ATC-CSCs and their capacity to initiate tumor formation. Our findings may open a new avenue for therapeutic development against ATC that targets INO80 in the CSCs through enhancing miRNA-148a levels.
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Affiliation(s)
- Weizhong Sheng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Yusheng Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Yuda Gong
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Tiangeng Dong
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Bo Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Weidong Gao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
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12
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INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer. Oncogene 2016; 36:1430-1439. [PMID: 27641337 DOI: 10.1038/onc.2016.311] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/20/2016] [Accepted: 07/25/2016] [Indexed: 01/04/2023]
Abstract
Epigenetic regulators are attractive targets for the development of new cancer therapies. Among them, the ATP-dependent chromatin remodeling complexes control the chromatin architecture and have important roles in gene regulation. They are often found to be mutated and de-regulated in cancers, but how they influence the cancer gene expression program during cancer initiation and progression is not fully understood. Here we show that the INO80 chromatin remodeling complex is required for oncogenic transcription and tumor growth in non-small-cell lung cancer (NSCLC). Ino80, the SWI/SNF ATPase in the complex, is highly expressed in NSCLC cells compared with normal lung epithelia cells. Further, its expression, as well as that of another subunit Ino80B, negatively correlates with disease prognosis in lung cancer patients. Functionally, INO80 silencing inhibits NSCLC cell proliferation and anchorage-independent growth in vitro and tumor formation in mouse xenografts. It occupies enhancer regions near lung cancer-associated genes, and its occupancy correlates with increased genome accessibility and enhanced expression of downstream genes. Together, our study defines a critical role of INO80 in promoting oncogenic transcription and NSCLC tumorigenesis, and reveals a potential treatment strategy for inhibiting the cancer transcription network by targeting the INO80 chromatin remodeling complex.
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13
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Abstract
Nucleosomes function to tightly package DNA into chromosomes, but the nucleosomal landscape becomes disrupted during active processes such as replication, transcription, and repair. The realization that many proteins responsible for chromatin regulation are frequently mutated in cancer has drawn attention to chromatin dynamics; however, the basic mechanisms whereby nucleosomes are disrupted and reassembled is incompletely understood. Here, I present an overview of chromatin dynamics as has been elucidated in model organisms, in which our understanding is most advanced. A basic understanding of chromatin dynamics during normal developmental processes can provide the context for understanding how this machinery can go awry during oncogenesis.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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14
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Messina G, Atterrato MT, Dimitri P. When chromatin organisation floats astray: theSrcapgene and Floating–Harbor syndrome. J Med Genet 2016; 53:793-797. [DOI: 10.1136/jmedgenet-2016-103842] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 02/29/2016] [Accepted: 03/29/2016] [Indexed: 01/19/2023]
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15
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Cavazza T, Vernos I. The RanGTP Pathway: From Nucleo-Cytoplasmic Transport to Spindle Assembly and Beyond. Front Cell Dev Biol 2016; 3:82. [PMID: 26793706 PMCID: PMC4707252 DOI: 10.3389/fcell.2015.00082] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/07/2015] [Indexed: 01/03/2023] Open
Abstract
The small GTPase Ran regulates the interaction of transport receptors with a number of cellular cargo proteins. The high affinity binding of the GTP-bound form of Ran to import receptors promotes cargo release, whereas its binding to export receptors stabilizes their interaction with the cargo. This basic mechanism linked to the asymmetric distribution of the two nucleotide-bound forms of Ran between the nucleus and the cytoplasm generates a switch like mechanism controlling nucleo-cytoplasmic transport. Since 1999, we have known that after nuclear envelope breakdown (NEBD) Ran and the above transport receptors also provide a local control over the activity of factors driving spindle assembly and regulating other aspects of cell division. The identification and functional characterization of RanGTP mitotic targets is providing novel insights into mechanisms essential for cell division. Here we review our current knowledge on the RanGTP system and its regulation and we focus on the recent advances made through the characterization of its mitotic targets. We then briefly review the novel functions of the pathway that were recently described. Altogether, the RanGTP system has moonlighting functions exerting a spatial control over protein interactions that drive specific functions depending on the cellular context.
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Affiliation(s)
- Tommaso Cavazza
- Cell and Developmental Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Isabelle Vernos
- Cell and Developmental Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Institució Catalana de Recerca I Estudis AvançatsBarcelona, Spain
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16
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Cao L, Ding J, Dong L, Zhao J, Su J, Wang L, Sui Y, Zhao T, Wang F, Jin J, Cai Y. Negative Regulation of p21Waf1/Cip1 by Human INO80 Chromatin Remodeling Complex Is Implicated in Cell Cycle Phase G2/M Arrest and Abnormal Chromosome Stability. PLoS One 2015; 10:e0137411. [PMID: 26340092 PMCID: PMC4560432 DOI: 10.1371/journal.pone.0137411] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/17/2015] [Indexed: 11/24/2022] Open
Abstract
We previously identified an ATP-dependent human Ino80 (INO80) chromatin remodeling complex which shares a set of core subunits with yeast Ino80 complex. Although research evidence has suggested that INO80 complex functions in gene transcription and genome stability, the precise mechanism remains unclear. Herein, based on gene expression profiles from the INO80 complex-knockdown in HeLa cells, we first demonstrate that INO80 complex negatively regulates the p21Waf1/Cip1 (p21) expression in a p53-mediated mechanism. In chromatin immunoprecipitation (ChIP) and a sequential ChIP (Re-ChIP) assays, we determined that the INO80 complex and p53 can bind to the same promoter region of p21 gene (-2.2kb and -1.0kb upstream of the p21 promoter region), and p53 is required for the recruitment of the INO80 complex to the p21 promoter. RNAi knockdown strategies of INO80 not only led to prolonged progression of cell cycle phase G2/M to G1, but it also resulted in abnormal chromosome stability. Interestingly, high expression of p21 was observed in most morphologically-changed cells, suggesting that negative regulation of p21 by INO80 complex might be implicated in maintaining the cell cycle process and chromosome stability. Together, our findings will provide a theoretical basis to further elucidate the cellular mechanisms of the INO80 complex.
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Affiliation(s)
- Lingling Cao
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Jian Ding
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Liguo Dong
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Jiayao Zhao
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Jiaming Su
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Lingyao Wang
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yi Sui
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Tong Zhao
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Fei Wang
- School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun, Jilin, China
- National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun City, Jilin, China
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin University, Changchun City, Jilin, China
- * E-mail: (JJ); (YC)
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun, Jilin, China
- National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun City, Jilin, China
- Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, Jilin University, Changchun City, Jilin, China
- * E-mail: (JJ); (YC)
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17
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Alatwi HE, Downs JA. Removal of H2A.Z by INO80 promotes homologous recombination. EMBO Rep 2015; 16:986-94. [PMID: 26142279 PMCID: PMC4552491 DOI: 10.15252/embr.201540330] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 11/09/2022] Open
Abstract
The mammalian INO80 remodelling complex facilitates homologous recombination (HR), but the mechanism by which it does this is unclear. Budding yeast INO80 can remove H2A.Z/H2B dimers from chromatin and replace them with H2A/H2B dimers. H2A.Z is actively incorporated at sites of damage in mammalian cells, raising the possibility that H2A.Z may need to be subsequently removed for resolution of repair. Here, we show that H2A.Z in human cells is indeed rapidly removed from chromatin flanking DNA damage by INO80. We also report that the histone chaperone ANP32E, which is implicated in removing H2AZ from chromatin, similarly promotes HR and appears to work on the same pathway as INO80 in these assays. Importantly, we demonstrate that the HR defect in cells depleted of INO80 or ANP32E can be rescued by H2A.Z co-depletion, suggesting that H2A.Z removal from chromatin is the primary function of INO80 and ANP32E in promoting homologous recombination.
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Affiliation(s)
- Hanan E Alatwi
- MRC Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, UK
| | - Jessica A Downs
- MRC Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, UK
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18
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Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C. Nat Commun 2015; 6:7108. [PMID: 25964121 PMCID: PMC4431590 DOI: 10.1038/ncomms8108] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/01/2015] [Indexed: 01/11/2023] Open
Abstract
INO80-C and SWR-C are conserved members of a subfamily of ATP-dependent chromatin remodeling enzymes that function in transcription and genome-maintenance pathways. A crucial role for these enzymes is to control chromosomal distribution of the H2A.Z histone variant. Here we use electron microscopy (EM) and two-dimensional (2D) class averaging to demonstrate that these remodeling enzymes have similar overall architectures. Each enzyme is characterized by a dynamic ‘tail’ domain and a compact ‘head’ that contains Rvb1/Rvb2 subunits organized as hexameric rings. EM class averages and mass spectrometry support the existence of single heterohexameric rings in both SWR-C and INO80-C. EM studies define the position of the Arp8/Arp4/Act1 module within INO80-C, and we find that this module enhances nucleosome binding affinity but is largely dispensable for remodeling activities. In contrast, the Ies6/Arp5 module is essential for INO80-C remodeling, and furthermore this module controls conformational changes that may couple nucleosome binding to remodeling.
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19
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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20
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Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol 2015; 16:178-89. [DOI: 10.1038/nrm3941] [Citation(s) in RCA: 650] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Wang L, Du Y, Ward JM, Shimbo T, Lackford B, Zheng X, Miao YL, Zhou B, Han L, Fargo DC, Jothi R, Williams CJ, Wade PA, Hu G. INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development. Cell Stem Cell 2014; 14:575-91. [PMID: 24792115 DOI: 10.1016/j.stem.2014.02.013] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/17/2013] [Accepted: 02/21/2014] [Indexed: 11/17/2022]
Abstract
The master transcription factors play integral roles in the pluripotency transcription circuitry of embryonic stem cells (ESCs). How they selectively activate expression of the pluripotency network while simultaneously repressing genes involved in differentiation is not fully understood. Here, we define a requirement for the INO80 complex, a SWI/SNF family chromatin remodeler, in ESC self-renewal, somatic cell reprogramming, and blastocyst development. We show that Ino80, the chromatin remodeling ATPase, co-occupies pluripotency gene promoters with the master transcription factors, and its occupancy is dependent on OCT4 and WDR5. At the pluripotency genes, Ino80 maintains an open chromatin architecture and licenses recruitment of Mediator and RNA polymerase II for gene activation. Our data reveal an essential role for INO80 in the expression of the pluripotency network and illustrate the coordination among chromatin remodeler, transcription factor, and histone-modifying enzyme in the regulation of the pluripotent state.
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Affiliation(s)
- Li Wang
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ying Du
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - James M Ward
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Takashi Shimbo
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Brad Lackford
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Xiaofeng Zheng
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yi-liang Miao
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Bingying Zhou
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leng Han
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Raja Jothi
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Carmen J Williams
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A Wade
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
| | - Guang Hu
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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22
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Zou S, Li J, Zhou H, Frech C, Jiang X, Chu JSC, Zhao X, Li Y, Li Q, Wang H, Hu J, Kong G, Wu M, Ding C, Chen N, Hu H. Mutational landscape of intrahepatic cholangiocarcinoma. Nat Commun 2014; 5:5696. [PMID: 25526346 DOI: 10.1038/ncomms6696] [Citation(s) in RCA: 284] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 10/29/2014] [Indexed: 12/11/2022] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a fatal primary liver cancer (PLC) that affects 5-10% of all PLCs. Here we sequence tumour and matching control sample pairs of a large cohort of 103 ICC patients in China, resulting in the identification of an ICC-specific somatic mutational signature that is associated with liver inflammation, fibrosis and cirrhosis. We further uncover 25 significantly mutated genes including eight potential driver genes (TP53, KRAS, IDH1, PTEN, ARID1A, EPPK1, ECE2 and FYN). We find that TP53-defective ICC patients are more likely to be HBsAg-seropositive, whereas mutations in the oncogene KRAS are nearly exclusively found in HBsAg-seronegative ICC patients. Three pathways (Ras/phosphatidylinositol-4,5-bisphosphate 3-kinase signalling, p53/cell cycle signalling and transforming growth factor-β/Smad signalling), genes important for epigenetic regulation and oxidative phosphorylation are substantially affected in ICC. We reveal mutations in this study that may be valuable for designing further studies, better diagnosis and effective therapies.
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Affiliation(s)
- Shanshan Zou
- Department of Hepatobiliary Medicine I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Jiarui Li
- 1] Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada [2] Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Huabang Zhou
- Department of Hepatobiliary Medicine I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Christian Frech
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Xiaolan Jiang
- Department of Hepatobiliary Medicine I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Jeffrey S C Chu
- Wuhan Frasergen Bioinformatics Co. Ltd, 666 Gaoxin Road, East Lake High-tech Zone, Wuhan 430075, China
| | - Xinyin Zhao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Yuqiong Li
- Department of Hepatobiliary Medicine I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Qiaomei Li
- Department of Hepatobiliary Medicine I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Hui Wang
- Department of Hepatobiliary Medicine I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Jingyi Hu
- School of Medicine, Jiao Tong University, Shanghai 200025, China
| | - Guanyi Kong
- Wuhan Frasergen Bioinformatics Co. Ltd, 666 Gaoxin Road, East Lake High-tech Zone, Wuhan 430075, China
| | - Mengchao Wu
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Chuanfan Ding
- Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Nansheng Chen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Heping Hu
- Department of Hepatobiliary Medicine I, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
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23
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Lopez-Bertoni H, Lal B, Li A, Caplan M, Guerrero-Cázares H, Eberhart CG, Quiñones-Hinojosa A, Glas M, Scheffler B, Laterra J, Li Y. DNMT-dependent suppression of microRNA regulates the induction of GBM tumor-propagating phenotype by Oct4 and Sox2. Oncogene 2014; 34:3994-4004. [PMID: 25328136 DOI: 10.1038/onc.2014.334] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 09/08/2014] [Accepted: 09/10/2014] [Indexed: 12/22/2022]
Abstract
Cancer stem-like cells represent poorly differentiated multipotent tumor-propagating cells that contribute disproportionately to therapeutic resistance and tumor recurrence. Transcriptional mechanisms that control the phenotypic conversion of tumor cells lacking tumor-propagating potential to tumor-propagating stem-like cells remain obscure. Here we show that the reprogramming transcription factors Oct4 and Sox2 induce glioblastoma cells to become stem-like and tumor-propagating via a mechanism involving direct DNA methyl transferase (DNMT) promoter transactivation, resulting in global DNA methylation- and DNMT-dependent downregulation of multiple microRNAs (miRNAs). We show that one such downregulated miRNA, miRNA-148a, inhibits glioblastoma cell stem-like properties and tumor-propagating potential. This study identifies a novel and targetable molecular circuit by which glioma cell stemness and tumor-propagating capacity are regulated.
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Affiliation(s)
- H Lopez-Bertoni
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - B Lal
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - A Li
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA
| | - M Caplan
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA
| | - H Guerrero-Cázares
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - C G Eberhart
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - A Quiñones-Hinojosa
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - M Glas
- Institute of Reconstructive Neurobiology, MediClin Robert Janker Klinik and University of Bonn Medical Center, Bonn, Germany.,Department of Neurology, MediClin Robert Janker Klinik and University of Bonn Medical Center, Bonn, Germany.,Clinical Cooperation Unit Neurooncology, MediClin Robert Janker Klinik and University of Bonn Medical Center, Bonn, Germany
| | - B Scheffler
- Institute of Reconstructive Neurobiology, MediClin Robert Janker Klinik and University of Bonn Medical Center, Bonn, Germany
| | - J Laterra
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Y Li
- Hugo W Moser Research Institute at Kennedy Krieger, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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24
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Shameer K, Klee EW, Dalenberg AK, Kullo IJ. Whole Exome Sequencing Implicates an
INO80D
Mutation in a Syndrome of Aortic Hypoplasia, Premature Atherosclerosis, and Arterial Stiffness. ACTA ACUST UNITED AC 2014; 7:607-14. [DOI: 10.1161/circgenetics.113.000233] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Massively parallel, high-throughput sequencing technology is helping to generate new insights into the genetic basis of human diseases. We used whole exome sequencing to identify the mutation underlying a syndrome affecting 2 siblings with aortic hypoplasia, calcific atherosclerosis, systolic hypertension, and premature cataract.
Methods and Results—
Exonic regions were captured and sequenced using a next-generation sequencing platform to generate 100 bases paired-end reads. A computational genomic data analysis pipeline was used to perform quality control, align reads to a reference genome, and identify genetic variants; findings were confirmed using a different exome analyses pipeline. The 2 siblings were homozygous for a rare missense mutation (Ser818Cys) in
INO80D
, a subunit of the human INO80 chromatin remodeling complex. Homozygosity mapping and Sanger sequencing confirmed that the mutation is located in one of the runs of homozygosity on chromosome 2.
INO80D
encodes a key subunit of the human IN080 complex, a multiprotein complex involved in DNA binding, chromatin modification, organization of chromosome structure, and ATP-dependent nucleosome sliding. By introducing a new disulphide-bond in the protein product and also disrupting the composition of low-complexity regions, the Ser818Cys mutation may affect INO80D function, protein–protein interactions, and chromatin remodeling.
Conclusions—
Our findings suggest a link between the Ser818Cys mutation in
INO80D
, a subunit of the human INO80 chromatin remodeling complex, and accelerated arterial aging.
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Affiliation(s)
- Khader Shameer
- From the Division of Cardiovascular Diseases (K.S., A.K.D., I.J.K.) and Biomedical Statistics and Informatics, Departments of Health Sciences Research and Laboratory Medicine and Pathology (E.W.K.), Mayo Clinic, Rochester MN
| | - Eric W. Klee
- From the Division of Cardiovascular Diseases (K.S., A.K.D., I.J.K.) and Biomedical Statistics and Informatics, Departments of Health Sciences Research and Laboratory Medicine and Pathology (E.W.K.), Mayo Clinic, Rochester MN
| | - Angela K. Dalenberg
- From the Division of Cardiovascular Diseases (K.S., A.K.D., I.J.K.) and Biomedical Statistics and Informatics, Departments of Health Sciences Research and Laboratory Medicine and Pathology (E.W.K.), Mayo Clinic, Rochester MN
| | - Iftikhar J. Kullo
- From the Division of Cardiovascular Diseases (K.S., A.K.D., I.J.K.) and Biomedical Statistics and Informatics, Departments of Health Sciences Research and Laboratory Medicine and Pathology (E.W.K.), Mayo Clinic, Rochester MN
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25
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Choukrallah MA, Matthias P. The Interplay between Chromatin and Transcription Factor Networks during B Cell Development: Who Pulls the Trigger First? Front Immunol 2014; 5:156. [PMID: 24782862 PMCID: PMC3990105 DOI: 10.3389/fimmu.2014.00156] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/25/2014] [Indexed: 01/25/2023] Open
Abstract
All mature blood cells derive from hematopoietic stem cells through gradual restriction of their cell fate potential and acquisition of specialized functions. Lineage specification and cell commitment require the establishment of specific transcriptional programs involving the activation of lineage-specific genes and the repression of lineage-inappropriate genes. This process requires the concerted action of transcription factors (TFs) and epigenetic modifying enzymes. Within the hematopoietic system, B lymphopoiesis is one of the most-studied differentiation programs. Loss of function studies allowed the identification of many TFs and epigenetic modifiers required for B cell development. The usage of systematic analytical techniques such as transcriptome determination, genome-wide mapping of TF binding and epigenetic modifications, and mass spectrometry analyses, allowed to gain a systemic description of the intricate networks that guide B cell development. However, the precise mechanisms governing the interaction between TFs and chromatin are still unclear. Generally, chromatin structure can be remodeled by some TFs but in turn can also regulate (i.e., prevent or promote) the binding of other TFs. This conundrum leads to the crucial questions of who is on first, when, and how. We review here the current knowledge about TF networks and epigenetic regulation during hematopoiesis, with an emphasis on B cell development, and discuss in particular the current models about the interplay between chromatin and TFs.
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Affiliation(s)
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research , Basel , Switzerland ; Faculty of Sciences, University of Basel , Basel , Switzerland
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26
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Billon P, Côté J. Precise deposition of histone H2A.Z in chromatin for genome expression and maintenance. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1819:290-302. [PMID: 24459731 DOI: 10.1016/j.bbagrm.2011.10.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Histone variant H2A.Z is essential in higher eukaryotes and has different functions in the cell. Several studies indicate that H2A.Z is found at specific loci in the genome such as regulatory-gene regions, where it poises genes for transcription. Itsdeposition creates chromatin regions with particular structural characteristics which could favor rapid transcription activation. This review focuses on the highly regulated mechanism of H2A.Z deposition in chromatin which is essential for genome integrity. Chaperones escort H2A.Z to large ATP-dependent chromatin remodeling enzymes which are responsible for its deposition/eviction. Over the last ten years, biochemical, genetic and genomic studies helped us understand the precise role of these complexes in this process. It hasbeen suggested that a cooperation occurs between histone acetyltransferase and chromatin remodeling activities to incorporate H2A.Z in chromatin. Its regulated deposition near centromeres and telomeres also shows its implication in chromosomal structure integrity and parallels a role in DNA damage response. Thedynamics of H2A.Z deposition/eviction at specific loci was shown to be critical for genome expression andmaintenance, thus cell fate. Altogether, recent findings reassert the importance of the regulated depositionof this histone variant. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.
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27
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Neuman SD, Ihry RJ, Gruetzmacher KM, Bashirullah A. INO80-dependent regression of ecdysone-induced transcriptional responses regulates developmental timing in Drosophila. Dev Biol 2014; 387:229-39. [PMID: 24468295 DOI: 10.1016/j.ydbio.2014.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 01/11/2014] [Indexed: 11/19/2022]
Abstract
Sequential pulses of the steroid hormone ecdysone regulate the major developmental transitions in Drosophila, and the duration of each developmental stage is determined by the length of time between ecdysone pulses. Ecdysone regulates biological responses by directly initiating target gene transcription. In turn, these transcriptional responses are known to be self-limiting, with mechanisms in place to ensure regression of hormone-dependent transcription. However, the biological significance of these transcriptional repression mechanisms remains unclear. Here we show that the chromatin remodeling protein INO80 facilitates transcriptional repression of ecdysone-regulated genes during prepupal development. In ino80 mutant animals, inefficient repression of transcriptional responses to the late larval ecdysone pulse delays the onset of the subsequent prepupal ecdysone pulse, resulting in a significantly longer prepupal stage. Conversely, increased expression of ino80 is sufficient to shorten the prepupal stage by increasing the rate of transcriptional repression. Furthermore, we demonstrate that enhancing the rate of regression of the mid-prepupal competence factor βFTZ-F1 is sufficient to determine the timing of head eversion and thus the duration of prepupal development. Although ino80 is conserved from yeast to humans, this study represents the first characterization of a bona fide ino80 mutation in any metazoan, raising the possibility that the functions of ino80 in transcriptional repression and developmental timing are evolutionarily conserved.
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Affiliation(s)
- Sarah D Neuman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA; Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Robert J Ihry
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA; Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kelly M Gruetzmacher
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA; College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Arash Bashirullah
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA; Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA.
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28
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Min JN, Tian Y, Xiao Y, Wu L, Li L, Chang S. The mINO80 chromatin remodeling complex is required for efficient telomere replication and maintenance of genome stability. Cell Res 2013; 23:1396-413. [PMID: 23979016 DOI: 10.1038/cr.2013.113] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/17/2013] [Accepted: 07/23/2013] [Indexed: 02/08/2023] Open
Abstract
The INO80 (inositol requiring mutant 80) chromatin remodeling complex plays important roles in transcriptional regulation and DNA replication and repair, and consists of several functional protein subunits, including the critical Ino80 ATPase catalytic subunit. While the function of INO80 has been studied in yeast and mammalian cell lines, we do not know how mIno80 contributes to the maintenance of genome stability to prevent cancer development in mice. Here, we use a conditional knockout approach to explore the cellular and organismal functions of mIno80. Deletion of mIno80 results in profound cellular proliferative defects and activation of p21-dependent cellular senescence. While mIno80 is required for efficient repair of DNA double strand breaks, its depletion did not impact upon the formation of γ-H2AX and 53BP1 DNA damage foci, or the activation of the ATM-CHK2-dependent DNA damage response. mIno80 deletion inhibited the generation of single-strand DNA, resulting in defects in homology-directed DNA repair (HDR) at telomeres. Fragile telomeres were prominent in mIno80(Δ/Δ) MEFs, suggesting that chromatin remodeling is required for efficient telomere replication. mIno80(-/-) mouse embryos die early during embryogenesis, while conditional deletion of mIno80 in adult mice results in weight loss and premature death. In a p53(-/-) tumor-prone background, mIno80 haploinsufficiency favored the development of sarcomas. Our studies suggest that the mIno80 chromatin remodeling complex plays important roles in telomere replication, HDR-mediated repair of dysfunctional telomeres, and maintenance of genome stability.
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Affiliation(s)
- Jin-Na Min
- Department of Laboratory Medicine and Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
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29
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Watanabe S, Peterson CL. Chromatin dynamics: flipping the switch on a chromatin remodeling machine. Cell Cycle 2013; 12:2337-8. [PMID: 23856580 PMCID: PMC3841306 DOI: 10.4161/cc.25704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Shinya Watanabe
- Program in Molecular Medicine; University of Massachusetts Medical School; Worcester, MA USA
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30
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Actin dosage lethality screening in yeast mediated by selective ploidy ablation reveals links to urmylation/wobble codon recognition and chromosome stability. G3-GENES GENOMES GENETICS 2013; 3:553-61. [PMID: 23450344 PMCID: PMC3583461 DOI: 10.1534/g3.113.005579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/15/2013] [Indexed: 12/16/2022]
Abstract
The actin cytoskeleton exists in a dynamic equilibrium with monomeric and filamentous states of its subunit protein actin. The spatial and temporal regulation of actin dynamics is critical to the many functions of actin. Actin levels are remarkably constant, suggesting that cells have evolved to function within a narrow range of actin concentrations. Here we report the results of screens in which we have increased actin levels in strains deleted for the ~4800 nonessential yeast genes using a technical advance called selective ploidy ablation. We detected 83 synthetic dosage interactions with actin, 78 resulted in reduced growth, whereas in 5 cases overexpression of actin suppressed the growth defects caused by the deleted genes. The genes were highly enriched in several classes, including transfer RNA wobble uridine modification, chromosome stability and segregation, cell growth, and cell division. We show that actin overexpression sequesters a limited pool of eEF1A, a bifunctional protein involved in aminoacyl-transfer RNA recruitment to the ribosome and actin filament cross-linking. Surprisingly, the largest class of genes is involved in chromosome stability and segregation. We show that actin mutants have chromosome segregation defects, suggesting a possible role in chromosome structure and function. Monomeric actin is a core component of the INO80 and SWR chromatin remodeling complexes and the NuA4 histone modification complex, and our results suggest these complexes may be sensitive to actin stoichiometry. We propose that the resulting effects on chromatin structure can lead to synergistic effects on chromosome stability in strains lacking genes important for chromosome maintenance.
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31
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Lu H, Cui JY, Gunewardena S, Yoo B, Zhong XB, Klaassen CD. Hepatic ontogeny and tissue distribution of mRNAs of epigenetic modifiers in mice using RNA-sequencing. Epigenetics 2012; 7:914-29. [PMID: 22772165 DOI: 10.4161/epi.21113] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Developmental regulation of gene expression is controlled by distinct epigenetic signatures catalyzed by various epigenetic modifiers. Little is known about the ontogeny and tissue distribution of these epigenetic modifiers. In the present study, we used a novel approach of RNA-sequencing to elucidate hepatic ontogeny and tissue distribution of mRNA expression of 142 epigenetic modifiers, including enzymes involved in DNA methylation/demethylation, histone acetylation/deacetylation, histone methylation/demethylation, histone phosphorylation and chromosome remodeling factors in male C57BL/6 mice. Livers from male C57BL/6 mice were collected at 12 ages from prenatal to adulthood. Many of these epigenetic modifiers were expressed at much higher levels in perinatal livers than adult livers, such as Dnmt1, Dnmt3a, Dnmt3b, Apobec3, Kat1, Ncoa4, Setd8, Ash2l, Dot1l, Cbx1, Cbx3, Cbx5, Cbx6, Ezh2, Suz12, Eed, Suv39h1, Suv420h2, Dek, Hdac1, Hdac2, Hdac7, Kdm2b, Kdm5c, Kdm7, Prmt1-5, Prmt7, Smarca4, Smarcb1, Chd4 and Ino80e. In contrast, hepatic mRNA expression of a few epigenetic modifiers increased during postnatal liver development, such as Smarca2, Kdm1b, Cbx7 and Chd3. In adult mice (60 d of age), most epigenetic modifiers were expressed at moderately (1-3-fold) higher levels in kidney and/or small intestine than liver. In conclusion, this study, for the first time, unveils developmental changes in mRNA abundance of all major known epigenetic modifiers in mouse liver. These data suggest that ontogenic changes in mRNA expression of epigenetic modifiers may play important roles in determining the addition and/or removal of corresponding epigenetic signatures during liver development.
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Affiliation(s)
- Hong Lu
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY, USA.
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