1
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Yang Z, Mameri A, Cattoglio C, Lachance C, Florez Ariza AJ, Luo J, Humbert J, Sudarshan D, Banerjea A, Galloy M, Fradet-Turcotte A, Lambert JP, Ranish JA, Côté J, Nogales E. Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. Science 2024; 385:eadl5816. [PMID: 39088653 DOI: 10.1126/science.adl5816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 05/25/2024] [Accepted: 06/25/2024] [Indexed: 08/03/2024]
Abstract
The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4, H2A, and H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the E1A binding protein P400 (EP400) subunit serves as a scaffold holding the different functional modules in specific positions, creating a distinct arrangement of the actin-related protein (ARP) module. EP400 interacts with the transformation/transcription domain-associated protein (TRRAP) subunit by using a footprint that overlaps with that of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly.
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Affiliation(s)
- Zhenlin Yang
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Amel Mameri
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Claudia Cattoglio
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, USA
| | - Jonathan Humbert
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Deepthi Sudarshan
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Arul Banerjea
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Maxime Galloy
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Amélie Fradet-Turcotte
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Jean-Philippe Lambert
- Endocrinology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | | | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division of the CHU de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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2
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Chen K, Wang L, Yu Z, Yu J, Ren Y, Wang Q, Xu Y. Structure of the human TIP60 complex. Nat Commun 2024; 15:7092. [PMID: 39154037 PMCID: PMC11330486 DOI: 10.1038/s41467-024-51259-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024] Open
Abstract
Mammalian TIP60 is a multi-functional enzyme with histone acetylation and histone dimer exchange activities. It plays roles in diverse cellular processes including transcription, DNA repair, cell cycle control, and embryonic development. Here we report the cryo-electron microscopy structures of the human TIP60 complex with the core subcomplex and TRRAP module refined to 3.2-Å resolution. The structures show that EP400 acts as a backbone integrating the motor module, the ARP module, and the TRRAP module. The RUVBL1-RUVBL2 hexamer serves as a rigid core for the assembly of EP400 ATPase and YL1 in the motor module. In the ARP module, an ACTL6A-ACTB heterodimer and an extra ACTL6A make hydrophobic contacts with EP400 HSA helix, buttressed by network interactions among DMAP1, EPC1, and EP400. The ARP module stably associates with the motor module but is flexibly tethered to the TRRAP module, exhibiting a unique feature of human TIP60. The architecture of the nucleosome-bound human TIP60 reveals an unengaged nucleosome that is located between the core subcomplex and the TRRAP module. Our work illustrates the molecular architecture of human TIP60 and provides architectural insights into how this complex is bound by the nucleosome.
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Affiliation(s)
- Ke Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Li Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Jiali Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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3
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Yamaguchi K, Nakagawa S, Furukawa Y. Understanding the role of BRD8 in human carcinogenesis. Cancer Sci 2024. [PMID: 38965933 DOI: 10.1111/cas.16263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/16/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024] Open
Abstract
The bromodomain is a conserved protein-protein interaction module that functions exclusively to recognize acetylated lysine residues on histones and other proteins. It is noteworthy that bromodomain-containing proteins are involved in transcriptional modulation by recruiting various transcription factors and/or protein complexes such as ATP-dependent chromatin remodelers and acetyltransferases. Bromodomain-containing protein 8 (BRD8), a molecule initially recognized as skeletal muscle abundant protein and thyroid hormone receptor coactivating protein of 120 kDa (TrCP120), was shown to be a subunit of the NuA4/TIP60-histone acetyltransferase complex. BRD8 has been reported to be upregulated in a subset of cancers and implicated in the regulation of cell proliferation as well as in the response to cytotoxic agents. However, little is still known about the underlying molecular mechanisms. In recent years, it has become increasingly clear that the bromodomain of BRD8 recognizes acetylated and/or nonacetylated histones H4 and H2AZ, and that BRD8 is associated with cancer development in both a NuA4/TIP60 complex-dependent and -independent manner. In this review, we will provide an overview of the current knowledge on the molecular function of BRD8, focusing on the biological role of the bromodomain of BRD8 in cancer cells.
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Affiliation(s)
- Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saya Nakagawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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4
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Laframboise SJ, Deneault LF, Denoncourt A, Downey M, Baetz K. Uncovering the Role of the Yeast Lysine Acetyltransferase NuA4 in the Regulation of Nuclear Shape and Lipid Metabolism. Mol Cell Biol 2024; 44:273-288. [PMID: 38961766 PMCID: PMC11253884 DOI: 10.1080/10985549.2024.2366206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/19/2024] [Indexed: 07/05/2024] Open
Abstract
Here, we report a novel role for the yeast lysine acetyltransferase NuA4 in regulating phospholipid availability for organelle morphology. Disruption of the NuA4 complex results in 70% of cells displaying nuclear deformations and nearly 50% of cells exhibiting vacuolar fragmentation. Cells deficient in NuA4 also show severe defects in the formation of nuclear-vacuole junctions (NJV), as well as a decrease in piecemeal microautophagy of the nucleus (PMN). To determine the cause of these defects we focused on Pah1, an enzyme that converts phosphatidic acid into diacylglycerol, favoring accumulation of lipid droplets over phospholipids that are used for membrane expansion. NuA4 subunit Eaf1 was required for Pah1 localization to the inner nuclear membrane and artificially tethering of Pah1 to the nuclear membrane rescued nuclear deformation and vacuole fragmentation defects, but not defects related to the formation of NVJs. Mutation of a NuA4-dependent acetylation site on Pah1 also resulted in aberrant Pah1 localization and defects in nuclear morphology and NVJ. Our work suggests a critical role for NuA4 in organelle morphology that is partially mediated through the regulation of Pah1 subcellular localization.
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Affiliation(s)
- Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Lauren F. Deneault
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Alix Denoncourt
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Downey
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
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5
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Kiss AE, Venkatasubramani AV, Pathirana D, Krause S, Sparr A, Hasenauer J, Imhof A, Müller M, Becker P. Processivity and specificity of histone acetylation by the male-specific lethal complex. Nucleic Acids Res 2024; 52:4889-4905. [PMID: 38407474 PMCID: PMC11109948 DOI: 10.1093/nar/gkae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
Acetylation of lysine 16 of histone H4 (H4K16ac) stands out among the histone modifications, because it decompacts the chromatin fiber. The metazoan acetyltransferase MOF (KAT8) regulates transcription through H4K16 acetylation. Antibody-based studies had yielded inconclusive results about the selectivity of MOF to acetylate the H4 N-terminus. We used targeted mass spectrometry to examine the activity of MOF in the male-specific lethal core (4-MSL) complex on nucleosome array substrates. This complex is part of the Dosage Compensation Complex (DCC) that activates X-chromosomal genes in male Drosophila. During short reaction times, MOF acetylated H4K16 efficiently and with excellent selectivity. Upon longer incubation, the enzyme progressively acetylated lysines 12, 8 and 5, leading to a mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains substrate-bound and continues to acetylate more N-terminal H4 lysines in a processive manner. The 4-MSL complex lacks non-coding roX RNA, a critical component of the DCC. Remarkably, addition of RNA to the reaction non-specifically suppressed H4 oligo-acetylation in favor of specific H4K16 acetylation. Because RNA destabilizes the MSL-nucleosome interaction in vitro we speculate that RNA accelerates enzyme-substrate turn-over in vivo, thus limiting the processivity of MOF, thereby increasing specific H4K16 acetylation.
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Affiliation(s)
- Anna E Kiss
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Anuroop V Venkatasubramani
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Dilan Pathirana
- Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Silke Krause
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Aline Campos Sparr
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Jan Hasenauer
- Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Axel Imhof
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Marisa Müller
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
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6
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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7
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Wachtel M, Surdez D, Grünewald TGP, Schäfer BW. Functional Classification of Fusion Proteins in Sarcoma. Cancers (Basel) 2024; 16:1355. [PMID: 38611033 PMCID: PMC11010897 DOI: 10.3390/cancers16071355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Sarcomas comprise a heterogeneous group of malignant tumors of mesenchymal origin. More than 80 entities are associated with different mesenchymal lineages. Sarcomas with fibroblastic, muscle, bone, vascular, adipocytic, and other characteristics are distinguished. Nearly half of all entities contain specific chromosomal translocations that give rise to fusion proteins. These are mostly pathognomonic, and their detection by various molecular techniques supports histopathologic classification. Moreover, the fusion proteins act as oncogenic drivers, and their blockade represents a promising therapeutic approach. This review summarizes the current knowledge on fusion proteins in sarcoma. We categorize the different fusion proteins into functional classes, including kinases, epigenetic regulators, and transcription factors, and describe their mechanisms of action. Interestingly, while fusion proteins acting as transcription factors are found in all mesenchymal lineages, the others have a more restricted pattern. Most kinase-driven sarcomas belong to the fibroblastic/myofibroblastic lineage. Fusion proteins with an epigenetic function are mainly associated with sarcomas of unclear differentiation, suggesting that epigenetic dysregulation leads to a major change in cell identity. Comparison of mechanisms of action reveals recurrent functional modes, including antagonism of Polycomb activity by fusion proteins with epigenetic activity and recruitment of histone acetyltransferases by fusion transcription factors of the myogenic lineage. Finally, based on their biology, we describe potential approaches to block the activity of fusion proteins for therapeutic intervention. Overall, our work highlights differences as well as similarities in the biology of fusion proteins from different sarcomas and provides the basis for a functional classification.
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Affiliation(s)
- Marco Wachtel
- Department of Oncology and Children’s Research Center, University Children’s Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
| | - Didier Surdez
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), CH-8008 Zurich, Switzerland
| | - Thomas G. P. Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Hopp-Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership between DKFZ and Heidelberg University Hospital, 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Beat W. Schäfer
- Department of Oncology and Children’s Research Center, University Children’s Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland
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8
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Lo TL, Wang Q, Nickson J, van Denderen BJW, Deveson Lucas D, Chai HX, Knott GJ, Weerasinghe H, Traven A. The C-terminal protein interaction domain of the chromatin reader Yaf9 is critical for pathogenesis of Candida albicans. mSphere 2024; 9:e0069623. [PMID: 38376217 PMCID: PMC10964406 DOI: 10.1128/msphere.00696-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
Fungal infections cause a large health burden but are treated by only a handful of antifungal drug classes. Chromatin factors have emerged as possible targets for new antifungals. These targets include the reader proteins, which interact with posttranslationally modified histones to influence DNA transcription and repair. The YEATS domain is one such reader recognizing both crotonylated and acetylated histones. Here, we performed a detailed structure/function analysis of the Candida albicans YEATS domain reader Yaf9, a subunit of the NuA4 histone acetyltransferase and the SWR1 chromatin remodeling complex. We have previously demonstrated that the homozygous deletion mutant yaf9Δ/Δ displays growth defects and is avirulent in mice. Here we show that a YEATS domain mutant expected to inactivate Yaf9's chromatin binding does not display strong phenotypes in vitro, nor during infection of immune cells or in a mouse systemic infection model, with only a minor virulence reduction in vivo. In contrast to the YEATS domain mutation, deletion of the C-terminal domain of Yaf9, a protein-protein interaction module necessary for its interactions with SWR1 and NuA4, phenocopies the null mutant. This shows that the C-terminal domain is essential for Yaf9 roles in vitro and in vivo, including C. albicans virulence. Our study informs on the strategies for therapeutic targeting of Yaf9, showing that approaches taken for the mammalian YEATS domains by disrupting their chromatin binding might not be effective in C. albicans, and provides a foundation for studying YEATS proteins in human fungal pathogens.IMPORTANCEThe scarcity of available antifungal drugs and rising resistance demand the development of therapies with new modes of action. In this context, chromatin regulation may be a target for novel antifungal therapeutics. To realize this potential, we must better understand the roles of chromatin regulators in fungal pathogens. Toward this goal, here, we studied the YEATS domain chromatin reader Yaf9 in Candida albicans. Yaf9 uses the YEATS domain for chromatin binding and a C-terminal domain to interact with chromatin remodeling complexes. By constructing mutants in these domains and characterizing their phenotypes, our data indicate that the Yaf9 YEATS domain might not be a suitable therapeutic drug target. Instead, the Yaf9 C-terminal domain is critical for C. albicans virulence. Collectively, our study informs how a class of chromatin regulators performs their cellular and pathogenesis roles in C. albicans and reveals strategies to inhibit them.
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Affiliation(s)
- Tricia L. Lo
- Department of Biochemistry and Molecular Biology and the Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Qi Wang
- Department of Biochemistry and Molecular Biology and the Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Joshua Nickson
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Bryce J. W. van Denderen
- Department of Biochemistry and Molecular Biology and the Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | | | - Her Xiang Chai
- Department of Biochemistry and Molecular Biology and the Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Gavin J. Knott
- Department of Biochemistry and Molecular Biology and the Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Harshini Weerasinghe
- Department of Biochemistry and Molecular Biology and the Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Ana Traven
- Department of Biochemistry and Molecular Biology and the Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
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9
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Vignesh P, Mahadevaiah C, Selvamuthu K, Mahadeva Swamy HK, Sreenivasa V, Appunu C. Comparative genome-wide characterization of salt responsive micro RNA and their targets through integrated small RNA and de novo transcriptome profiling in sugarcane and its wild relative Erianthus arundinaceus. 3 Biotech 2024; 14:24. [PMID: 38162015 PMCID: PMC10756875 DOI: 10.1007/s13205-023-03867-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024] Open
Abstract
Soil salinity and saline irrigation water are major constraints in sugarcane affecting the production of cane and sugar yield. To understand the salinity induced responses and to identify novel genomic resources, integrated de novo transcriptome and small RNA sequencing in sugarcane wild relative, Erianthus arundinaceus salt tolerant accession IND 99-907 and salt-sensitive sugarcane genotype Co 97010 were performed. A total of 362 known miRNAs belonging to 62 families and 353 miRNAs belonging to 63 families were abundant in IND 99-907 and Co 97010 respectively. The miRNA families such as miR156, miR160, miR166, miR167, miR169, miR171, miR395, miR399, miR437 and miR5568 were the most abundant with more than ten members in both genotypes. The differential expression analysis of miRNA reveals that 221 known miRNAs belonging to 48 families and 130 known miRNAs belonging to 42 families were differentially expressed in IND 99-907 and Co 97010 respectively. A total of 12,693 and 7982 miRNA targets against the monoploid mosaic genome and a total of 15,031 and 12,152 miRNA targets against the de novo transcriptome were identified for differentially expressed known miRNAs of IND 99-907 and Co 97010 respectively. The gene ontology (GO) enrichment analysis of the miRNA targets revealed that 24, 12 and 14 enriched GO terms (FDR < 0.05) for biological process, molecular function and cellular component respectively. These miRNAs have many targets that associated in regulation of biotic and abiotic stresses. Thus, the genomic resources generated through this study are useful for sugarcane crop improvement through biotechnological and advanced breeding approaches. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03867-7.
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Affiliation(s)
- Palanisamy Vignesh
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Channappa Mahadevaiah
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
- ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bangalore, 560089 India
| | - Kannan Selvamuthu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | | | - Venkatarayappa Sreenivasa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Chinnaswamy Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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10
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Barman P, Chakraborty P, Bhaumik R, Bhaumik SR. UPS writes a new saga of SAGA. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194981. [PMID: 37657588 PMCID: PMC10843445 DOI: 10.1016/j.bbagrm.2023.194981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023]
Abstract
SAGA (Spt-Ada-Gcn5-Acetyltransferase), an evolutionarily conserved transcriptional co-activator among eukaryotes, is a large multi-subunit protein complex with two distinct enzymatic activities, namely HAT (Histone acetyltransferase) and DUB (De-ubiquitinase), and is targeted to the promoter by the gene-specific activator proteins for histone covalent modifications and PIC (Pre-initiation complex) formation in enhancing transcription (or gene activation). Targeting of SAGA to the gene promoter is further facilitated by the 19S RP (Regulatory particle) of the 26S proteasome (that is involved in targeted degradation of protein via ubiquitylation) in a proteolysis-independent manner. Moreover, SAGA is also recently found to be regulated by the 26S proteasome in a proteolysis-dependent manner via the ubiquitylation of its Sgf73/ataxin-7 component that is required for SAGA's integrity and DUB activity (and hence transcription), and is linked to various diseases including neurodegenerative disorders and cancer. Thus, SAGA itself and its targeting to the active gene are regulated by the UPS (Ubiquitin-proteasome system) with implications in diseases.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Pritam Chakraborty
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Rhea Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale IL-62901, USA.
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11
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Fréchard A, Faux C, Hexnerova R, Crucifix C, Papai G, Smirnova E, McKeon C, Ping FLY, Helmlinger D, Schultz P, Ben-Shem A. The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification. Nat Struct Mol Biol 2023; 30:1337-1345. [PMID: 37550452 DOI: 10.1038/s41594-023-01056-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/26/2023] [Indexed: 08/09/2023]
Abstract
Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles in both transcription and DNA-damage repair. NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither the molecular mechanism of this activity nor its physiological importance are known. Here we report the structure of the Pichia pastoris NuA4 complex, with its core resolved at 3.4-Å resolution. Three subunits, Epl1, Eaf1 and Swc4, intertwine to form a stable platform that coordinates all other modules. The HAT module is firmly anchored into the core while retaining the ability to stretch out over a long distance. We provide structural, biochemical and genetic evidence that an unfolded linker region of the Epl1 subunit is critical for this long-range activity. Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. Our work lays the foundations for a mechanistic understanding of NuA4's regulatory role and elucidates how its essential long-range activity is attained.
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Affiliation(s)
- Alexander Fréchard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Céline Faux
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Rozalie Hexnerova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Corinne Crucifix
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Gabor Papai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Ekaterina Smirnova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France
| | - Conor McKeon
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Florie Lo Ying Ping
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Dominique Helmlinger
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France.
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France.
| | - Adam Ben-Shem
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Integrated Structural Biology Department, Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
- Equipe labellisée Ligue Contre le Cancer, Illkirch, France.
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12
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Pan Y, Hu C, Hou LJ, Chen YL, Shi J, Liu JC, Zhou JQ. Swc4 protects nucleosome-free rDNA, tDNA and telomere loci to inhibit genome instability. DNA Repair (Amst) 2023; 127:103512. [PMID: 37230009 DOI: 10.1016/j.dnarep.2023.103512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/17/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
In the baker's yeast Saccharomyces cerevisiae, NuA4 and SWR1-C, two multisubunit complexes, are involved in histone acetylation and chromatin remodeling, respectively. Eaf1 is the assembly platform subunit of NuA4, Swr1 is the assembly platform and catalytic subunit of SWR1-C, while Swc4, Yaf9, Arp4 and Act1 form a functional module, and is present in both NuA4 and SWR1 complexes. ACT1 and ARP4 are essential for cell survival. Deletion of SWC4, but not YAF9, EAF1 or SWR1 results in a severe growth defect, but the underlying mechanism remains largely unknown. Here, we show that swc4Δ, but not yaf9Δ, eaf1Δ, or swr1Δ cells display defects in DNA ploidy and chromosome segregation, suggesting that the defects observed in swc4Δ cells are independent of NuA4 or SWR1-C integrity. Swc4 is enriched in the nucleosome-free regions (NFRs) of the genome, including characteristic regions of RDN5s, tDNAs and telomeres, independently of Yaf9, Eaf1 or Swr1. In particular, rDNA, tDNA and telomere loci are more unstable and prone to recombination in the swc4Δ cells than in wild-type cells. Taken together, we conclude that the chromatin associated Swc4 protects nucleosome-free chromatin of rDNA, tDNA and telomere loci to ensure genome integrity.
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Affiliation(s)
- Yue Pan
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin-Jun Hou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Long Chen
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiantao Shi
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jin-Qiu Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
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13
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Li X, Mei Q, Yu Q, Wang M, He F, Xiao D, Liu H, Ge F, Yu X, Li S. The TORC1 activates Rpd3L complex to deacetylate Ino80 and H2A.Z and repress autophagy. SCIENCE ADVANCES 2023; 9:eade8312. [PMID: 36888706 PMCID: PMC9995077 DOI: 10.1126/sciadv.ade8312] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Autophagy is a critical process to maintain homeostasis, differentiation, and development. How autophagy is tightly regulated by nutritional changes is poorly understood. Here, we identify chromatin remodeling protein Ino80 and histone variant H2A.Z as the deacetylation targets for histone deacetylase Rpd3L complex and uncover how they regulate autophagy in response to nutrient availability. Mechanistically, Rpd3L deacetylates Ino80 K929, which protects Ino80 from being degraded by autophagy. The stabilized Ino80 promotes H2A.Z eviction from autophagy-related genes, leading to their transcriptional repression. Meanwhile, Rpd3L deacetylates H2A.Z, which further blocks its deposition into chromatin to repress the transcription of autophagy-related genes. Rpd3-mediated deacetylation of Ino80 K929 and H2A.Z is enhanced by the target of rapamycin complex 1 (TORC1). Inactivation of TORC1 by nitrogen starvation or rapamycin inhibits Rpd3L, leading to induction of autophagy. Our work provides a mechanism for chromatin remodelers and histone variants in modulating autophagy in response to nutrient availability.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qianyun Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Min Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Fei He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Duncheng Xiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Huan Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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14
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Hsieh E, Janssens DH, Paddison PJ, Browne EP, Henikoff S, OhAinle M, Emerman M. A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency. PLoS Pathog 2023; 19:e1011101. [PMID: 36706161 PMCID: PMC9907829 DOI: 10.1371/journal.ppat.1011101] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/08/2023] [Accepted: 01/05/2023] [Indexed: 01/28/2023] Open
Abstract
Transcriptional silencing of latent HIV-1 proviruses entails complex and overlapping mechanisms that pose a major barrier to in vivo elimination of HIV-1. We developed a new latency CRISPR screening strategy, called Latency HIV-CRISPR which uses the packaging of guideRNA-encoding lentiviral vector genomes into the supernatant of budding virions as a direct readout of factors involved in the maintenance of HIV-1 latency. We developed a custom guideRNA library targeting epigenetic regulatory genes and paired the screen with and without a latency reversal agent-AZD5582, an activator of the non-canonical NFκB pathway-to examine a combination of mechanisms controlling HIV-1 latency. A component of the Nucleosome Acetyltransferase of H4 histone acetylation (NuA4 HAT) complex, ING3, acts in concert with AZD5582 to activate proviruses in J-Lat cell lines and in a primary CD4+ T cell model of HIV-1 latency. We found that the knockout of ING3 reduces acetylation of the H4 histone tail and BRD4 occupancy on the HIV-1 LTR. However, the combination of ING3 knockout accompanied with the activation of the non-canonical NFκB pathway via AZD5582 resulted in a dramatic increase in initiation and elongation of RNA Polymerase II on the HIV-1 provirus in a manner that is nearly unique among all cellular promoters.
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Affiliation(s)
- Emily Hsieh
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Derek H. Janssens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Patrick J. Paddison
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Edward P. Browne
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Steve Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Molly OhAinle
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Michael Emerman
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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15
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Abstract
Nucleosome acetyltransferase of H4 (NuA4), one of two major histone acetyltransferase complexes in Saccharomyces cerevisiae specifically acetylates histone H2A and H4, resulting in increased transcriptional activity. Here we present a 3.8-4.0 Å resolution structure of the NuA4 complex from cryoelectron microscopy and associated biochemical studies. The determined structure comprises six subunits and appropriately 5,000 amino acids, with a backbone formed by subunits Eaf1 and Eaf2 spanning from an Actin-Arp4 module to a platform subunit Tra1. Seven subunits are missing from the cryo-EM map. The locations of missing components, Yaf9, and three subunits of the Piccolo module Esa1, Yng2, and Eaf6 were determined. Biochemical studies showed that the Piccolo module and the complete NuA4 exhibit comparable histone acetyltransferase activities, but the Piccolo module binds to nucleosomes, whereas the complete NuA4 does not. The interaction lifetime of NuA4 and nucleosome is evidently short, possibly because of subunits of the NuA4 complex that diminish the affinity of the Piccolo module for the nucleosome, enabling rapid movement from nucleosome to nucleosome.
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16
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Lu PYT, Kirlin AC, Aristizabal MJ, Brewis HT, Lévesque N, Setiaputra DT, Avvakumov N, Benschop JJ, Groot Koerkamp M, Holstege FCP, Krogan NJ, Yip CK, Côté J, Kobor MS. A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans. Genetics 2022; 222:iyac136. [PMID: 36066422 PMCID: PMC9630986 DOI: 10.1093/genetics/iyac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 lysine acetyltransferase complex acetylates histone and nonhistone proteins and functions in transcription regulation, cell cycle progression, and DNA repair. NuA4 harbors an interesting duality in that its catalytic module can function independently and distinctly as picNuA4. At the molecular level, picNuA4 anchors to its bigger brother via physical interactions between the C-terminus of Epl1 and the HSA domain of Eaf1, the NuA4 central scaffolding subunit. This is reflected at the regulatory level, as picNuA4 can be liberated genetically from NuA4 by disrupting the Epl1-Eaf1 interaction. As such, removal of either Eaf1 or the Epl1 C-terminus offers a unique opportunity to elucidate the contributions of Eaf1 and Epl1 to NuA4 biology and in turn their roles in balancing picNuA4 and NuA4 activities. Using high-throughput genetic and gene expression profiling, and targeted functional assays to compare eaf1Δ and epl1-CΔ mutants, we found that EAF1 and EPL1 had both overlapping and distinct roles. Strikingly, loss of EAF1 or its HSA domain led to a significant decrease in the amount of picNuA4, while loss of the Epl1 C-terminus increased picNuA4 levels, suggesting starkly opposing effects on picNuA4 regulation. The eaf1Δ epl1-CΔ double mutants resembled the epl1-CΔ single mutants, indicating that Eaf1's role in picNuA4 regulation depended on the Epl1 C-terminus. Key aspects of this regulation were evolutionarily conserved, as truncating an Epl1 homolog in human cells increased the levels of other picNuA4 subunits. Our findings suggested a model in which distinct aspects of the Epl1-Eaf1 interaction regulated picNuA4 amount and activity.
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Affiliation(s)
- Phoebe Y T Lu
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Alyssa C Kirlin
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Maria J Aristizabal
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Hilary T Brewis
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Nancy Lévesque
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Dheva T Setiaputra
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nikita Avvakumov
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Joris J Benschop
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | | | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht 3584 CS, The Netherlands
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jacques Côté
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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17
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Zukin SA, Marunde MR, Popova IK, Soczek KM, Nogales E, Patel AB. Structure and flexibility of the yeast NuA4 histone acetyltransferase complex. eLife 2022; 11:e81400. [PMID: 36263929 PMCID: PMC9643008 DOI: 10.7554/elife.81400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 protein complex acetylates histones H4 and H2A to activate both transcription and DNA repair. We report the 3.1-Å resolution cryo-electron microscopy structure of the central hub of NuA4, which flexibly tethers the histone acetyltransferase (HAT) and Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) modules. The hub contains the large Tra1 subunit and a core that includes Swc4, Arp4, Act1, Eaf1, and the C-terminal region of Epl1. Eaf1 stands out as the primary scaffolding factor that interacts with the Tra1, Swc4, and Epl1 subunits and contributes the conserved HSA helix to the Arp module. Using nucleosome-binding assays, we find that the HAT module, which is anchored to the core through Epl1, recognizes H3K4me3 nucleosomes with hyperacetylated H3 tails, while the TINTIN module, anchored to the core via Eaf1, recognizes nucleosomes that have hyperacetylated H2A and H4 tails. Together with the known interaction of Tra1 with site-specific transcription factors, our data suggest a model in which Tra1 recruits NuA4 to specific genomic sites then allowing the flexible HAT and TINTIN modules to select nearby nucleosomes for acetylation.
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Affiliation(s)
- Stefan A Zukin
- College of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Irina K Popova
- EpiCypher, Inc, Research Triangle ParkDurhamUnited States
| | - Katarzyna M Soczek
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Avinash B Patel
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
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18
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Structure of the NuA4 acetyltransferase complex bound to the nucleosome. Nature 2022; 610:569-574. [PMID: 36198799 DOI: 10.1038/s41586-022-05303-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022]
Abstract
Deoxyribonucleic acid in eukaryotes wraps around the histone octamer to form nucleosomes1, the fundamental unit of chromatin. The N termini of histone H4 interact with nearby nucleosomes and play an important role in the formation of high-order chromatin structure and heterochromatin silencing2-4. NuA4 in yeast and its homologue Tip60 complex in mammalian cells are the key enzymes that catalyse H4 acetylation, which in turn regulates chromatin packaging and function in transcription activation and DNA repair5-10. Here we report the cryo-electron microscopy structure of NuA4 from Saccharomyces cerevisiae bound to the nucleosome. NuA4 comprises two major modules: the catalytic histone acetyltransferase (HAT) module and the transcription activator-binding (TRA) module. The nucleosome is mainly bound by the HAT module and is positioned close to a polybasic surface of the TRA module, which is important for the optimal activity of NuA4. The nucleosomal linker DNA carrying the upstream activation sequence is oriented towards the conserved, transcription activator-binding surface of the Tra1 subunit, which suggests a potential mechanism of NuA4 to act as a transcription co-activator. The HAT module recognizes the disk face of the nucleosome through the H2A-H2B acidic patch and nucleosomal DNA, projecting the catalytic pocket of Esa1 to the N-terminal tail of H4 and supporting its function in selective acetylation of H4. Together, our findings illustrate how NuA4 is assembled and provide mechanistic insights into nucleosome recognition and transcription co-activation by a HAT.
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19
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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: 6] [Impact Index Per Article: 3.0] [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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20
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Lashgari A, Kougnassoukou Tchara PE, Lambert JP, Côté J. New insights into the DNA repair pathway choice with NuA4/TIP60. DNA Repair (Amst) 2022; 113:103315. [PMID: 35278769 DOI: 10.1016/j.dnarep.2022.103315] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 11/03/2022]
Abstract
In eukaryotic cells, DNA double-strand breaks (DSBs) can be repaired through two main pathways, non-homologous end-joining (NHEJ) or homologous recombination (HR). The selection of the repair pathway choice is governed by an antagonistic relationship between repair factors specific to each pathway, in a cell cycle-dependent manner. The molecular mechanisms of this decision implicate post-translational modifications of chromatin surrounding the break. Here, we discuss the recent advances regarding the function of the NuA4/TIP60 histone acetyltransferase/chromatin remodeling complex during DSBs repair. In particular, we emphasise the contribution of NuA4/TIP60 in repair pathway choice, in collaboration with the SAGA acetyltransferase complex, and how they regulate chromatin dynamics, modify non-histone substrates to allow DNA end resection and recombination.
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Affiliation(s)
- Anahita Lashgari
- St-Patrick Research Group in Basic Oncology, Canada; Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada
| | - Pata-Eting Kougnassoukou Tchara
- Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada
| | - Jean-Philippe Lambert
- Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada.
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Canada; Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada.
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21
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Barry RM, Sacco O, Mameri A, Stojaspal M, Kartsonis W, Shah P, De Ioannes P, Hofr C, Côté J, Sfeir A. Rap1 regulates TIP60 function during fate transition between two-cell-like and pluripotent states. Genes Dev 2022; 36:313-330. [PMID: 35210222 PMCID: PMC8973845 DOI: 10.1101/gad.349039.121] [Citation(s) in RCA: 6] [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: 10/07/2021] [Accepted: 02/08/2022] [Indexed: 01/05/2023]
Abstract
In mammals, the conserved telomere binding protein Rap1 serves a diverse set of nontelomeric functions, including activation of the NF-kB signaling pathway, maintenance of metabolic function in vivo, and transcriptional regulation. Here, we uncover the mechanism by which Rap1 modulates gene expression. Using a separation-of-function allele, we show that Rap1 transcriptional regulation is largely independent of TRF2-mediated binding to telomeres and does not involve direct binding to genomic loci. Instead, Rap1 interacts with the TIP60/p400 complex and modulates its histone acetyltransferase activity. Notably, we show that deletion of Rap1 in mouse embryonic stem cells increases the fraction of two-cell-like cells. Specifically, Rap1 enhances the repressive activity of Tip60/p400 across a subset of two-cell-stage genes, including Zscan4 and the endogenous retrovirus MERVL. Preferential up-regulation of genes proximal to MERVL elements in Rap1-deficient settings implicates these endogenous retroviral elements in the derepression of proximal genes. Altogether, our study reveals an unprecedented link between Rap1 and the TIP60/p400 complex in the regulation of pluripotency.
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Affiliation(s)
- Raymond Mario Barry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Olivia Sacco
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Amel Mameri
- St-Patrick Research Group in Basic Oncology; CHU de Québec-Université Laval Research Center-Oncology Division, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Martin Stojaspal
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - William Kartsonis
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - Pooja Shah
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York 10016, USA
| | - Pablo De Ioannes
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Ctirad Hofr
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Scientific Incubator, 612 65 Brno, Czech Republic
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology; CHU de Québec-Université Laval Research Center-Oncology Division, Laval University Cancer Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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22
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CaSWC4 regulates the immunity-thermotolerance tradeoff by recruiting CabZIP63/CaWRKY40 to target genes and activating chromatin in pepper. PLoS Genet 2022; 18:e1010023. [PMID: 35226664 PMCID: PMC8884482 DOI: 10.1371/journal.pgen.1010023] [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: 07/28/2021] [Accepted: 01/10/2022] [Indexed: 11/19/2022] Open
Abstract
Pepper (Capsicum annuum) responds differently to high temperature stress (HTS) and Ralstonia solanacearum infection (RSI) but employs some shared transcription factors (TFs), such as CabZIP63 and CaWRKY40, in both cases. How the plant activates and balances these distinct responses, however, was unclear. Here, we show that the protein CaSWC4 interacts with CaRUVBL2 and CaTAF14b and they all act positively in pepper response to RSI and thermotolerance. CaSWC4 activates chromatin of immunity or thermotolerance related target genes of CaWRKY40 or CabZIP63 by promoting deposition of H2A.Z, H3K9ac and H4K5ac, simultaneously recruits CabZIP63 and CaWRKY40 through physical interaction and brings them to their targets (immunity- or thermotolerance-related genes) via binding AT-rich DNA element. The above process relies on the recruitment of CaRUVBL2 and TAF14 by CaSWC4 via physical interaction, which occurs at loci of immunity related target genes only when the plants are challenged with RSI, and at loci of thermotolerance related target genes only upon HTS. Collectively, our data suggest that CaSWC4 regulates rapid, accurate responses to both RSI and HTS by modulating chromatin of specific target genes opening and recruiting the TFs, CaRUVBL2 and CaTAF14b to the specific target genes, thereby helping achieve the balance between immunity and thermotolerance.
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23
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NuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis. Nat Commun 2022; 13:277. [PMID: 35022409 PMCID: PMC8755797 DOI: 10.1038/s41467-021-27882-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/21/2021] [Indexed: 12/19/2022] Open
Abstract
Nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, but remains poorly characterized in plants. Here, we describe Arabidopsis homologs of the NuA4 scaffold proteins Enhancer of Polycomb-Like 1 (AtEPL1) and Esa1-Associated Factor 1 (AtEAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors, suggesting that NuA4 activates nuclear plastid genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished genome-wide in Atepl1, while another active chromatin mark, H3K9 acetylation (H3K9ac), is locally enhanced. Expression of many chloroplast-related genes depends on NuA4, as they are downregulated with loss of H4ac and H2A.Zac. Finally, we demonstrate that NuA4 promotes H2A.Z deposition and by doing so prevents spurious activation of stress response genes. Function of nucleosomal acetyltransferase of H4 (NuA4), one major complex of HAT, remains unclear in plants. Here, the authors generate mutants targeting two components of the putative NuA4 complex in Arabidopsis (EAF1 and EPL1) and show their roles in photosynthesis genes regulation through H4K5ac and H2A.Z acetylation.
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24
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Zhang J, Gundu A, Strahl BD. Recognition of acetylated histone by Yaf9 regulates metabolic cycling of transcription initiation and chromatin regulatory factors. Genes Dev 2021; 35:1678-1692. [PMID: 34819351 PMCID: PMC8653784 DOI: 10.1101/gad.348904.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/02/2021] [Indexed: 12/14/2022]
Abstract
How transcription programs rapidly adjust to changing metabolic and cellular cues remains poorly defined. Here, we reveal a function for the Yaf9 component of the SWR1-C and NuA4 chromatin regulatory complexes in maintaining timely transcription of metabolic genes across the yeast metabolic cycle (YMC). By reading histone acetylation during the oxidative and respiratory phase of the YMC, Yaf9 recruits SWR1-C and NuA4 complexes to deposit H2A.Z and acetylate H4, respectively. Increased H2A.Z and H4 acetylation during the oxidative phase promotes transcriptional initiation and chromatin machinery occupancy and is associated with reduced RNA polymerase II levels at genes-a pattern reversed during transition from oxidative to reductive metabolism. Prevention of Yaf9-H3 acetyl reading disrupted this pattern of transcriptional and chromatin regulator recruitment and impaired the timely transcription of metabolic genes. Together, these findings reveal that Yaf9 contributes to a dynamic chromatin and transcription initiation factor signature that is necessary for the proper regulation of metabolic gene transcription during the YMC. They also suggest that unique regulatory mechanisms of transcription exist at distinct metabolic states.
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Affiliation(s)
- Jibo Zhang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Aakanksha Gundu
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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25
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Razzaq I, Berg MD, Jiang Y, Genereaux J, Uthayakumar D, Kim GH, Agyare-Tabbi M, Halder V, Brandl CJ, Lajoie P, Shapiro RS. The SAGA and NuA4 component Tra1 regulates Candida albicans drug resistance and pathogenesis. Genetics 2021; 219:iyab131. [PMID: 34849885 PMCID: PMC8633099 DOI: 10.1093/genetics/iyab131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/02/2021] [Indexed: 11/14/2022] Open
Abstract
Candida albicans is the most common cause of death from fungal infections. The emergence of resistant strains reducing the efficacy of first-line therapy with echinocandins, such as caspofungin calls for the identification of alternative therapeutic strategies. Tra1 is an essential component of the SAGA and NuA4 transcriptional co-activator complexes. As a PIKK family member, Tra1 is characterized by a C-terminal phosphoinositide 3-kinase domain. In Saccharomyces cerevisiae, the assembly and function of SAGA and NuA4 are compromised by a Tra1 variant (Tra1Q3) with three arginine residues in the putative ATP-binding cleft changed to glutamine. Whole transcriptome analysis of the S. cerevisiae tra1Q3 strain highlights Tra1's role in global transcription, stress response, and cell wall integrity. As a result, tra1Q3 increases susceptibility to multiple stressors, including caspofungin. Moreover, the same tra1Q3 allele in the pathogenic yeast C. albicans causes similar phenotypes, suggesting that Tra1 broadly mediates the antifungal response across yeast species. Transcriptional profiling in C. albicans identified 68 genes that were differentially expressed when the tra1Q3 strain was treated with caspofungin, as compared to gene expression changes induced by either tra1Q3 or caspofungin alone. Included in this set were genes involved in cell wall maintenance, adhesion, and filamentous growth. Indeed, the tra1Q3 allele reduces filamentation and other pathogenesis traits in C. albicans. Thus, Tra1 emerges as a promising therapeutic target for fungal infections.
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Affiliation(s)
- Iqra Razzaq
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Matthew D Berg
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Yuwei Jiang
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Deeva Uthayakumar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Grace H Kim
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Michelle Agyare-Tabbi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Viola Halder
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Rebecca S Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
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26
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Ahmad S, Côté V, Cheng X, Bourriquen G, Sapountzi V, Altaf M, Côté J. Antagonistic relationship of NuA4 with the non-homologous end-joining machinery at DNA damage sites. PLoS Genet 2021; 17:e1009816. [PMID: 34543274 PMCID: PMC8483352 DOI: 10.1371/journal.pgen.1009816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 09/30/2021] [Accepted: 09/09/2021] [Indexed: 11/19/2022] Open
Abstract
The NuA4 histone acetyltransferase complex, apart from its known role in gene regulation, has also been directly implicated in the repair of DNA double-strand breaks (DSBs), favoring homologous recombination (HR) in S/G2 during the cell cycle. Here, we investigate the antagonistic relationship of NuA4 with non-homologous end joining (NHEJ) factors. We show that budding yeast Rad9, the 53BP1 ortholog, can inhibit NuA4 acetyltransferase activity when bound to chromatin in vitro. While we previously reported that NuA4 is recruited at DSBs during the S/G2 phase, we can also detect its recruitment in G1 when genes for Rad9 and NHEJ factors Yku80 and Nej1 are mutated. This is accompanied with the binding of single-strand DNA binding protein RPA and Rad52, indicating DNA end resection in G1 as well as recruitment of the HR machinery. This NuA4 recruitment to DSBs in G1 depends on Mre11-Rad50-Xrs2 (MRX) and Lcd1/Ddc2 and is linked to the hyper-resection phenotype of NHEJ mutants. It also implicates NuA4 in the resection-based single-strand annealing (SSA) repair pathway along Rad52. Interestingly, we identified two novel non-histone acetylation targets of NuA4, Nej1 and Yku80. Acetyl-mimicking mutant of Nej1 inhibits repair of DNA breaks by NHEJ, decreases its interaction with other core NHEJ factors such as Yku80 and Lif1 and favors end resection. Altogether, these results establish a strong reciprocal antagonistic regulatory function of NuA4 and NHEJ factors in repair pathway choice and suggests a role of NuA4 in alternative repair mechanisms in situations where some DNA-end resection can occur in G1. DNA double-strand breaks (DSBs) are one of the most harmful form of DNA damage. Cells employ two major repair pathways to resolve DSBs: Homologous Recombination (HR) and Non-Homologous End Joining (NHEJ). Here we wanted to dissect further the role played by the NuA4 (Nucleosome acetyltransferase of histone H4) complex in the repair of DSBs. Budding yeast NuA4 complex, like its mammalian homolog TIP60 complex, has been shown to favor repair by HR. Here, we show that indeed budding yeast NuA4 and components of the NHEJ repair pathway share an antagonistic relationship. Deletion of NHEJ components enables increased recruitment of NuA4 in the vicinity of DSBs, possible through two independent mechanisms, where NuA4 favors the end resection process which implicates it in repair by single-strand annealing (SSA), an alternate homology-based repair pathway. Additionally, we also present two NHEJ core components as new targets of NuA4 acetyltransferase activity and suggest that these acetylation events can disassemble the NHEJ repair complex from DSBs, favoring repair by HR. Our study demonstrates the importance of NuA4 in the modulation of DSB repair pathway choice.
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Affiliation(s)
- Salar Ahmad
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Valérie Côté
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Gaëlle Bourriquen
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Vasileia Sapountzi
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Mohammed Altaf
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, Canada
- * E-mail:
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27
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Cheng X, Côté V, Côté J. NuA4 and SAGA acetyltransferase complexes cooperate for repair of DNA breaks by homologous recombination. PLoS Genet 2021; 17:e1009459. [PMID: 34228704 PMCID: PMC8284799 DOI: 10.1371/journal.pgen.1009459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/16/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin modifying complexes play important yet not fully defined roles in DNA repair processes. The essential NuA4 histone acetyltransferase (HAT) complex is recruited to double-strand break (DSB) sites and spreads along with DNA end resection. As predicted, NuA4 acetylates surrounding nucleosomes upon DSB induction and defects in its activity correlate with altered DNA end resection and Rad51 recombinase recruitment. Importantly, we show that NuA4 is also recruited to the donor sequence during recombination along with increased H4 acetylation, indicating a direct role during strand invasion/D-loop formation after resection. We found that NuA4 cooperates locally with another HAT, the SAGA complex, during DSB repair as their combined action is essential for DNA end resection to occur. This cooperation of NuA4 and SAGA is required for recruitment of ATP-dependent chromatin remodelers, targeted acetylation of repair factors and homologous recombination. Our work reveals a multifaceted and conserved cooperation mechanism between acetyltransferase complexes to allow repair of DNA breaks by homologous recombination. DNA double-strand breaks (DSBs) are among the most dangerous types of DNA lesions as they can produce genomic instability that leads to cancer and genetic diseases. It is therefore crucial to understand the precise molecular mechanisms used by cells to detect and repair this type of damages. Homologous recombination using sister chromatid as template is the most accurate pathway to repair these breaks but has to occur within the context of the DNA compacted structure in chromosomes. Here, we show that two enzymes, NuA4 and SAGA, that acetylate the structural components of chromosomes in the vicinity of the DNA breaks are together essential for recombination-mediated repair to occur. We found that they are recruited at an early step after damage detection and their action allows subsequent remodeling of local structural organisation by other enzymes, providing DNA access to the recombination machinery. These results highlight the cooperation of enzymes for a same goal, providing robustness in the repair process as only the loss of both leads to major defects.
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Affiliation(s)
- Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Valérie Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
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Liu JC, Li QJ, He MH, Hu C, Dai P, Meng FL, Zhou BO, Zhou JQ. Swc4 positively regulates telomere length independently of its roles in NuA4 and SWR1 complexes. Nucleic Acids Res 2021; 48:12792-12803. [PMID: 33270890 PMCID: PMC7736797 DOI: 10.1093/nar/gkaa1150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2020] [Accepted: 11/10/2020] [Indexed: 01/25/2023] Open
Abstract
Telomeres at the ends of eukaryotic chromosomes are essential for genome integrality and stability. In order to identify genes that sustain telomere maintenance independently of telomerase recruitment, we have exploited the phenotype of over-long telomeres in the cells that express Cdc13-Est2 fusion protein, and examined 195 strains, in which individual non-essential gene deletion causes telomere shortening. We have identified 24 genes whose deletion results in dramatic failure of Cdc13-Est2 function, including those encoding components of telomerase, Yku, KEOPS and NMD complexes, as well as quite a few whose functions are not obvious in telomerase activity regulation. We have characterized Swc4, a shared subunit of histone acetyltransferase NuA4 and chromatin remodeling SWR1 (SWR1-C) complexes, in telomere length regulation. Deletion of SWC4, but not other non-essential subunits of either NuA4 or SWR1-C, causes significant telomere shortening. Consistently, simultaneous disassembly of NuA4 and SWR1-C does not affect telomere length. Interestingly, inactivation of Swc4 in telomerase null cells accelerates both telomere shortening and senescence rates. Swc4 associates with telomeric DNA in vivo, suggesting a direct role of Swc4 at telomeres. Taken together, our work reveals a distinct role of Swc4 in telomere length regulation, separable from its canonical roles in both NuA4 and SWR1-C.
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Affiliation(s)
- Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian-Jin Li
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming-Hong He
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Can Hu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Pengfei Dai
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Fei-Long Meng
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo O Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Scacchetti A, Becker PB. Variation on a theme: Evolutionary strategies for H2A.Z exchange by SWR1-type remodelers. Curr Opin Cell Biol 2020; 70:1-9. [PMID: 33217681 DOI: 10.1016/j.ceb.2020.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023]
Abstract
Histone variants are a universal means to alter the biochemical properties of nucleosomes, implementing local changes in chromatin structure. H2A.Z, one of the most conserved histone variants, is incorporated into chromatin by SWR1-type nucleosome remodelers. Here, we summarize recent advances toward understanding the transcription-regulatory roles of H2A.Z and of the remodeling enzymes that govern its dynamic chromatin incorporation. Tight transcriptional control guaranteed by H2A.Z nucleosomes depends on the context provided by other histone variants or chromatin modifications, such as histone acetylation. The functional cooperation of SWR1-type remodelers with NuA4 histone acetyltransferase complexes, a recurring theme during evolution, is structurally implemented by species-specific strategies.
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Affiliation(s)
- Alessandro Scacchetti
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-Universität, Munich, Germany.
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Kafer GR, Tanaka Y, Rillo-Bohn R, Shimizu E, Hasegawa K, Carlton PM. Sequential peripheral enrichment of H2A.Zac and H3K9me2 during trophoblast differentiation in human embryonic stem cells. J Cell Sci 2020; 133:jcs.245282. [PMID: 33199519 DOI: 10.1242/jcs.245282] [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: 02/16/2020] [Accepted: 10/27/2020] [Indexed: 11/20/2022] Open
Abstract
During the transition from pluripotency to a lineage-committed state, chromatin undergoes large-scale changes in structure, involving covalent modification of histone tails, use of histone variants and gene position changes with respect to the nuclear periphery. Here, using high-resolution microscopy and quantitative image analysis, we surveyed a panel of histone modifications for changes in nuclear peripheral enrichment during differentiation of human embryonic stem cells to a trophoblast-like lineage. We found two dynamic modifications at the nuclear periphery, acetylation of histone H2A.Z (H2A.Zac), and dimethylation of histone H3 at lysine 9 (H3K9me2). We demonstrate successive peripheral enrichment of these markers, with H2A.Zac followed by H3K9me2, over the course of 4 days. We find that H3K9me2 increases concomitantly with, but independently of, expression of lamin A, since deletion of lamin A did not affect H3K9me2 enrichment. We further show that inhibition of histone deacetylases causes persistent and increased H2A.Z acetylation at the periphery, delayed H3K9me2 enrichment and failure to differentiate. Our results show a concerted change in the nature of peripheral chromatin occurs upon differentiation into the trophoblast state.
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Affiliation(s)
- Georgia Rose Kafer
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Yoshihisa Tanaka
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Regina Rillo-Bohn
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Eiko Shimizu
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Kouichi Hasegawa
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Peter M Carlton
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
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31
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Walden EA, Fong RY, Pham TT, Knill H, Laframboise SJ, Huard S, Harper ME, Baetz K. Phenomic screen identifies a role for the yeast lysine acetyltransferase NuA4 in the control of Bcy1 subcellular localization, glycogen biosynthesis, and mitochondrial morphology. PLoS Genet 2020; 16:e1009220. [PMID: 33253187 PMCID: PMC7728387 DOI: 10.1371/journal.pgen.1009220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 12/10/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022] Open
Abstract
Cellular metabolism is tightly regulated by many signaling pathways and processes, including lysine acetylation of proteins. While lysine acetylation of metabolic enzymes can directly influence enzyme activity, there is growing evidence that lysine acetylation can also impact protein localization. As the Saccharomyces cerevisiae lysine acetyltransferase complex NuA4 has been implicated in a variety of metabolic processes, we have explored whether NuA4 controls the localization and/or protein levels of metabolic proteins. We performed a high-throughput microscopy screen of over 360 GFP-tagged metabolic proteins and identified 23 proteins whose localization and/or abundance changed upon deletion of the NuA4 scaffolding subunit, EAF1. Within this, three proteins were required for glycogen synthesis and 14 proteins were associated with the mitochondria. We determined that in eaf1Δ cells the transcription of glycogen biosynthesis genes is upregulated resulting in increased proteins and glycogen production. Further, in the absence of EAF1, mitochondria are highly fused, increasing in volume approximately 3-fold, and are chaotically distributed but remain functional. Both the increased glycogen synthesis and mitochondrial elongation in eaf1Δ cells are dependent on Bcy1, the yeast regulatory subunit of PKA. Surprisingly, in the absence of EAF1, Bcy1 localization changes from being nuclear to cytoplasmic and PKA activity is altered. We found that NuA4-dependent localization of Bcy1 is dependent on a lysine residue at position 313 of Bcy1. However, the glycogen accumulation and mitochondrial elongation phenotypes of eaf1Δ, while dependent on Bcy1, were not fully dependent on Bcy1-K313 acetylation state and subcellular localization of Bcy1. As NuA4 is highly conserved with the human Tip60 complex, our work may inform human disease biology, revealing new avenues to investigate the role of Tip60 in metabolic diseases.
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Affiliation(s)
- Elizabeth A. Walden
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Roger Y. Fong
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Trang T. Pham
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Hana Knill
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sarah Jane Laframboise
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Sylvain Huard
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Canada
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32
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Numata A, Kwok HS, Zhou QL, Li J, Tirado-Magallanes R, Angarica VE, Hannah R, Park J, Wang CQ, Krishnan V, Rajagopalan D, Zhang Y, Zhou S, Welner RS, Osato M, Jha S, Bohlander SK, Göttgens B, Yang H, Benoukraf T, Lough JW, Bararia D, Tenen DG. Lysine acetyltransferase Tip60 is required for hematopoietic stem cell maintenance. Blood 2020; 136:1735-1747. [PMID: 32542325 PMCID: PMC7544546 DOI: 10.1182/blood.2019001279] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic stem cells (HSCs) have the potential to replenish the blood system for the lifetime of the organism. Their 2 defining properties, self-renewal and differentiation, are tightly regulated by the epigenetic machineries. Using conditional gene-knockout models, we demonstrated a critical requirement of lysine acetyltransferase 5 (Kat5, also known as Tip60) for murine HSC maintenance in both the embryonic and adult stages, which depends on its acetyltransferase activity. Genome-wide chromatin and transcriptome profiling in murine hematopoietic stem and progenitor cells revealed that Tip60 colocalizes with c-Myc and that Tip60 deletion suppress the expression of Myc target genes, which are associated with critical biological processes for HSC maintenance, cell cycling, and DNA repair. Notably, acetylated H2A.Z (acH2A.Z) was enriched at the Tip60-bound active chromatin, and Tip60 deletion induced a robust reduction in the acH2A.Z/H2A.Z ratio. These results uncover a critical epigenetic regulatory layer for HSC maintenance, at least in part through Tip60-dependent H2A.Z acetylation to activate Myc target genes.
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Affiliation(s)
- Akihiko Numata
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Hui Si Kwok
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Qi-Ling Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | | | - Rebecca Hannah
- Department of Haematology, Wellcome and Medical Research Council Cambridge Stem Cell Institute, and
- Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Jihye Park
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Chelsia Qiuxia Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Vaidehi Krishnan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Deepa Rajagopalan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yanzhou Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Siqin Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Robert S Welner
- Hematology Oncology, Department of Medicine, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Stefan K Bohlander
- Leukaemia and Blood Cancer Research Unit, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Berthold Göttgens
- Department of Haematology, Wellcome and Medical Research Council Cambridge Stem Cell Institute, and
- Cambridge Institute for Medical Research, Cambridge University, Cambridge, United Kingdom
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St John's, NL, Canada
| | - John W Lough
- Department of Cell Biology, Neurobiology, and Anatomy, and the Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI; and
| | - Deepak Bararia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA
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Abstract
Chromatin is a highly dynamic structure that closely relates with gene expression in eukaryotes. ATP-dependent chromatin remodelling, histone post-translational modification and DNA methylation are the main ways that mediate such plasticity. The histone variant H2A.Z is frequently encountered in eukaryotes, and can be deposited or removed from nucleosomes by chromatin remodelling complex SWR1 or INO80, respectively, leading to altered chromatin state. H2A.Z has been found to be involved in a diverse range of biological processes, including genome stability, DNA repair and transcriptional regulation. Due to their formidable production of secondary metabolites, filamentous fungi play outstanding roles in pharmaceutical production, food safety and agriculture. During the last few years, chromatin structural changes were proven to be a key factor associated with secondary metabolism in fungi. However, studies on the function of H2A.Z are scarce. Here, we summarize current knowledge of H2A.Z functions with a focus on filamentous fungi. We propose that H2A.Z is a potential target involved in the regulation of secondary metabolite biosynthesis by fungi.
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34
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Scacchetti A, Schauer T, Reim A, Apostolou Z, Campos Sparr A, Krause S, Heun P, Wierer M, Becker PB. Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms. eLife 2020; 9:e56325. [PMID: 32432549 PMCID: PMC7239659 DOI: 10.7554/elife.56325] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/23/2020] [Indexed: 12/11/2022] Open
Abstract
Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene.
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Affiliation(s)
- Alessandro Scacchetti
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Tamas Schauer
- Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Alexander Reim
- Department of Proteomics and Signal Transduction, Max Planck Institute of BiochemistryMunichGermany
| | - Zivkos Apostolou
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Aline Campos Sparr
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Silke Krause
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
| | - Patrick Heun
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of EdinburghEdinburghUnited Kingdom
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of BiochemistryMunichGermany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-UniversityMunichGermany
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35
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Kraus AJ, Vanselow JT, Lamer S, Brink BG, Schlosser A, Siegel TN. Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes. Nat Commun 2020; 11:1498. [PMID: 32198348 PMCID: PMC7083915 DOI: 10.1038/s41467-020-15274-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/01/2020] [Indexed: 12/29/2022] Open
Abstract
Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histones or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization in Trypanosoma brucei, we identified 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we found TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription. Histone modification and deposition are key regulators of transcription. Here, Kraus et al. provide a quantitative histone acetylome for Trypanosoma brucei, identify histone modifications enriched at transcription start sites, and show how H4 and H2A.Z acetylation affect histone deposition and transcription in trypanosomes.
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Affiliation(s)
- Amelie J Kraus
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany.,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.,Research Center for Infectious Diseases, University of Würzburg, 97080, Würzburg, Germany.,Institute for Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany.,German Federal Institute for Risk Assessment, Unit Safety of Chemicals, Department Chemicals and Product Safety, Berlin, Germany
| | - Stephanie Lamer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - Benedikt G Brink
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany.,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - T Nicolai Siegel
- Department of Veterinary Sciences, Experimental Parasitology, Ludwig-Maximilians-Universität München, 80752, Munich, Germany. .,Biomedical Center Munich, Department of Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany. .,Research Center for Infectious Diseases, University of Würzburg, 97080, Würzburg, Germany.
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36
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Cao C, Cao Z, Yu P, Zhao Y. Genome-wide identification for genes involved in sodium dodecyl sulfate toxicity in Saccharomyces cerevisiae. BMC Microbiol 2020; 20:34. [PMID: 32066383 PMCID: PMC7027087 DOI: 10.1186/s12866-020-1721-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/06/2020] [Indexed: 11/26/2022] Open
Abstract
Background Sodium dodecyl sulfate (SDS) is one of the most widely used anionic alkyl sulfate surfactants. Toxicological information on SDS is accumulating, however, mechanisms of SDS toxicity regulation remain poorly understood. In this study, the relationship between the SDS-sensitive mutants and their intracellular ROS levels has been investigated. Results Through a genome-scale screen, we have identified 108 yeast single-gene deletion mutants that are sensitive to 0.03% SDS. These genes were predominantly related to the cellular processes of metabolism, cell cycle and DNA processing, cellular transport, transport facilities and transport routes, transcription and the protein with binding function or cofactor requirement (structural or catalytic). Measurement of the intracellular ROS (reactive oxygen species) levels of these SDS-sensitive mutants showed that about 79% of SDS-sensitive mutants accumulated significantly higher intracellular ROS levels than the wild-type cells under SDS stress. Moreover, SDS could generate oxidative damage and up-regulate several antioxidant defenses genes, and some of the SDS-sensitive genes were involved in this process. Conclusion This study provides insight on yeast genes involved in SDS tolerance and the elevated intracellular ROS caused by SDS stress, which is a potential way to understand the detoxification mechanisms of SDS by yeast cells.
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Affiliation(s)
- Chunlei Cao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Zhengfeng Cao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Peibin Yu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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37
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Zhao H, Wang Y, Yang C, Zhou J, Wang L, Yi K, Li Y, Wang Q, Shi J, Kang C, Zeng L. EGFR-vIII downregulated H2AZK4/7AC though the PI3K/AKT-HDAC2 axis to regulate cell cycle progression. Clin Transl Med 2020; 9:10. [PMID: 31993801 PMCID: PMC6987283 DOI: 10.1186/s40169-020-0260-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/13/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The EGFR-vIII mutation is the most common malignant event in GBM. Epigenetic reprogramming in EGFR-activated GBM has recently been suggested to downregulate the expression of tumour suppressor genes. Histone acetylation is important for chromatin structure and function. However, the role and biological function of H2AZK4/7AC in tumours have not yet been clarified. RESULTS In our study, we found that EGFR-vIII negatively regulated H2AZK4/7AC expression though the PI3K/AKT-HDAC2 axis. Because HDAC1 and HDAC2 are highly homologous enzymes that usually form multi-protein complexes for transcriptional regulation and epigenetic landscaping, we simultaneously knocked out HDAC1 and HDAC2 and found that H2AZK4/7AC and H3K27AC were upregulated, which partially released EGFR-vIII-mediated inhibition of USP11, negative regulator of cell cycle. In addition, we demonstrated in vitro and in vivo that FK228 induced G1/S transition arrest in GBM with EGFR-vIII mutation. FK228 could enhance anti-tumour activity by upregulating expression of the tumour suppressor USP11 in GBM cells. CONCLUSIONS EGFR-vIII mutation downregulates H2AZK4/7AC and H3K27AC, inhibiting USP11 expression though the PI3K/AKT-HDAC1/2 axis. FK228 is an effective and promising treatment for GBM with EGFR-vIII mutation.
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Affiliation(s)
- Hongyu Zhao
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yunfei Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, China
| | - Chao Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, China
| | - Junhu Zhou
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, China
| | - Lin Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, China
| | - Kaikai Yi
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, China
| | - Yansheng Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, China
| | - Qixue Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, China
| | - Jin Shi
- Department of Neurosurgery, Second Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Key Laboratory of Post-trauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin, 300052, China.
| | - Liang Zeng
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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38
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Lei B, Berger F. H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity. PLANT COMMUNICATIONS 2020; 1:100015. [PMID: 33404536 PMCID: PMC7747964 DOI: 10.1016/j.xplc.2019.100015] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/13/2019] [Accepted: 12/11/2019] [Indexed: 05/16/2023]
Abstract
The eukaryotic nucleosome prevents access to the genome. Convergently evolving histone isoforms, also called histone variants, form diverse families that are enriched over distinct features of plant genomes. Among the diverse families of plant histone variants, H2A.Z exclusively marks genes. Here we review recent research progress on the genome-wide distribution patterns and deposition of H2A.Z in plants as well as its association with histone modifications and roles in plant chromatin regulation. We also discuss some hypotheses that explain the different findings about the roles of H2A.Z in plants.
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39
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Espinosa-Cores L, Bouza-Morcillo L, Barrero-Gil J, Jiménez-Suárez V, Lázaro A, Piqueras R, Jarillo JA, Piñeiro M. Insights Into the Function of the NuA4 Complex in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:125. [PMID: 32153620 PMCID: PMC7047200 DOI: 10.3389/fpls.2020.00125] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/28/2020] [Indexed: 05/14/2023]
Abstract
Chromatin remodeling plays a key role in the establishment and maintenance of gene expression patterns essential for plant development and responses to environmental factors. Post-translational modification of histones, including acetylation, is one of the most relevant chromatin remodeling mechanisms that operate in eukaryotic cells. Histone acetylation is an evolutionarily conserved chromatin signature commonly associated with transcriptional activation. Histone acetylation levels are tightly regulated through the antagonistic activity of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In plants, different families of HATs are present, including the MYST family, which comprises homologs of the catalytic subunit of the Nucleosome Acetyltransferase of H4 (NuA4) complex in yeast. This complex mediates acetylation of histones H4, H2A, and H2A.Z, and is involved in transcriptional regulation, heterochromatin silencing, cell cycle progression, and DNA repair in yeast. In Arabidopsis and, other plant species, homologs for most of the yeast NuA4 subunits are present and although the existence of this complex has not been demonstrated yet, compelling evidence supports the notion that this type of HAT complex functions from mosses to angiosperms. Recent proteomic studies show that several Arabidopsis homologs of NuA4 components, including the assembly platform proteins and the catalytic subunit, are associated in vivo with additional members of this complex suggesting that a NuA4-like HAT complex is present in plants. Furthermore, the functional characterization of some Arabidopsis NuA4 subunits has uncovered the involvement of these proteins in the regulation of different plant biological processes. Interestingly, for most of the mutant plants deficient in subunits of this complex characterized so far, conspicuous defects in flowering time are observed, suggesting a role for NuA4 in the control of this plant developmental program. Moreover, the participation of Arabidopsis NuA4 homologs in other developmental processes, such as gametophyte development, as well as in cell proliferation and stress and hormone responses, has also been reported. In this review, we summarize the current state of knowledge on plant putative NuA4 subunits and discuss the latest progress concerning the function of this chromatin modifying complex.
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Elías-Villalobos A, Toullec D, Faux C, Séveno M, Helmlinger D. Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in yeast. Nat Commun 2019; 10:5237. [PMID: 31748520 PMCID: PMC6868236 DOI: 10.1038/s41467-019-13243-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022] Open
Abstract
Transcription initiation involves the coordinated activities of large multimeric complexes, but little is known about their biogenesis. Here we report several principles underlying the assembly and topological organization of the highly conserved SAGA and NuA4 co-activator complexes, which share the Tra1 subunit. We show that Tra1 contributes to the overall integrity of NuA4, whereas, within SAGA, it specifically controls the incorporation of the de-ubiquitination module (DUB), as part of an ordered assembly pathway. Biochemical and functional analyses reveal the mechanism by which Tra1 specifically interacts with either SAGA or NuA4. Finally, we demonstrate that Hsp90 and its cochaperone TTT promote Tra1 de novo incorporation into both complexes, indicating that Tra1, the sole pseudokinase of the PIKK family, shares a dedicated chaperone machinery with its cognate kinases. Overall, our work brings mechanistic insights into the assembly of transcriptional complexes and reveals the contribution of dedicated chaperones to this process. Transcription initiation involves the coordinated assembly and activity of large multimeric complexes. Here the authors report on the chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in fission yeast, providing insight into the de novo assembly of transcriptional complexes and the contribution of dedicated chaperones to this process.
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Affiliation(s)
| | - Damien Toullec
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Céline Faux
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Martial Séveno
- BioCampus Montpellier, CNRS, INSERM, University of Montpellier, Montpellier, France
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Roles of the INO80 and SWR1 Chromatin Remodeling Complexes in Plants. Int J Mol Sci 2019; 20:ijms20184591. [PMID: 31533258 PMCID: PMC6770637 DOI: 10.3390/ijms20184591] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic genes are packed into a dynamic but stable nucleoprotein structure called chromatin. Chromatin-remodeling and modifying complexes generate a dynamic chromatin environment that ensures appropriate DNA processing and metabolism in various processes such as gene expression, as well as DNA replication, repair, and recombination. The INO80 and SWR1 chromatin remodeling complexes (INO80-c and SWR1-c) are ATP-dependent complexes that modulate the incorporation of the histone variant H2A.Z into nucleosomes, which is a critical step in eukaryotic gene regulation. Although SWR1-c has been identified in plants, plant INO80-c has not been successfully isolated and characterized. In this review, we will focus on the functions of the SWR1-c and putative INO80-c (SWR1/INO80-c) multi-subunits and multifunctional complexes in Arabidopsis thaliana. We will describe the subunit compositions of the SWR1/INO80-c and the recent findings from the standpoint of each subunit and discuss their involvement in regulating development and environmental responses in Arabidopsis.
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Klein BJ, Ahmad S, Vann KR, Andrews FH, Mayo ZA, Bourriquen G, Bridgers JB, Zhang J, Strahl BD, Côté J, Kutateladze TG. Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain. Nucleic Acids Res 2019; 46:421-430. [PMID: 29145630 PMCID: PMC5758897 DOI: 10.1093/nar/gkx1151] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 10/31/2017] [Indexed: 12/15/2022] Open
Abstract
Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac stabilizes the complex. The side chain of K27ac inserts between two aromatic residues, mutation of which abrogates the interaction in vitro and leads in vivo to phenotypes similar to YAF9 deletion, including loss of SWR1-dependent incorporation of variant histone H2A.Z. Our findings reveal the molecular basis for the recognition of H3K27ac by a YEATS reader and underscore the importance of this interaction in mediating Yaf9 function within the NuA4 and SWR1 complexes.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Salar Ahmad
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, CHU de Québec Research Center-Oncology Axis, Quebec City, Québec G1R 3S3, Canada
| | - Kendra R Vann
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zachary A Mayo
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Gaelle Bourriquen
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, CHU de Québec Research Center-Oncology Axis, Quebec City, Québec G1R 3S3, Canada
| | - Joseph B Bridgers
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jinyong Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, CHU de Québec Research Center-Oncology Axis, Quebec City, Québec G1R 3S3, Canada
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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43
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Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
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Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
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Noguchi C, Singh T, Ziegler MA, Peake JD, Khair L, Aza A, Nakamura TM, Noguchi E. The NuA4 acetyltransferase and histone H4 acetylation promote replication recovery after topoisomerase I-poisoning. Epigenetics Chromatin 2019; 12:24. [PMID: 30992049 PMCID: PMC6466672 DOI: 10.1186/s13072-019-0271-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 04/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone acetylation plays an important role in DNA replication and repair because replicating chromatin is subject to dynamic changes in its structures. However, its precise mechanism remains elusive. In this report, we describe roles of the NuA4 acetyltransferase and histone H4 acetylation in replication fork protection in the fission yeast Schizosaccharomyces pombe. RESULTS Downregulation of NuA4 subunits renders cells highly sensitive to camptothecin, a compound that induces replication fork breakage. Defects in NuA4 function or mutations in histone H4 acetylation sites lead to impaired recovery of collapsed replication forks and elevated levels of Rad52 DNA repair foci, indicating the role of histone H4 acetylation in DNA replication and fork repair. We also show that Vid21 interacts with the Swi1-Swi3 replication fork protection complex and that Swi1 stabilizes Vid21 and promotes efficient histone H4 acetylation. Furthermore, our genetic analysis demonstrates that loss of Swi1 further sensitizes NuA4 and histone H4 mutant cells to replication fork breakage. CONCLUSION Considering that Swi1 plays a critical role in replication fork protection, our results indicate that NuA4 and histone H4 acetylation promote repair of broken DNA replication forks.
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Affiliation(s)
- Chiaki Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Tanu Singh
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Fox Chase Cancer Center, Philadelphia, USA
| | - Melissa A Ziegler
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Jasmine D Peake
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Lyne Khair
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA.,University of Massachusetts Medical School, Worcester, USA
| | - Ana Aza
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Toru M Nakamura
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.
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45
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Jiang Y, Berg MD, Genereaux J, Ahmed K, Duennwald ML, Brandl CJ, Lajoie P. Sfp1 links TORC1 and cell growth regulation to the yeast SAGA‐complex component Tra1 in response to polyQ proteotoxicity. Traffic 2019; 20:267-283. [DOI: 10.1111/tra.12637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Yuwei Jiang
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| | - Matthew D. Berg
- Department of BiochemistryThe University of Western Ontario London Ontario Canada
| | - Julie Genereaux
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
- Department of BiochemistryThe University of Western Ontario London Ontario Canada
| | - Khadija Ahmed
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| | - Martin L. Duennwald
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
- Department of Pathology and Laboratory MedicineThe University of Western Ontario London Ontario Canada
| | | | - Patrick Lajoie
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
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46
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Cheung ACM, Díaz-Santín LM. Share and share alike: the role of Tra1 from the SAGA and NuA4 coactivator complexes. Transcription 2019; 10:37-43. [PMID: 30375921 PMCID: PMC6351133 DOI: 10.1080/21541264.2018.1530936] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 01/12/2023] Open
Abstract
SAGA and NuA4 are coactivator complexes required for transcription on chromatin. Although they contain different enzymatic and biochemical activities, both contain the large Tra1 subunit. Recent electron microscopy studies have resolved the complete structure of Tra1 and its integration in SAGA/NuA4, providing important insight into Tra1 function.
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Affiliation(s)
- Alan C. M. Cheung
- Department of Structural and Molecular Biology, University College London, Institute of Structural and Molecular Biology, London, UK
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, UK
| | - Luis Miguel Díaz-Santín
- Department of Structural and Molecular Biology, University College London, Institute of Structural and Molecular Biology, London, UK
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, UK
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47
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Hodges AJ, Plummer DA, Wyrick JJ. NuA4 acetyltransferase is required for efficient nucleotide excision repair in yeast. DNA Repair (Amst) 2018; 73:91-98. [PMID: 30473425 DOI: 10.1016/j.dnarep.2018.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/02/2018] [Accepted: 11/12/2018] [Indexed: 12/13/2022]
Abstract
The nucleotide excision repair (NER) pathway is critical for removing damage induced by ultraviolet (UV) light and other helix-distorting lesions from cellular DNA. While efficient NER is critical to avoid cell death and mutagenesis, NER activity is inhibited in chromatin due to the association of lesion-containing DNA with histone proteins. Histone acetylation has emerged as an important mechanism for facilitating NER in chromatin, particularly acetylation catalyzed by the Spt-Ada-Gcn5 acetyltransferase (SAGA); however, it is not known if other histone acetyltransferases (HATs) promote NER activity in chromatin. Here, we report that the essential Nucleosome Acetyltransferase of histone H4 (NuA4) complex is required for efficient NER in Saccharomyces cerevisiae. Deletion of the non-essential Yng2 subunit of the NuA4 complex causes a general defect in repair of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast; in contrast, deletion of the Sas3 catalytic subunit of the NuA3 complex does not affect repair. Rapid depletion of the essential NuA4 catalytic subunit Esa1 using the anchor-away method also causes a defect in NER, particularly at the heterochromatic HML locus. We show that disrupting the Sds3 subunit of the Rpd3L histone deacetylase (HDAC) complex rescued the repair defect associated with loss of Esa1 activity, suggesting that NuA4-catalyzed acetylation is important for efficient NER in heterochromatin.
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Affiliation(s)
- Amelia J Hodges
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, United States
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, United States
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, United States; Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, United States.
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48
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Klages-Mundt NL, Kumar A, Zhang Y, Kapoor P, Shen X. The Nature of Actin-Family Proteins in Chromatin-Modifying Complexes. Front Genet 2018; 9:398. [PMID: 30319687 PMCID: PMC6167448 DOI: 10.3389/fgene.2018.00398] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/31/2018] [Indexed: 01/25/2023] Open
Abstract
Actin is not only one of the most abundant proteins in eukaryotic cells, but also one of the most versatile. In addition to its familiar involvement in enabling contraction and establishing cellular motility and scaffolding in the cytosol, actin has well-documented roles in a variety of processes within the confines of the nucleus, such as transcriptional regulation and DNA repair. Interestingly, monomeric actin as well as actin-related proteins (Arps) are found as stoichiometric subunits of a variety of chromatin remodeling complexes and histone acetyltransferases, raising the question of precisely what roles they serve in these contexts. Actin and Arps are present in unique combinations in chromatin modifiers, helping to establish structural integrity of the complex and enabling a wide range of functions, such as recruiting the complex to nucleosomes to facilitate chromatin remodeling and promoting ATPase activity of the catalytic subunit. Actin and Arps are also thought to help modulate chromatin dynamics and maintain higher-order chromatin structure. Moreover, the presence of actin and Arps in several chromatin modifiers is necessary for promoting genomic integrity and an effective DNA damage response. In this review, we discuss the involvement of actin and Arps in these nuclear complexes that control chromatin remodeling and histone modifications, while also considering avenues for future study to further shed light on their functional importance.
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Affiliation(s)
- Naeh L Klages-Mundt
- Science Park Research Division, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Ashok Kumar
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Yuexuan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Prabodh Kapoor
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Xuetong Shen
- Science Park Research Division, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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Phospho-dependent recruitment of the yeast NuA4 acetyltransferase complex by MRX at DNA breaks regulates RPA dynamics during resection. Proc Natl Acad Sci U S A 2018; 115:10028-10033. [PMID: 30224481 DOI: 10.1073/pnas.1806513115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The KAT5 (Tip60/Esa1) histone acetyltransferase is part of NuA4, a large multifunctional complex highly conserved from yeast to mammals that targets lysines on H4 and H2A (X/Z) tails for acetylation. It is essential for cell viability, being a key regulator of gene expression, cell proliferation, and stem cell renewal and an important factor for genome stability. The NuA4 complex is directly recruited near DNA double-strand breaks (DSBs) to facilitate repair, in part through local chromatin modification and interplay with 53BP1 during the DNA damage response. While NuA4 is detected early after appearance of the lesion, its precise mechanism of recruitment remains to be defined. Here, we report a stepwise recruitment of yeast NuA4 to DSBs first by a DNA damage-induced phosphorylation-dependent interaction with the Xrs2 subunit of the Mre11-Rad50-Xrs2 (MRX) complex bound to DNA ends. This is followed by a DNA resection-dependent spreading of NuA4 on each side of the break along with the ssDNA-binding replication protein A (RPA). Finally, we show that NuA4 can acetylate RPA and regulate the dynamics of its binding to DNA, hence targeting locally both histone and nonhistone proteins for lysine acetylation to coordinate repair.
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50
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Wang X, Zhu W, Chang P, Wu H, Liu H, Chen J. Merge and separation of NuA4 and SWR1 complexes control cell fate plasticity in Candida albicans. Cell Discov 2018; 4:45. [PMID: 30109121 PMCID: PMC6089883 DOI: 10.1038/s41421-018-0043-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/11/2018] [Accepted: 05/25/2018] [Indexed: 12/16/2022] Open
Abstract
Phenotypic plasticity is common in development. Candida albicans, a polymorphic fungal pathogen of humans, possesses the unique ability to achieve rapid and reversible cell fate between unicellular form (yeast) and multicellular form (hypha) in response to environmental cues. The NuA4 histone acetyltransferase activity and Hda1 histone deacetylase activity have been reported to be required for hyphal initiation and maintenance. However, how Hda1 and NuA4 regulate hyphal elongation is not clear. NuA4 histone acetyltransferase and SWR1 chromatin remodeling complexes are conserved from yeast to human, which may have merged together to form a larger TIP60 complex since the origin of metazoan. In this study, we show a dynamic merge and separation of NuA4 and SWR1 complexes in C. albicans. NuA4 and SWR1 merge together in yeast state and separate into two distinct complexes in hyphal state. We demonstrate that acetylation of Eaf1 K173 controls the interaction between the two complexes. The YEATS domain of Yaf9 in C. albicans can recognize an acetyl-lysine of the Eaf1 and mediate the Yaf9-Eaf1 interaction. The reversible acetylation and deacetylation of Eaf1 by Esa1 and Hda1 control the merge and separation of NuA4 and SWR1, and this regulation is triggered by Brg1 recruitment of Hda1 to chromatin in response nutritional signals that sustain hyphal elongation. We have also observed an orchestrated promoter association of Esa1, Hda1, Swr1, and H2A.Z during the reversible yeast-hyphae transitions. This is the first discovery of a regulated merge of the NuA4 and SWR1 complexes that controls cell fate determination and this regulation may be conserved in polymorphic fungi.
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Affiliation(s)
- Xiongjun Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031 China
| | - Wencheng Zhu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031 China
| | - Peng Chang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031 China
| | - Hongyu Wu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031 China
| | - Haoping Liu
- Department of Biological Chemistry, University of California, Irvine, CA 92697 USA
| | - Jiangye Chen
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031 China
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