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Vivo M, Rosti V, Cervone S, Lanzuolo C. Chromatin plasticity in mechanotransduction. Curr Opin Cell Biol 2024; 88:102376. [PMID: 38810318 DOI: 10.1016/j.ceb.2024.102376] [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: 02/02/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024]
Abstract
Living organisms can detect and respond to physical forces at the cellular level. The pathways that transmit these forces to the nucleus allow cells to react quickly and consistently to environmental changes. Mechanobiology involves the interaction between physical forces and biological processes and is crucial for driving embryonic development and adapting to environmental cues during adulthood. Molecular studies have shown that cells can sense mechanical signals directly through membrane receptors linked to the cytoskeleton or indirectly through biochemical cascades that can influence gene expression for environmental adaptation. This review will explore the role of epigenetic modifications, emphasizing the 3D genome architecture and nuclear structures as responders to mechanical stimuli, which ensure cellular memory and adaptability. Understanding how mechanical cues are transduced and regulate cell functioning, governing processes such as cell programming and reprogramming, is essential for advancing our knowledge of human diseases.
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Affiliation(s)
- Maria Vivo
- Università degli Studi di Salerno, Fisciano, Italy.
| | - Valentina Rosti
- Institute of Biomedical Technologies, National Research Council (CNR), Milan, Italy; INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Sara Cervone
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council (CNR), Milan, Italy; INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy.
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2
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Sen B, Xie Z, Thomas MD, Pattenden SG, Howard S, McGrath C, Styner M, Uzer G, Furey TS, Rubin J. Nuclear actin structure regulates chromatin accessibility. Nat Commun 2024; 15:4095. [PMID: 38750021 PMCID: PMC11096319 DOI: 10.1038/s41467-024-48580-y] [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: 08/28/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Polymerized β-actin may provide a structural basis for chromatin accessibility and actin transport into the nucleus can guide mesenchymal stem cell (MSC) differentiation. Using MSC, we show that using CK666 to inhibit Arp2/3 directed secondary actin branching results in decreased nuclear actin structure, and significantly alters chromatin access measured with ATACseq at 24 h. The ATAC-seq results due to CK666 are distinct from those caused by cytochalasin D (CytoD), which enhances nuclear actin structure. In addition, nuclear visualization shows Arp2/3 inhibition decreases pericentric H3K9me3 marks. CytoD, alternatively, induces redistribution of H3K27me3 marks centrally. Such alterations in chromatin landscape are consistent with differential gene expression associated with distinctive differentiation patterns. Further, knockdown of the non-enzymatic monomeric actin binding protein, Arp4, leads to extensive chromatin unpacking, but only a modest increase in transcription, indicating an active role for actin-Arp4 in transcription. These data indicate that dynamic actin remodeling can regulate chromatin interactions.
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Affiliation(s)
- Buer Sen
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Zhihui Xie
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Michelle D Thomas
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samantha G Pattenden
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sean Howard
- Department of Mechanical and Biomedical Engineering, Boise State University, Boise, ID, USA
| | - Cody McGrath
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Maya Styner
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Gunes Uzer
- Department of Mechanical and Biomedical Engineering, Boise State University, Boise, ID, USA
| | - Terrence S Furey
- Departments of Genetics and Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Janet Rubin
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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3
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Stephan OOH. Effects of environmental stress factors on the actin cytoskeleton of fungi and plants: Ionizing radiation and ROS. Cytoskeleton (Hoboken) 2023; 80:330-355. [PMID: 37066976 DOI: 10.1002/cm.21758] [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: 01/16/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 04/18/2023]
Abstract
Actin is an abundant and multifaceted protein in eukaryotic cells that has been detected in the cytoplasm as well as in the nucleus. In cooperation with numerous interacting accessory-proteins, monomeric actin (G-actin) polymerizes into microfilaments (F-actin) which constitute ubiquitous subcellular higher order structures. Considering the extensive spatial dimensions and multifunctionality of actin superarrays, the present study analyses the issue if and to what extent environmental stress factors, specifically ionizing radiation (IR) and reactive oxygen species (ROS), affect the cellular actin-entity. In that context, this review particularly surveys IR-response of fungi and plants. It examines in detail which actin-related cellular constituents and molecular pathways are influenced by IR and related ROS. This comprehensive survey concludes that the general integrity of the total cellular actin cytoskeleton is a requirement for IR-tolerance. Actin's functions in genome organization and nuclear events like chromatin remodeling, DNA-repair, and transcription play a key role. Beyond that, it is highly significant that the macromolecular cytoplasmic and cortical actin-frameworks are affected by IR as well. In response to IR, actin-filament bundling proteins (fimbrins) are required to stabilize cables or patches. In addition, the actin-associated factors mediating cellular polarity are essential for IR-survivability. Moreover, it is concluded that a cellular homeostasis system comprising ROS, ROS-scavengers, NADPH-oxidases, and the actin cytoskeleton plays an essential role here. Consequently, besides the actin-fraction which controls crucial genome-integrity, also the portion which facilitates orderly cellular transport and polarized growth has to be maintained in order to survive IR.
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Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Bavaria, 91058, Germany
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4
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Horníková L, Bruštíková K, Huérfano S, Forstová J. Nuclear Cytoskeleton in Virus Infection. Int J Mol Sci 2022; 23:ijms23010578. [PMID: 35009004 PMCID: PMC8745530 DOI: 10.3390/ijms23010578] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 02/04/2023] Open
Abstract
The nuclear lamina is the main component of the nuclear cytoskeleton that maintains the integrity of the nucleus. However, it represents a natural barrier for viruses replicating in the cell nucleus. The lamina blocks viruses from being trafficked to the nucleus for replication, but it also impedes the nuclear egress of the progeny of viral particles. Thus, viruses have evolved mechanisms to overcome this obstacle. Large viruses induce the assembly of multiprotein complexes that are anchored to the inner nuclear membrane. Important components of these complexes are the viral and cellular kinases phosphorylating the lamina and promoting its disaggregation, therefore allowing virus egress. Small viruses also use cellular kinases to induce lamina phosphorylation and the subsequent disruption in order to facilitate the import of viral particles during the early stages of infection or during their nuclear egress. Another component of the nuclear cytoskeleton, nuclear actin, is exploited by viruses for the intranuclear movement of their particles from the replication sites to the nuclear periphery. This study focuses on exploitation of the nuclear cytoskeleton by viruses, although this is just the beginning for many viruses, and promises to reveal the mechanisms and dynamic of physiological and pathological processes in the nucleus.
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5
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Goelzer M, Goelzer J, Ferguson ML, Neu CP, Uzer G. Nuclear envelope mechanobiology: linking the nuclear structure and function. Nucleus 2021; 12:90-114. [PMID: 34455929 PMCID: PMC8432354 DOI: 10.1080/19491034.2021.1962610] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
The nucleus, central to cellular activity, relies on both direct mechanical input as well as its molecular transducers to sense external stimuli and respond by regulating intra-nuclear chromatin organization that determines cell function and fate. In mesenchymal stem cells of musculoskeletal tissues, changes in nuclear structures are emerging as a key modulator of their differentiation and proliferation programs. In this review we will first introduce the structural elements of the nucleoskeleton and discuss the current literature on how nuclear structure and signaling are altered in relation to environmental and tissue level mechanical cues. We will focus on state-of-the-art techniques to apply mechanical force and methods to measure nuclear mechanics in conjunction with DNA, RNA, and protein visualization in living cells. Ultimately, combining real-time nuclear deformations and chromatin dynamics can be a powerful tool to study mechanisms of how forces affect the dynamics of genome function.
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Affiliation(s)
- Matthew Goelzer
- Materials Science and Engineering, Boise State University, Boise, ID, US
| | | | - Matthew L. Ferguson
- Biomolecular Science, Boise State University, Boise, ID, US
- Physics, Boise State University, Boise, ID, US
| | - Corey P. Neu
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, US
| | - Gunes Uzer
- Mechanical and Biomedical Engineering, Boise State University, Boise, ID, US
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6
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Nuclear actin dynamics in gene expression and genome organization. Semin Cell Dev Biol 2020; 102:105-112. [DOI: 10.1016/j.semcdb.2019.10.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/28/2019] [Accepted: 10/24/2019] [Indexed: 11/19/2022]
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7
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The Actin-Family Protein Arp4 Is a Novel Suppressor for the Formation and Functions of Nuclear F-Actin. Cells 2020; 9:cells9030758. [PMID: 32204557 PMCID: PMC7140684 DOI: 10.3390/cells9030758] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/06/2020] [Accepted: 03/17/2020] [Indexed: 12/20/2022] Open
Abstract
The crosstalk between actin and actin-related proteins (Arps), namely Arp2 and Arp3, plays a central role in facilitating actin polymerization in the cytoplasm and also in the nucleus. Nuclear F-actin is required for transcriptional regulation, double-strand break repair, and nuclear organization. The formation of nuclear F-actin is highly dynamic, suggesting the involvement of positive and negative regulators for nuclear actin polymerization. While actin assembly factors for nuclear F-actin have been recently described, information about inhibitory factors is still limited. The actin-related protein Arp4 which is predominantly localized in the nucleus, has been previously identified as an integral subunit of multiple chromatin modulation complexes, where it forms a heterodimer with monomeric actin. Therefore, we tested whether Arp4 functions as a suppressor of nuclear F-actin formation. The knockdown of Arp4 (Arp4 KD) led to an increase in nuclear F-actin formation in NIH3T3 cells, and purified Arp4 potently inhibited F-actin formation in mouse nuclei transplanted into Xenopus laevis oocytes. Consistently, Arp4 KD facilitated F-actin-inducible gene expression (e.g., OCT4) and DNA damage repair. Our results suggest that Arp4 has a critical role in the formation and functions of nuclear F-actin.
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8
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Venit T, Mahmood SR, Endara-Coll M, Percipalle P. Nuclear actin and myosin in chromatin regulation and maintenance of genome integrity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 355:67-108. [DOI: 10.1016/bs.ircmb.2020.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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9
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Lambert MW. The functional importance of lamins, actin, myosin, spectrin and the LINC complex in DNA repair. Exp Biol Med (Maywood) 2019; 244:1382-1406. [PMID: 31581813 PMCID: PMC6880146 DOI: 10.1177/1535370219876651] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Three major proteins in the nucleoskeleton, lamins, actin, and spectrin, play essential roles in maintenance of nuclear architecture and the integrity of the nuclear envelope, in mechanotransduction and mechanical coupling between the nucleoskeleton and cytoskeleton, and in nuclear functions such as regulation of gene expression, transcription and DNA replication. Less well known, but critically important, are the role these proteins play in DNA repair. The A-type and B-type lamins, nuclear actin and myosin, spectrin and the LINC (linker of nucleoskeleton and cytoskeleton) complex each function in repair of DNA damage utilizing various repair pathways. The lamins play a role in repair of DNA double-strand breaks (DSBs) by nonhomologous end joining (NHEJ) or homologous recombination (HR). Actin is involved in repair of DNA DSBs and interacts with myosin in facilitating relocalization of these DSBs in heterochromatin for HR repair. Nonerythroid alpha spectrin (αSpII) plays a critical role in repair of DNA interstrand cross-links (ICLs) where it acts as a scaffold in recruitment of repair proteins to sites of damage and is important in the initial damage recognition and incision steps of the repair process. The LINC complex contributes to the repair of DNA DSBs and ICLs. This review will address the important functions of these proteins in the DNA repair process, their mechanism of action, and the profound impact a defect or deficiency in these proteins has on cellular function. The critical roles of these proteins in DNA repair will be further emphasized by discussing the human disorders and the pathophysiological changes that result from or are related to deficiencies in these proteins. The demonstrated function for each of these proteins in the DNA repair process clearly indicates that there is another level of complexity that must be considered when mechanistically examining factors crucial for DNA repair.
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Affiliation(s)
- Muriel W Lambert
- Department of Pathology, Immunology and Laboratory
Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
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10
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Caridi CP, Plessner M, Grosse R, Chiolo I. Nuclear actin filaments in DNA repair dynamics. Nat Cell Biol 2019; 21:1068-1077. [PMID: 31481797 PMCID: PMC6736642 DOI: 10.1038/s41556-019-0379-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
Recent development of innovative tools for live imaging of actin filaments (F-actin) enabled the detection of surprising nuclear structures responding to various stimuli, challenging previous models that actin is substantially monomeric in the nucleus. We review these discoveries, focusing on double-strand break (DSB) repair responses. These studies revealed a remarkable network of nuclear filaments and regulatory mechanisms coordinating chromatin dynamics with repair progression and led to a paradigm shift by uncovering the directed movement of repair sites.
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Affiliation(s)
| | - Matthias Plessner
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg im Breisgau, Germany
- CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Freiburg, Freiburg im Breisgau, Germany
- CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA.
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11
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Sidorenko E, Vartiainen MK. Nucleoskeletal regulation of transcription: Actin on MRTF. Exp Biol Med (Maywood) 2019; 244:1372-1381. [PMID: 31142145 DOI: 10.1177/1535370219854669] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Myocardin-related transcription factor A (MRTF-A) and serum response factor (SRF) form an essential transcriptional complex that regulates the expression of many cytoskeletal genes in response to dynamic changes in the actin cytoskeleton. The nucleoskeleton, a “dynamic network of networks,” consists of numerous proteins that contribute to nuclear shape and to its various functions, including gene expression. In this review, we will discuss recent work that has identified many nucleoskeletal proteins, such as nuclear lamina and lamina-associated proteins, nuclear actin, and the linker of the cytoskeleton and nucleoskeleton complex as important regulators of MRTF-A/SRF transcriptional activity, especially in the context of mechanical control of transcription. Impact statement Regulation of gene expression is a fundamental cellular process that ensures the appropriate response of a cell to its surroundings. Alongside biochemical signals, mechanical cues, such as substrate rigidity, have been recognized as key regulators of gene expression. Nucleoskeletal components play an important role in mechanoresponsive transcription, particularly in controlling the activity of MRTF-A/SRF transcription factors. This ensures that the cell can balance the internal and external mechanical forces by fine-tuning the expression of cytoskeletal genes.
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Affiliation(s)
- Ekaterina Sidorenko
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Maria K Vartiainen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
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12
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Viita T, Kyheröinen S, Prajapati B, Virtanen J, Frilander MJ, Varjosalo M, Vartiainen MK. Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing. J Cell Sci 2019; 132:jcs226852. [PMID: 30890647 PMCID: PMC6503952 DOI: 10.1242/jcs.226852] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/05/2019] [Indexed: 12/25/2022] Open
Abstract
In addition to its essential functions within the cytoskeleton, actin also localizes to the cell nucleus, where it is linked to many important nuclear processes from gene expression to maintenance of genomic integrity. However, the molecular mechanisms by which actin operates in the nucleus remain poorly understood. Here, we have used two complementary mass spectrometry (MS) techniques, AP-MS and BioID, to identify binding partners for nuclear actin. Common high-confidence interactions highlight the role of actin in chromatin-remodeling complexes and identify the histone-modifying complex human Ada-Two-A-containing (hATAC) as a novel actin-containing nuclear complex. Actin binds directly to the hATAC subunit KAT14, and modulates its histone acetyl transferase activity in vitro and in cells. Transient interactions detected through BioID link actin to several steps of transcription as well as to RNA processing. Alterations in nuclear actin levels disturb alternative splicing in minigene assays, likely by affecting the transcription elongation rate. This interactome analysis thus identifies both novel direct binding partners and functional roles for nuclear actin, as well as forms a platform for further mechanistic studies on how actin operates during essential nuclear processes.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Tiina Viita
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Salla Kyheröinen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Bina Prajapati
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Jori Virtanen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
- Proteomics Unit, University of Helsinki, Helsinki 00014, Finland
| | - Maria K Vartiainen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
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13
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Hurst V, Shimada K, Gasser SM. Nuclear Actin and Actin-Binding Proteins in DNA Repair. Trends Cell Biol 2019; 29:462-476. [PMID: 30954333 DOI: 10.1016/j.tcb.2019.02.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/27/2022]
Abstract
Nuclear actin has been implicated in a variety of DNA-related processes including chromatin remodeling, transcription, replication, and DNA repair. However, the mechanistic understanding of actin in these processes has been limited, largely due to a lack of research tools that address the roles of nuclear actin specifically, that is, distinct from its cytoplasmic functions. Recent findings support a model for homology-directed DNA double-strand break (DSB) repair in which a complex of ARP2 and ARP3 (actin-binding proteins 2 and 3) binds at the break and works with actin to promote DSB clustering and homology-directed repair. Further, it has been reported that relocalization of heterochromatic DSBs to the nuclear periphery in Drosophila is ARP2/3 dependent and actin-myosin driven. Here we provide an overview of the role of nuclear actin and actin-binding proteins in DNA repair, critically evaluating the experimental tools used and potential indirect effects.
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Affiliation(s)
- Verena Hurst
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, CH-4056 Basel, Switzerland
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, CH-4056 Basel, Switzerland.
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14
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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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15
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Brahma S, Ngubo M, Paul S, Udugama M, Bartholomew B. The Arp8 and Arp4 module acts as a DNA sensor controlling INO80 chromatin remodeling. Nat Commun 2018; 9:3309. [PMID: 30120252 PMCID: PMC6098158 DOI: 10.1038/s41467-018-05710-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023] Open
Abstract
Nuclear actin and actin-related proteins (Arps) are key components of chromatin remodeling and modifying complexes. Although Arps are essential for the functions of chromatin remodelers, their specific roles and mechanisms are unclear. Here we define the nucleosome binding interfaces and functions of the evolutionarily conserved Arps in the yeast INO80 chromatin remodeling complex. We show that the N-terminus of Arp8, C-terminus of Arp4 and the HSA domain of Ino80 bind extranucleosomal DNA 37-51 base pairs from the edge of nucleosomes and function as a DNA-length sensor that regulates nucleosome sliding by INO80. Disruption of Arp8 and Arp4 binding to DNA uncouples ATP hydrolysis from nucleosome mobilization by disengaging Arp5 from the acidic patch on histone H2A-H2B and the Ino80-ATPase domain from the Super-helical Location (SHL) -6 of nucleosomes. Our data suggest a functional interplay between INO80's Arp8-Arp4-actin and Arp5 modules in sensing the DNA length separating nucleosomes and regulating nucleosome positioning.
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Affiliation(s)
- Sandipan Brahma
- Department of Epigenetics & Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.,Center for Cancer Epigenetics, MD Anderson Cancer Center, Smithville, TX, 78957, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Mzwanele Ngubo
- Department of Epigenetics & Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.,Center for Cancer Epigenetics, MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Somnath Paul
- Department of Epigenetics & Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.,Center for Cancer Epigenetics, MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Maheshi Udugama
- Department of Biochemistry and Molecular Biology, Southern Illinois University, 1245 Lincoln Drive, Carbondale, 62901, USA.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, 3800, Australia
| | - Blaine Bartholomew
- Department of Epigenetics & Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA. .,Center for Cancer Epigenetics, MD Anderson Cancer Center, Smithville, TX, 78957, USA.
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16
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Nuclear actin: ancient clue to evolution in eukaryotes? Histochem Cell Biol 2018; 150:235-244. [DOI: 10.1007/s00418-018-1693-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2018] [Indexed: 12/31/2022]
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17
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Morozov AA, Bedoshvili YD, Popova MS, Likhoshway YV. Novel subfamilies of actin-regulating proteins. Mar Genomics 2017; 37:128-134. [PMID: 29074263 DOI: 10.1016/j.margen.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/28/2017] [Accepted: 10/11/2017] [Indexed: 02/07/2023]
Abstract
Ability of actin to polymerise and depolymerise makes it essential to key functions of eukaryotic cell. The functioning of actin is controlled by a host of regulatory proteins, the repertoire of which in diatoms is known to remarkably differ from other organisms. We have performed a phylogenetic analysis of 521 actin and actin-related proteins' aminoacid sequences, as well as 190 sequences of gelsolin family proteins from various genomic and transcriptomic datasets. Based on the results of this analysis, as well as on the presence of clade-specific indels in some of the actin-related proteins, we describe a novel ARP subfamily, dubbed ARP12, which is specific to heterokonts and related organisms. We also describe two novel diatom-specific subfamilies, dGRC1 and dGRC2, among short gelsolin repeat-containing proteins.
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Affiliation(s)
- A A Morozov
- Cell Ultrastructure Dept., Limnological Institute SB RAS, Irkutsk, Russia.
| | - Ye D Bedoshvili
- Cell Ultrastructure Dept., Limnological Institute SB RAS, Irkutsk, Russia
| | - M S Popova
- Cell Ultrastructure Dept., Limnological Institute SB RAS, Irkutsk, Russia
| | - Ye V Likhoshway
- Cell Ultrastructure Dept., Limnological Institute SB RAS, Irkutsk, Russia
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18
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Klopf E, Schmidt HA, Clauder-Münster S, Steinmetz LM, Schüller C. INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res 2017; 45:3752-3766. [PMID: 28025392 PMCID: PMC5397147 DOI: 10.1093/nar/gkw1292] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/13/2016] [Indexed: 12/19/2022] Open
Abstract
The conserved INO80 chromatin remodeling complex is involved in regulation of DNA damage repair, replication and transcription. It is commonly recruited to the transcription start region and contributes to the establishment of promoter-proximal nucleosomes. We find a substantial influence of INO80 on nucleosome dynamics and gene expression during stress induced transcription. Transcription induced by osmotic stress leads to genome-wide remodeling of promoter proximal nucleosomes. INO80 function is required for timely return of evicted nucleosomes to the 5΄ end of induced genes. Reduced INO80 function in Arp8-deficient cells leads to correlated prolonged transcription and nucleosome eviction. INO80 and the related complex SWR1 regulate incorporation of the H2A.Z isoform at promoter proximal nucleosomes. However, H2A.Z seems not to influence osmotic stress induced gene regulation. Furthermore, we show that high rates of transcription promote INO80 recruitment to promoter regions, suggesting a connection between active transcription and promoter proximal nucleosome remodeling. In addition, we find that absence of INO80 enhances bidirectional promoter activity at highly induced genes and expression of a number of stress induced transcripts. We suggest that INO80 has a direct repressive role via promoter proximal nucleosome remodeling to limit high levels of transcription in yeast.
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Affiliation(s)
- Eva Klopf
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Medical University of Vienna, University of Vienna, Campus Vienna Biocenter 5 (VBC5), 1030 Vienna, Austria
| | - Sandra Clauder-Münster
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph Schüller
- Department of Applied Genetics and Cell Biology (DAGZ), University of Natural Resources and Life Sciences, Vienna (BOKU), UFT-Campus Tulln, Konrad Lorenz Strasse 24, 3430 Tulln, Austria
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19
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Marom R, Jain M, Burrage LC, Song IW, Graham BH, Brown CW, Stevens SJC, Stegmann APA, Gunter AT, Kaplan JD, Gavrilova RH, Shinawi M, Rosenfeld JA, Bae Y, Tran AA, Chen Y, Lu JT, Gibbs RA, Eng C, Yang Y, Rousseau J, de Vries BBA, Campeau PM, Lee B. Heterozygous variants in ACTL6A, encoding a component of the BAF complex, are associated with intellectual disability. Hum Mutat 2017. [PMID: 28649782 DOI: 10.1002/humu.23282] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pathogenic variants in genes encoding components of the BRG1-associated factor (BAF) chromatin remodeling complex have been associated with intellectual disability syndromes. We identified heterozygous, novel variants in ACTL6A, a gene encoding a component of the BAF complex, in three subjects with varying degrees of intellectual disability. Two subjects have missense variants affecting highly conserved amino acid residues within the actin-like domain. Missense mutations in the homologous region in yeast actin were previously reported to be dominant lethal and were associated with impaired binding of the human ACTL6A to β-actin and BRG1. A third subject has a splicing variant that creates an in-frame deletion. Our findings suggest that the variants identified in our subjects may have a deleterious effect on the function of the protein by disturbing the integrity of the BAF complex. Thus, ACTL6A gene mutation analysis should be considered in patients with intellectual disability, learning disabilities, or developmental language disorder.
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Affiliation(s)
- Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mahim Jain
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - I-Wen Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Brett H Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chester W Brown
- Department of Pediatrics/Genetics Division, University of Tennessee Health Science Center Memphis, Memphis, Tennessee
| | - Servi J C Stevens
- Department of Human Genetics, Maastricht University Hospital, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Maastricht University Hospital, Maastricht, The Netherlands
| | - Andrew T Gunter
- Department of Pediatrics, Division of Medical Genetics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Julie D Kaplan
- Department of Pediatrics, Division of Medical Genetics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Ralitza H Gavrilova
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota.,Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yangjin Bae
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alyssa A Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yuqing Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justine Rousseau
- Department of Pediatrics, CHU Ste-Justine and University of Montreal, Montreal, Canada
| | - Bert B A de Vries
- Department of Human Genetics and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philippe M Campeau
- Department of Pediatrics, CHU Ste-Justine and University of Montreal, Montreal, Canada
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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20
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Characterizing the molecular architectures of chromatin-modifying complexes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1613-1622. [PMID: 28652207 DOI: 10.1016/j.bbapap.2017.06.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/09/2017] [Accepted: 06/21/2017] [Indexed: 11/23/2022]
Abstract
Eukaryotic cells package their genome in the form of a DNA-protein complex known as chromatin. This organization not only condenses the genome to fit within the confines of the nucleus, but also provides a platform for a cell to regulate accessibility to different gene sequences. The basic packaging element of chromatin is the nucleosome, which consists of 146 base pairs of DNA wrapped around histone proteins. One major means that a cell regulates chromatin structure is by depositing post-translational modifications on nucleosomal histone proteins, and thereby altering internucleosomal interactions and/or binding to different chromatin associated factors. These chromatin modifications are often catalyzed by multi-subunit enzyme complexes, whose large size, sophisticated composition, and inherent conformational flexibility pose significant technical challenges to their biochemical and structural characterization. Multiple structural approaches including nuclear magnetic resonance spectroscopy, X-ray crystallography, single-particle electron microscopy, and crosslinking coupled to mass spectrometry are often used synergistically to probe the overall architecture, subunit organization, and catalytic mechanisms of these macromolecular assemblies. In this review, we highlight several recent chromatin-modifying complexes studies that embodies this multipronged structural approach, and explore common themes amongst them. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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21
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Willhoft O, McCormack EA, Aramayo RJ, Bythell-Douglas R, Ocloo L, Zhang X, Wigley DB. Crosstalk within a functional INO80 complex dimer regulates nucleosome sliding. eLife 2017; 6. [PMID: 28585918 PMCID: PMC5472440 DOI: 10.7554/elife.25782] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/03/2017] [Indexed: 01/17/2023] Open
Abstract
Several chromatin remodellers have the ability to space nucleosomes on DNA. For ISWI remodellers, this involves an interplay between H4 histone tails, the AutoN and NegC motifs of the motor domains that together regulate ATPase activity and sense the length of DNA flanking the nucleosome. By contrast, the INO80 complex also spaces nucleosomes but is not regulated by H4 tails and lacks the AutoN and NegC motifs. Instead nucleosome sliding requires cooperativity between two INO80 complexes that monitor DNA length simultaneously on either side of the nucleosome during sliding. The C-terminal domain of the human Ino80 subunit (Ino80CTD) binds cooperatively to DNA and dimerisation of these domains provides crosstalk between complexes. ATPase activity, rather than being regulated, instead gradually becomes uncoupled as nucleosome sliding reaches an end point and this is controlled by the Ino80CTD. A single active ATPase motor within the dimer is sufficient for sliding. DOI:http://dx.doi.org/10.7554/eLife.25782.001
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Affiliation(s)
- Oliver Willhoft
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Elizabeth A McCormack
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Ricardo J Aramayo
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Rohan Bythell-Douglas
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Lorraine Ocloo
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Xiaodong Zhang
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
| | - Dale B Wigley
- Department of Medicine, Section of Structural Biology, Imperial College London, London, United Kingdom
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22
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Misu S, Takebayashi M, Miyamoto K. Nuclear Actin in Development and Transcriptional Reprogramming. Front Genet 2017; 8:27. [PMID: 28326098 PMCID: PMC5339334 DOI: 10.3389/fgene.2017.00027] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 02/20/2017] [Indexed: 12/20/2022] Open
Abstract
Actin is a highly abundant protein in eukaryotic cells and dynamically changes its polymerized states with the help of actin-binding proteins. Its critical function as a constituent of cytoskeleton has been well-documented. Growing evidence demonstrates that actin is also present in nuclei, referred to as nuclear actin, and is involved in a number of nuclear processes, including transcriptional regulation and chromatin remodeling. The contribution of nuclear actin to transcriptional regulation can be explained by its direct interaction with transcription machineries and chromatin remodeling factors and by controlling the activities of transcription factors. In both cases, polymerized states of nuclear actin affect the transcriptional outcome. Nuclear actin also plays an important role in activating strongly silenced genes in somatic cells for transcriptional reprogramming. When these nuclear functions of actin are considered, it is plausible to speculate that nuclear actin is also implicated in embryonic development, in which numerous genes need to be activated in a well-coordinated manner. In this review, we especially focus on nuclear actin's roles in transcriptional activation, reprogramming and development, including stem cell differentiation and we discuss how nuclear actin can be an important player in development and cell differentiation.
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Affiliation(s)
- Shinji Misu
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University Kinokawa-shi, Japan
| | - Marina Takebayashi
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University Kinokawa-shi, Japan
| | - Kei Miyamoto
- Laboratory of Molecular Developmental Biology, Faculty of Biology-Oriented Science and Technology, Kindai University Kinokawa-shi, Japan
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23
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Takahashi Y, Murakami H, Akiyama Y, Katoh Y, Oma Y, Nishijima H, Shibahara KI, Igarashi K, Harata M. Actin Family Proteins in the Human INO80 Chromatin Remodeling Complex Exhibit Functional Roles in the Induction of Heme Oxygenase-1 with Hemin. Front Genet 2017; 8:17. [PMID: 28270832 PMCID: PMC5318382 DOI: 10.3389/fgene.2017.00017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 02/06/2017] [Indexed: 11/13/2022] Open
Abstract
Nuclear actin family proteins, comprising of actin and actin-related proteins (Arps), are essential functional components of the multiple chromatin remodeling complexes. The INO80 chromatin remodeling complex, which is evolutionarily conserved and has roles in transcription, DNA replication and repair, consists of actin and actin-related proteins Arp4, Arp5, and Arp8. We generated Arp5 knockout (KO) and Arp8 KO cells from the human Nalm-6 pre-B cell line and used these KO cells to examine the roles of Arp5 and Arp8 in the transcriptional regulation mediated by the INO80 complex. In both of Arp5 KO and Arp8 KO cells, the oxidative stress-induced expression of HMOX1 gene, encoding for heme oxygenase-1 (HO-1), was significantly impaired. Consistent with these observations, chromatin immunoprecipitation (ChIP) assay revealed that oxidative stress caused an increase in the binding of the INO80 complex to the regulatory sites of HMOX1 in wild-type cells. The binding of INO80 complex to chromatin was reduced in Arp8 KO cells compared to that in the wild-type cells. On the other hand, the binding of INO80 complex to chromatin in Arp5 KO cells was similar to that in the wild-type cells even under the oxidative stress condition. However, both remodeling of chromatin at the HMOX1 regulatory sites and binding of a transcriptional activator to these sites were impaired in Arp5 KO cells, indicating that Arp5 is required for the activation of the INO80 complex. Collectively, these results suggested that these nuclear Arps play indispensable roles in the function of the INO80 chromatin remodeling complex.
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Affiliation(s)
- Yuichiro Takahashi
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University Sendai, Japan
| | - Hirokazu Murakami
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University Sendai, Japan
| | - Yusuke Akiyama
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University Sendai, Japan
| | - Yasutake Katoh
- Department of Biochemistry, Graduate School of Medicine, Tohoku University Sendai, Japan
| | - Yukako Oma
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University Sendai, Japan
| | - Hitoshi Nishijima
- Department of Integrated Genetics, National Institute of GeneticsMishima, Japan; Division of Molecular Immunology, Institute of Advanced Medical Sciences, Tokushima UniversityTokushima, Japan
| | - Kei-Ichi Shibahara
- Department of Integrated Genetics, National Institute of Genetics Mishima, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Graduate School of Medicine, Tohoku UniversitySendai, Japan; Japan Agency for Medical Research and DevelopmentTokyo, Japan
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University Sendai, Japan
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24
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Diverse functions for different forms of nuclear actin. Curr Opin Cell Biol 2017; 46:33-38. [PMID: 28092729 DOI: 10.1016/j.ceb.2016.12.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/23/2016] [Accepted: 12/12/2016] [Indexed: 12/31/2022]
Abstract
In addition to its essential roles as part of the cytoskeleton, actin has also been linked to many processes in the nucleus. Recent data has demonstrated the presence of both monomeric and polymeric actin in the nucleus, and implied distinct functional roles for these actin pools. Monomeric actin seems to be involved in regulation of gene expression through transcription factors, chromatin regulating complexes and RNA polymerases. In addition to cytoplasmic actin regulators, nuclear proteins, such as emerin, can regulate actin polymerization properties specifically in this compartment. Besides of structural roles, nuclear actin filaments may be required for organizing the nuclear contents and for the maintenance of genomic integrity.
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25
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Abstract
Although most people still associate actin mainly with the cytoskeleton, several lines of evidence, with the earliest studies dating back to decades ago, have emphasized the importance of actin also inside the cell nucleus. Actin has been linked to many gene expression processes from gene activation to chromatin remodeling, but also to maintenance of genomic integrity and intranuclear movement of chromosomes and chromosomal loci. Recent advances in visualizing different forms and dynamic properties of nuclear actin have clearly advanced our understanding of the basic concepts by which actin operates in the nucleus. In this chapter we address the different breakthroughs in nuclear actin studies, as well as discuss the regulation nuclear actin and the importance of nuclear actin dynamics in relation to its different nuclear functions. Our aim is to highlight the fact that actin should be considered as an essential component of the cell nucleus, and its nuclear actions should be taken into account also in experiments on cytoplasmic actin networks.
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Affiliation(s)
- Tiina Viita
- Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, 56, Helsinki, Finland
| | - Maria K Vartiainen
- Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, 56, Helsinki, Finland.
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26
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Volokh OI, Derkacheva NI, Studitsky VM, Sokolova OS. Structural studies of chromatin remodeling factors. Mol Biol 2016. [DOI: 10.1134/s0026893316060212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Abstract
Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT-associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus.
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28
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Willhoft O, Bythell-Douglas R, McCormack EA, Wigley DB. Synergy and antagonism in regulation of recombinant human INO80 chromatin remodeling complex. Nucleic Acids Res 2016; 44:8179-88. [PMID: 27257055 PMCID: PMC5041457 DOI: 10.1093/nar/gkw509] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 05/23/2016] [Indexed: 12/30/2022] Open
Abstract
We have purified a minimal core human Ino80 complex from recombinant protein expressed in insect cells. The complex comprises one subunit each of an N-terminally truncated Ino80, actin, Arp4, Arp5, Arp8, Ies2 and Ies6, together with a single heterohexamer of the Tip49a and Tip49b proteins. This core complex has nucleosome sliding activity that is similar to that of endogenous human and yeast Ino80 complexes and is also inhibited by inositol hexaphosphate (IP6). We show that IP6 is a non-competitive inhibitor that acts by blocking the stimulatory effect of nucleosomes on the ATPase activity. The IP6 binding site is located within the C-terminal region of the Ino80 subunit. We have also prepared complexes lacking combinations of Ies2 and Arp5/Ies6 subunits that reveal regulation imposed by each of them individually and synergistically that couples ATP hydrolysis to nucleosome sliding. This coupling between Ies2 and Arp5/Ies6 can be overcome in a bypass mutation of the Arp5 subunit that is active in the absence of Ies2. These studies reveal several underlying mechanisms for regulation of ATPase activity involving a complex interplay between these protein subunits and IP6 that in turn controls nucleosome sliding.
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Affiliation(s)
- Oliver Willhoft
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Rohan Bythell-Douglas
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Elizabeth A McCormack
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Dale B Wigley
- Section of Structural Biology, Department of Medicine, Imperial College London, London SW7 2AZ, UK
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29
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Actin, actin-binding proteins, and actin-related proteins in the nucleus. Histochem Cell Biol 2016; 145:373-88. [PMID: 26847179 DOI: 10.1007/s00418-015-1400-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2015] [Indexed: 10/25/2022]
Abstract
Extensive research in the past decade has significantly broadened our view about the role actin plays in the life of the cell and added novel aspects to actin research. One of these new aspects is the discovery of the existence of nuclear actin which became evident only recently. Nuclear activities including transcriptional activation in the case of all three RNA polymerases, editing and nuclear export of mRNAs, and chromatin remodeling all depend on actin. It also became clear that there is a fine-tuned equilibrium between cytoplasmic and nuclear actin pools and that this balance is ensured by an export-import system dedicated to actin. After over half a century of research on conventional actin and its organizing partners in the cytoplasm, it was also an unexpected finding that the nucleus contains more than 30 actin-binding proteins and new classes of actin-related proteins which are not able to form filaments but had evolved nuclear-specific functions. The actin-binding and actin-related proteins in the nucleus have been linked to RNA transcription and processing, nuclear transport, and chromatin remodeling. In this paper, we attempt to provide an overview of the wide range of information that is now available about actin, actin-binding, and actin-related proteins in the nucleus.
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30
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Geer MA, Fitzgerald MC. Characterization of the Saccharomyces cerevisiae ATP-Interactome using the iTRAQ-SPROX Technique. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:233-243. [PMID: 26530046 DOI: 10.1007/s13361-015-1290-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/01/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
The stability of proteins from rates of oxidation (SPROX) technique was used in combination with an isobaric mass tagging strategy to identify adenosine triphosphate (ATP) interacting proteins in the Saccharomyces cerevisiae proteome. The SPROX methodology utilized in this work enabled 373 proteins in a yeast cell lysate to be assayed for ATP interactions (both direct and indirect) using the non-hydrolyzable ATP analog, adenylyl imidodiphosphate (AMP-PNP). A total of 28 proteins were identified with AMP-PNP-induced thermodynamic stability changes. These protein hits included 14 proteins that were previously annotated as ATP-binding proteins in the Saccharomyces Genome Database (SGD). The 14 non-annotated ATP-binding proteins included nine proteins that were previously found to be ATP-sensitive in an earlier SPROX study using a stable isotope labeling with amino acids in cell culture (SILAC)-based approach. A bioinformatics analysis of the protein hits identified here and in the earlier SILAC-SPROX experiments revealed that many of the previously annotated ATP-binding protein hits were kinases, ligases, and chaperones. In contrast, many of the newly discovered ATP-sensitive proteins were not from these protein classes, but rather were hydrolases, oxidoreductases, and nucleic acid-binding proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- M Ariel Geer
- Department of Chemistry, Duke University, Durham, NC, 27708-0346, USA
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31
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Yao W, Beckwith SL, Zheng T, Young T, Dinh VT, Ranjan A, Morrison AJ. Assembly of the Arp5 (Actin-related Protein) Subunit Involved in Distinct INO80 Chromatin Remodeling Activities. J Biol Chem 2015; 290:25700-9. [PMID: 26306040 DOI: 10.1074/jbc.m115.674887] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/06/2022] Open
Abstract
ATP-dependent chromatin remodeling, which repositions and restructures nucleosomes, is essential to all DNA-templated processes. The INO80 chromatin remodeling complex is an evolutionarily conserved complex involved in diverse cellular processes, including transcription, DNA repair, and replication. The functional diversity of the INO80 complex can, in part, be attributed to specialized activities of distinct subunits that compose the complex. Furthermore, structural analyses have identified biochemically discrete subunit modules that assemble along the Ino80 ATPase scaffold. Of particular interest is the Saccharomyces cerevisiae Arp5-Ies6 module located proximal to the Ino80 ATPase and the Rvb1-Rvb2 helicase module needed for INO80-mediated in vitro activity. In this study we demonstrate that the previously uncharacterized Ies2 subunit is required for Arp5-Ies6 association with the catalytic components of the INO80 complex. In addition, Arp5-Ies6 module assembly with the INO80 complex is dependent on distinct conserved domains within Arp5, Ies6, and Ino80, including the spacer region within the Ino80 ATPase domain. Arp5-Ies6 interacts with chromatin via assembly with the INO80 complex, as IES2 and INO80 deletion results in loss of Arp5-Ies6 chromatin association. Interestingly, ectopic addition of the wild-type Arp5-Ies6 module stimulates INO80-mediated ATP hydrolysis and nucleosome sliding in vitro. However, the addition of mutant Arp5 lacking unique insertion domains facilitates ATP hydrolysis in the absence of nucleosome sliding. Collectively, these results define the requirements of Arp5-Ies6 assembly, which are needed to couple ATP hydrolysis to productive nucleosome movement.
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Affiliation(s)
- Wei Yao
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Sean L Beckwith
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Tina Zheng
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Thomas Young
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Van T Dinh
- From the Department of Biology, Stanford University, Stanford California 94305 and
| | - Anand Ranjan
- Laboratory of Biochemistry and Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Ashby J Morrison
- From the Department of Biology, Stanford University, Stanford California 94305 and
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Andreatta ME, Levine JA, Foy SG, Guzman LD, Kosinski LJ, Cordes MHJ, Masel J. The Recent De Novo Origin of Protein C-Termini. Genome Biol Evol 2015; 7:1686-701. [PMID: 26002864 PMCID: PMC4494051 DOI: 10.1093/gbe/evv098] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Protein-coding sequences can arise either from duplication and divergence of existing sequences, or de novo from noncoding DNA. Unfortunately, recently evolved de novo genes can be hard to distinguish from false positives, making their study difficult. Here, we study a more tractable version of the process of conversion of noncoding sequence into coding: the co-option of short segments of noncoding sequence into the C-termini of existing proteins via the loss of a stop codon. Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes. We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic. We find one putative gene fusion that turns out, on close inspection, to be the product of replicated assembly errors, further highlighting the issue of false positives in the study of rare events. Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure.
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Affiliation(s)
- Matthew E Andreatta
- Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN
| | - Joshua A Levine
- Department of Ecology & Evolutionary Biology, University of Arizona
| | - Scott G Foy
- Department of Ecology & Evolutionary Biology, University of Arizona
| | - Lynette D Guzman
- Department of Ecology & Evolutionary Biology, University of Arizona Present address: Program in Mathematics Education, Michigan State University, MI
| | - Luke J Kosinski
- Biochemistry and Molecular & Cellular Biology Graduate Program, University of Arizona
| | | | - Joanna Masel
- Department of Ecology & Evolutionary Biology, University of Arizona
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Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C. Nat Commun 2015; 6:7108. [PMID: 25964121 PMCID: PMC4431590 DOI: 10.1038/ncomms8108] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/01/2015] [Indexed: 01/11/2023] Open
Abstract
INO80-C and SWR-C are conserved members of a subfamily of ATP-dependent chromatin remodeling enzymes that function in transcription and genome-maintenance pathways. A crucial role for these enzymes is to control chromosomal distribution of the H2A.Z histone variant. Here we use electron microscopy (EM) and two-dimensional (2D) class averaging to demonstrate that these remodeling enzymes have similar overall architectures. Each enzyme is characterized by a dynamic ‘tail’ domain and a compact ‘head’ that contains Rvb1/Rvb2 subunits organized as hexameric rings. EM class averages and mass spectrometry support the existence of single heterohexameric rings in both SWR-C and INO80-C. EM studies define the position of the Arp8/Arp4/Act1 module within INO80-C, and we find that this module enhances nucleosome binding affinity but is largely dispensable for remodeling activities. In contrast, the Ies6/Arp5 module is essential for INO80-C remodeling, and furthermore this module controls conformational changes that may couple nucleosome binding to remodeling.
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Osakabe A, Takahashi Y, Murakami H, Otawa K, Tachiwana H, Oma Y, Nishijima H, Shibahara KI, Kurumizaka H, Harata M. DNA binding properties of the actin-related protein Arp8 and its role in DNA repair. PLoS One 2014; 9:e108354. [PMID: 25299602 PMCID: PMC4191963 DOI: 10.1371/journal.pone.0108354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 08/26/2014] [Indexed: 12/05/2022] Open
Abstract
Actin and actin-related proteins (Arps), which are members of the actin family, are essential components of many of these remodeling complexes. Actin, Arp4, Arp5, and Arp8 are found to be evolutionarily conserved components of the INO80 chromatin remodeling complex, which is involved in transcriptional regulation, DNA replication, and DNA repair. A recent report showed that Arp8 forms a module in the INO80 complex and this module can directly capture a nucleosome. In the present study, we showed that recombinant human Arp8 binds to DNAs, and preferentially binds to single-stranded DNA. Analysis of the binding of adenine nucleotides to Arp8 mutants suggested that the ATP-binding pocket, located in the evolutionarily conserved actin fold, plays a regulatory role in the binding of Arp8 to DNA. To determine the cellular function of Arp8, we derived tetracycline-inducible Arp8 knockout cells from a cultured human cell line. Analysis of results obtained after treating these cells with aphidicolin and camptothecin revealed that Arp8 is involved in DNA repair. Together with the previous observation that Arp8, but not γ-H2AX, is indispensable for recruiting INO80 complex to DSB in human, results of our study suggest an individual role for Arp8 in DNA repair.
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Affiliation(s)
- Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yuichiro Takahashi
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hirokazu Murakami
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Kenji Otawa
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Yukako Oma
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hitoshi Nishijima
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Kei-ich Shibahara
- Department of Integrated Genetics, National Institute of Genetics, Mishima, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- * E-mail: (HK); (MH)
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- * E-mail: (HK); (MH)
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35
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Gerhold CB, Gasser SM. INO80 and SWR complexes: relating structure to function in chromatin remodeling. Trends Cell Biol 2014; 24:619-31. [PMID: 25088669 DOI: 10.1016/j.tcb.2014.06.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 02/04/2023]
Abstract
Virtually all DNA-dependent processes require selective and controlled access to the DNA sequence. Governing this access are sophisticated molecular machines, nucleosome remodelers, which regulate the composition and structure of chromatin, allowing conversion from open to closed states. In most cases these multisubunit remodelers operate in concert to organize chromatin structure by depositing, moving, evicting, or selectively altering nucleosomes in an ATP-dependent manner. Despite sharing a conserved domain architecture, chromatin remodelers differ significantly in how they bind to their nucleosomal substrates. Recent structural studies link specific interactions between nucleosomes and remodelers to the diverse tasks they carry out. We review here insights into the modular organization of the INO80 family of nucleosome remodelers. Understanding their structural diversity will help to shed light on how these related ATPases modify their nucleosomal substrates.
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Affiliation(s)
- Christian B Gerhold
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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36
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Rubenstein PA, Wen KK. Insights into the effects of disease-causing mutations in human actins. Cytoskeleton (Hoboken) 2014; 71:211-29. [PMID: 24574087 DOI: 10.1002/cm.21169] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/13/2013] [Accepted: 02/19/2014] [Indexed: 01/04/2023]
Abstract
Mutations in all six actins in humans have now been shown to cause diseases. However, a number of factors have made it difficult to gain insight into how the changes in actin functions brought about by these pathogenic mutations result in the disease phenotype. These include the presence of multiple actins in the same cell, limited accessibility to pure mutant material, and complexities associated with the structures and their component cells that manifest the diseases. To try to circumvent these difficulties, investigators have turned to the use of model systems. This review describes these various approaches, the initial results obtained using them, and the insight they have provided into allosteric mechanisms that govern actin function. Although results so far have not explained a particular disease phenotype at the molecular level, they have provided valuable insight into actin function at the mechanistic level which can be utilized in the future to delineate the molecular bases of these different actinopathies.
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Affiliation(s)
- Peter A Rubenstein
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, Iowa
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37
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Rajakylä EK, Vartiainen MK. Rho, nuclear actin, and actin-binding proteins in the regulation of transcription and gene expression. Small GTPases 2014; 5:e27539. [PMID: 24603113 DOI: 10.4161/sgtp.27539] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Actin cytoskeleton is one of the main targets of Rho GTPases, which act as molecular switches on many signaling pathways. During the past decade, actin has emerged as an important regulator of gene expression. Nuclear actin plays a key role in transcription, chromatin remodeling, and pre-mRNA processing. In addition, the "status" of the actin cytoskeleton is used as a signaling intermediate by at least the MKL1-SRF and Hippo-pathways, which culminate in the transcriptional regulation of cytoskeletal and growth-promoting genes, respectively. Rho GTPases may therefore regulate gene expression by controlling either cytoplasmic or nuclear actin dynamics. Although the regulation of nuclear actin polymerization is still poorly understood, many actin-binding proteins, which are downstream effectors of Rho, are found in the nuclear compartment. In this review, we discuss the possible mechanisms and key proteins that may mediate the transcriptional regulation by Rho GTPases through actin.
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Affiliation(s)
- Eeva Kaisa Rajakylä
- Program in Cell and Molecular Biology; Institute of Biotechnology; University of Helsinki; Helsinki, Finland
| | - Maria K Vartiainen
- Program in Cell and Molecular Biology; Institute of Biotechnology; University of Helsinki; Helsinki, Finland
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38
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Abstract
A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).
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Affiliation(s)
- Blaine Bartholomew
- University of Texas MD Anderson Cancer Center, Department of Molecular Carcinogenesis, Smithville, Texas 78957;
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39
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Abstract
Arp5 suppresses myocardin activity through both direct binding to myocardin and binding to SRF to prevent transcriptional activation of myogenic genes by the myocardin–SRF complex. Myocardin (Myocd) and Myocd-related transcription factors (MRTFs) are robust coactivators of serum response factor (SRF). RPEL motifs are monomeric globular actin (G-actin) binding elements that regulate MRTF localization and activity. However, the function of the RPEL motif in Myocd is largely unknown because of its low affinity for G-actin. Here, we demonstrated that the Myocd RPEL motif bound to actin-related protein 5 (Arp5) instead of conventional actin, resulting in a significant suppression of Myocd activity. In addition, Arp5 bound to a DNA binding domain of SRF via its C-terminal sequence and prevented the association of the Myocd–SRF complex with the promoter regions of smooth muscle genes. Well-differentiated smooth muscle cells mainly expressed a specific splicing variant of arp5; therefore, the protein level of Arp5 was markedly reduced by partial messenger RNA decay and translational suppression. In dedifferentiated smooth muscle cells, Arp5 knockdown restored the differentiated phenotype via Myocd activation. Thus, Arp5 is a key regulator of Myocd activity.
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Affiliation(s)
- Tsuyoshi Morita
- Department of Neuroscience, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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40
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Lobsiger J, Hunziker Y, Richmond TJ. Structure of the full-length yeast Arp7-Arp9 heterodimer. ACTA ACUST UNITED AC 2014; 70:310-6. [PMID: 24531465 DOI: 10.1107/s1399004713027417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/06/2013] [Indexed: 11/11/2022]
Abstract
The nuclear actin-related proteins Arp7 and Arp9 are components of the yeast SWI/SNF and RSC chromatin-remodelling complexes. The 3.1 Å resolution crystal structure reported here shows that the full-length Arp7 and Arp9 proteins exist as a dimer without a requirement for additional polypeptides. Of the 11 actin-related proteins, Arp7 and Arp9 are the only two directly demonstrated to form a dimer within this family. The Arp7-Arp9 heterodimer is unlikely to form an actin-like filament based on modelling using the structure. The Arp7-Arp9 structure reveals that its dimerization interface is not altered when bound in a complex with the SWI/SNF Snf2 HSA domain and the regulatory protein Rtt102.
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Affiliation(s)
- Joel Lobsiger
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Schafmattstrasse 20, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Yvonne Hunziker
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Schafmattstrasse 20, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Timothy J Richmond
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Schafmattstrasse 20, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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41
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Nguyen V, Ranjan A, Stengel F, Wei D, Aebersold R, Wu C, Leschziner A. Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Cell 2013; 154:1220-31. [PMID: 24034246 PMCID: PMC3776929 DOI: 10.1016/j.cell.2013.08.018] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/24/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022]
Abstract
The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.
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Affiliation(s)
- Vu Q. Nguyen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anand Ranjan
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Florian Stengel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8092, Switzerland
- Faculty of Science, University of Zurich, Zurich 8057, Switzerland
| | - Carl Wu
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
| | - Andres E. Leschziner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Corresponding author
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42
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Tosi A, Haas C, Herzog F, Gilmozzi A, Berninghausen O, Ungewickell C, Gerhold CB, Lakomek K, Aebersold R, Beckmann R, Hopfner KP. Structure and subunit topology of the INO80 chromatin remodeler and its nucleosome complex. Cell 2013; 154:1207-19. [PMID: 24034245 DOI: 10.1016/j.cell.2013.08.016] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 06/05/2013] [Accepted: 08/12/2013] [Indexed: 11/16/2022]
Abstract
INO80/SWR1 family chromatin remodelers are complexes composed of >15 subunits and molecular masses exceeding 1 MDa. Their important role in transcription and genome maintenance is exchanging the histone variants H2A and H2A.Z. We report the architecture of S. cerevisiae INO80 using an integrative approach of electron microscopy, crosslinking and mass spectrometry. INO80 has an embryo-shaped head-neck-body-foot architecture and shows dynamic open and closed conformations. We can assign an Rvb1/Rvb2 heterododecamer to the head in close contact with the Ino80 Snf2 domain, Ies2, and the Arp5 module at the neck. The high-affinity nucleosome-binding Nhp10 module localizes to the body, whereas the module that contains actin, Arp4, and Arp8 maps to the foot. Structural and biochemical analyses indicate that the nucleosome is bound at the concave surface near the neck, flanked by the Rvb1/2 and Arp8 modules. Our analysis establishes a structural and functional framework for this family of large remodelers.
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Affiliation(s)
- Alessandro Tosi
- Department of Biochemistry, Ludwig-Maximilian University, 81377 Munich, Germany; Gene Center, Ludwig-Maximilian University, 81377 Munich, Germany
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43
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Kapoor P, Shen X. Mechanisms of nuclear actin in chromatin-remodeling complexes. Trends Cell Biol 2013; 24:238-46. [PMID: 24246764 DOI: 10.1016/j.tcb.2013.10.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 10/04/2013] [Accepted: 10/22/2013] [Indexed: 10/26/2022]
Abstract
The mystery of nuclear actin has puzzled biologists for decades largely due to the lack of defined experimental systems. However, the development of actin-containing chromatin-modifying complexes as a defined genetic and biochemical system in the past decade has provided an unprecedented opportunity to dissect the mechanism of actin in the nucleus. Although the established functions of actin mostly rely on its dynamic polymerization, the novel finding of the mechanism of action of actin in the INO80 chromatin-remodeling complex suggests a conceptually distinct mode of actin that functions as a monomer. In this review we highlight the new paradigm and discuss how actin interaction with chromatin suggests a fundamental divergence between conventional cytoplasmic actin and nuclear actin. Furthermore, we provide how this framework could be applied to investigations of nuclear actin in other actin-containing chromatin-modifying complexes.
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Affiliation(s)
- Prabodh Kapoor
- Department of Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA
| | - Xuetong Shen
- Department of Molecular Carcinogenesis, Science Park Research Division, The University of Texas M.D. Anderson Cancer Center, Smithville, TX 78957, USA.
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44
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Turegun B, Kast DJ, Dominguez R. Subunit Rtt102 controls the conformation of the Arp7/9 heterodimer and its interactions with nucleotide and the catalytic subunit of SWI/SNF remodelers. J Biol Chem 2013; 288:35758-68. [PMID: 24189066 DOI: 10.1074/jbc.m113.514083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromatin-remodeling complexes are assembled around a catalytic subunit that contains a central ATPase domain and flanking sequences that recruit auxiliary subunits. The catalytic subunits of SWI/SNF remodelers recruit Arp7/9 through a helicase/SANT-associated (HSA) domain N-terminal to the ATPase domain. Arp7/9-containing remodelers also carry the auxiliary subunit Rtt102, but the role of this subunit is poorly understood. Here, we show that Rtt102 binds with nanomolar affinity to the Arp7/9 heterodimer and modulates its conformation and interactions with the ATPase subunit and nucleotide. When bound to Rtt102, Arp7/9 interacts with a shorter segment of the HSA domain. Structural analysis by small-angle x-ray scattering further shows that when bound to Rtt102, the complex of Arp7/9 with the catalytic subunit assumes a more stable compact conformation. We also found that Arp7, Arp9, and Arp7/9 interact very weakly with ATP, but Rtt102 promotes high-affinity ATP binding to a single site in the heterodimer. Collectively, the results establish a function for subunit Rtt102 as a stabilizing factor for the Arp7/9 heterodimer, enhancing its interaction with nucleotide and controlling the conformation of SWI/SNF remodelers in an Arp7/9-dependent manner.
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45
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To be or not to be assembled: progressing into nuclear actin filaments. Nat Rev Mol Cell Biol 2013; 14:693-7. [PMID: 24088744 DOI: 10.1038/nrm3681] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The paradigm states that cytoplasmic actin operates as filaments and nuclear actin is mainly monomeric, acting as a scaffold in transcription complexes. However, why should a powerful function of actin, namely polymerization, not be used in the nucleus? Recent progress in the field forces us to rethink this issue, as many actin filament assembly proteins have been linked to nuclear functions and new experimental approaches have provided the first direct visualizations of polymerized nuclear actin.
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46
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Miyamoto K, Gurdon JB. Transcriptional regulation and nuclear reprogramming: roles of nuclear actin and actin-binding proteins. Cell Mol Life Sci 2013; 70:3289-302. [PMID: 23275942 PMCID: PMC3753470 DOI: 10.1007/s00018-012-1235-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 12/03/2012] [Accepted: 12/04/2012] [Indexed: 12/18/2022]
Abstract
Proper regulation of transcription is essential for cells to acquire and maintain cell identity. Transcriptional activation plays a central role in gene regulation and can be modulated by introducing transcriptional activators such as transcription factors. Activators act on their specific target genes to induce transcription. Reprogramming experiments have revealed that as cells become differentiated, some genes are highly silenced and even introduction of activators that target these silenced genes does not induce transcription. This can be explained by chromatin-based repression that restricts access of transcriptional activators to silenced genes. Transcriptional activation from these genes can be accomplished by opening chromatin, in addition to providing activators. Once a de novo transcription network is established, cells are differentiated or reprogrammed to a new cell type. Emerging evidence suggests that actin in the nucleus (nuclear actin) and nuclear actin-binding proteins are implicated in these transcriptional regulatory processes. This review summarizes roles of nuclear actin and actin-binding proteins in transcriptional regulation. We also discuss possible functions of nuclear actin during reprogramming in the context of transcription and chromatin remodeling.
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Affiliation(s)
- Kei Miyamoto
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
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47
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Treisman R. Shedding light on nuclear actin dynamics and function. Trends Biochem Sci 2013; 38:376-7. [PMID: 23810602 DOI: 10.1016/j.tibs.2013.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 01/08/2023]
Abstract
The functions of nuclear actin have been a mystery for many years. Recent papers demonstrate that the nuclear and cytoplasmic actin pools are in dynamic communication, but that not all nuclear actin freely exchanges. Extracellular signals can induce changes in nuclear actin dynamics, affecting activity of the myocardin-related transcription factor (MRTF) transcriptional coactivators, which reversibly bind G-actin. By contrast, actin is stably associated with the Ino80 chromatin remodelling complex, where it plays a role in the recognition of nucleosome linker DNA.
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Affiliation(s)
- Richard Treisman
- CR-UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.
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48
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Skarp KP, Huet G, Vartiainen MK. Steady-state nuclear actin levels are determined by export competent actin pool. Cytoskeleton (Hoboken) 2013; 70:623-34. [PMID: 23749625 DOI: 10.1002/cm.21116] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/22/2013] [Accepted: 05/23/2013] [Indexed: 12/18/2022]
Abstract
A number of studies in the last decade have irrevocably promoted actin into a fully fledged member of the nuclear compartment, where it, among other crucial tasks, facilitates transcription and chromatin remodeling. Changes in nuclear actin levels have been linked to different cellular processes: decreased nuclear actin to quiescence and increased nuclear actin to differentiation. Importin 9 and exportin 6 transport factors are responsible for the continuous nucleocytoplasmic shuttling of actin, but the mechanisms, which result in modulated actin levels, have not been characterized. We find that in cells growing under normal growth conditions, the levels of nuclear actin vary considerably from cell to cell. To understand the basis for this, we have extensively quantified several cellular parameters while at the same time recording the import and export rates of green fluorescent protein (GFP)-tagged actin. Surprisingly, our dataset shows that the ratio of nuclear to cytoplasmic fluorescence intensity, but not nuclear shape, size, cytoplasm size, or their ratio, correlates negatively with both import and export rate of actin. This suggests that high-nuclear actin content is maintained by both diminished import and export. The high nuclear actin containing cells still show high mobility of actin, but it is not export competent, suggesting increased binding of actin to nuclear complexes. Creation of such export incompetent actin pool would ensure enough actin is retained in the nucleus and make it available for the various nuclear functions described for actin.
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Affiliation(s)
- Kari-Pekka Skarp
- Program in Cell and Molecular Biology, Institute of Biotechnology, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
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49
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50
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Actin dosage lethality screening in yeast mediated by selective ploidy ablation reveals links to urmylation/wobble codon recognition and chromosome stability. G3-GENES GENOMES GENETICS 2013; 3:553-61. [PMID: 23450344 PMCID: PMC3583461 DOI: 10.1534/g3.113.005579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/15/2013] [Indexed: 12/16/2022]
Abstract
The actin cytoskeleton exists in a dynamic equilibrium with monomeric and filamentous states of its subunit protein actin. The spatial and temporal regulation of actin dynamics is critical to the many functions of actin. Actin levels are remarkably constant, suggesting that cells have evolved to function within a narrow range of actin concentrations. Here we report the results of screens in which we have increased actin levels in strains deleted for the ~4800 nonessential yeast genes using a technical advance called selective ploidy ablation. We detected 83 synthetic dosage interactions with actin, 78 resulted in reduced growth, whereas in 5 cases overexpression of actin suppressed the growth defects caused by the deleted genes. The genes were highly enriched in several classes, including transfer RNA wobble uridine modification, chromosome stability and segregation, cell growth, and cell division. We show that actin overexpression sequesters a limited pool of eEF1A, a bifunctional protein involved in aminoacyl-transfer RNA recruitment to the ribosome and actin filament cross-linking. Surprisingly, the largest class of genes is involved in chromosome stability and segregation. We show that actin mutants have chromosome segregation defects, suggesting a possible role in chromosome structure and function. Monomeric actin is a core component of the INO80 and SWR chromatin remodeling complexes and the NuA4 histone modification complex, and our results suggest these complexes may be sensitive to actin stoichiometry. We propose that the resulting effects on chromatin structure can lead to synergistic effects on chromosome stability in strains lacking genes important for chromosome maintenance.
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