51
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Caridi CP, D'Agostino C, Ryu T, Zapotoczny G, Delabaere L, Li X, Khodaverdian VY, Amaral N, Lin E, Rau AR, Chiolo I. Nuclear F-actin and myosins drive relocalization of heterochromatic breaks. Nature 2018; 559:54-60. [PMID: 29925946 PMCID: PMC6051730 DOI: 10.1038/s41586-018-0242-8] [Citation(s) in RCA: 243] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 05/18/2018] [Indexed: 12/13/2022]
Abstract
Heterochromatin mainly comprises repeated DNA sequences that are prone to ectopic recombination. In Drosophila cells, 'safe' repair of heterochromatic double-strand breaks by homologous recombination relies on the relocalization of repair sites to the nuclear periphery before strand invasion. The mechanisms responsible for this movement were unknown. Here we show that relocalization occurs by directed motion along nuclear actin filaments assembled at repair sites by the Arp2/3 complex. Relocalization requires nuclear myosins associated with the heterochromatin repair complex Smc5/6 and the myosin activator Unc45, which is recruited to repair sites by Smc5/6. ARP2/3, actin nucleation and myosins also relocalize heterochromatic double-strand breaks in mouse cells. Defects in this pathway result in impaired heterochromatin repair and chromosome rearrangements. These findings identify de novo nuclear actin filaments and myosins as effectors of chromatin dynamics for heterochromatin repair and stability in multicellular eukaryotes.
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Affiliation(s)
- Christopher P Caridi
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Carla D'Agostino
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Taehyun Ryu
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Grzegorz Zapotoczny
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Laetitia Delabaere
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Xiao Li
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Varandt Y Khodaverdian
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Nuno Amaral
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Karolinska Institute, Stockholm, Sweden
| | - Emily Lin
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Alesandra R Rau
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Irene Chiolo
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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52
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Roukos V. Actin proteins assemble to protect the genome. Nature 2018; 559:35-37. [PMID: 29959411 DOI: 10.1038/d41586-018-05339-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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53
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Xie X, Almuzzaini B, Drou N, Kremb S, Yousif A, Farrants AKÖ, Gunsalus K, Percipalle P. β-Actin-dependent global chromatin organization and gene expression programs control cellular identity. FASEB J 2018; 32:1296-1314. [PMID: 29101221 DOI: 10.1096/fj.201700753r] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During differentiation and development, cell fate and identity are established by waves of genetic reprogramming. Although the mechanisms are largely unknown, during these events, dynamic chromatin reorganization is likely to ensure that multiple genes involved in the same cellular functions are coregulated, depending on the nuclear environment. In this study, using high-content screening of embryonic fibroblasts from a β-actin knockout (KO) mouse, we found major chromatin rearrangements and changes in histone modifications, such as methylated histone (H)3-lysine-(K)9. Genome-wide H3K9 trimethylation-(Me)3 landscape changes correlate with gene up- and down-regulation in β-actin KO cells. Mechanistically, we found loss of chromatin association by the Brahma-related gene ( Brg)/Brahma-associated factor (BAF) chromatin remodeling complex subunit Brg1 in the absence of β-actin. This actin-dependent chromatin reorganization was concomitant with the up-regulation of sets of genes involved in angiogenesis, cytoskeletal organization, and myofibroblast features in β-actin KO cells. Some of these genes and phenotypes were gained in a β-actin dose-dependent manner. Moreover, reintroducing a nuclear localization signal-containing β-actin in the knockout cells affected nuclear features and gene expression. Our results suggest that, by affecting the genome-wide organization of heterochromatin through the chromatin-binding activity of the BAF complex, β-actin plays an essential role in the determination of gene expression programs and cellular identity.-Xie, X., Almuzzaini, B., Drou, N., Kremb, S., Yousif, A., Östlund Farrants, A.-K., Gunsalus, K., Percipalle, P. β-Actin-dependent global chromatin organization and gene expression programs control cellular identity.
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Affiliation(s)
- Xin Xie
- Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates
| | - Bader Almuzzaini
- Medical Genomic Research Department, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Nizar Drou
- NYUAD Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates
| | - Stephan Kremb
- NYUAD Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates
| | - Ayman Yousif
- NYUAD Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates
| | | | - Kristin Gunsalus
- Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,NYUAD Center for Genomics and Systems Biology, Abu Dhabi, United Arab Emirates.,Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - Piergiorgio Percipalle
- Biology Program, New York University Abu Dhabi (NYUAD), Abu Dhabi, United Arab Emirates.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; and
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54
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Houthaeve G, Robijns J, Braeckmans K, De Vos WH. Bypassing Border Control: Nuclear Envelope Rupture in Disease. Physiology (Bethesda) 2018; 33:39-49. [DOI: 10.1152/physiol.00029.2017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 11/22/2022] Open
Abstract
Recent observations in laminopathy patient cells and cancer cells have revealed that the nuclear envelope (NE) can transiently rupture during interphase. NE rupture leads to an uncoordinated exchange of nuclear and cytoplasmic material, thereby deregulating cellular homeostasis. Moreover, concurrently inflicted DNA damage could prime rupture-prone cells for genome instability. Thus, NE rupture may represent a novel pathogenic mechanism that has far-reaching consequences for cell and organism physiology.
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Affiliation(s)
- Gaëlle Houthaeve
- Department of Veterinary Sciences, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Joke Robijns
- Department of Veterinary Sciences, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, Belgium
| | - Winnok H. De Vos
- Department of Veterinary Sciences, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
- Department of Molecular Biotechnology, Cell Systems and Imaging Research Group (CSI), Ghent University, Ghent, Belgium
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55
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Gothe HJ, Minneker V, Roukos V. Dynamics of Double-Strand Breaks: Implications for the Formation of Chromosome Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:27-38. [PMID: 29956289 DOI: 10.1007/978-981-13-0593-1_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Illegitimate joining of chromosome breaks can lead to the formation of chromosome translocations, a catastrophic type of genome rearrangements that often plays key roles in tumorigenesis. Emerging evidence suggests that the mobility of broken DNA loci can be an important determinant in partner search and clustering of individual breaks, events that can influence translocation frequency. We summarize here the recent literature on the mechanisms that regulate chromatin movement, focusing on studies exploring the motion properties of double-strand breaks in the context of chromatin, the functional consequences for DNA repair, and the formation of chromosome fusions.
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56
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Shah FR, Bhat YA, Wani AH. Subnuclear distribution of proteins: Links with genome architecture. Nucleus 2018; 9:42-55. [PMID: 28910577 PMCID: PMC5973252 DOI: 10.1080/19491034.2017.1361578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 02/08/2023] Open
Abstract
Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, differentiation and disease. However, the principles governing the 3D chromatin architecture are just beginning to get unraveled. The nucleus has very high concentration of proteins and these proteins are either diffusely distributed throughout the nucleus, or aggregated in the form of foci/bodies/clusters/speckles or in combination of both. Several evidences suggest that the distribution of proteins within the nuclear space is linked to the organization and function of genome. Here, we describe advances made in understanding the relationship between subnuclear distribution of proteins and genome architecture.
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Affiliation(s)
- Fouziya R. Shah
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Younus A. Bhat
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Ajazul H. Wani
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
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57
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Szczesny SE, Mauck RL. The Nuclear Option: Evidence Implicating the Cell Nucleus in Mechanotransduction. J Biomech Eng 2017; 139:2592356. [PMID: 27918797 DOI: 10.1115/1.4035350] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Indexed: 02/06/2023]
Abstract
Biophysical stimuli presented to cells via microenvironmental properties (e.g., alignment and stiffness) or external forces have a significant impact on cell function and behavior. Recently, the cell nucleus has been identified as a mechanosensitive organelle that contributes to the perception and response to mechanical stimuli. However, the specific mechanotransduction mechanisms that mediate these effects have not been clearly established. Here, we offer a comprehensive review of the evidence supporting (and refuting) three hypothetical nuclear mechanotransduction mechanisms: physical reorganization of chromatin, signaling at the nuclear envelope, and altered cytoskeletal structure/tension due to nuclear remodeling. Our goal is to provide a reference detailing the progress that has been made and the areas that still require investigation regarding the role of nuclear mechanotransduction in cell biology. Additionally, we will briefly discuss the role that mathematical models of cell mechanics can play in testing these hypotheses and in elucidating how biophysical stimulation of the nucleus drives changes in cell behavior. While force-induced alterations in signaling pathways involving lamina-associated polypeptides (LAPs) (e.g., emerin and histone deacetylase 3 (HDAC3)) and transcription factors (TFs) located at the nuclear envelope currently appear to be the most clearly supported mechanism of nuclear mechanotransduction, additional work is required to examine this process in detail and to more fully test alternative mechanisms. The combination of sophisticated experimental techniques and advanced mathematical models is necessary to enhance our understanding of the role of the nucleus in the mechanotransduction processes driving numerous critical cell functions.
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Affiliation(s)
- Spencer E Szczesny
- Department of Orthopaedic Surgery, University of Pennsylvania, 424 Stemmler Hall, 36th Street and Hamilton Walk, Philadelphia, PA 19104; Translational Musculoskeletal Research Center, Corporal Michael J. Crescenz Veterans Affairs Medical Center, 3900 Woodland Avenue, Philadelphia, PA 19104
| | - Robert L Mauck
- Department of Orthopaedic Surgery, University of Pennsylvania, 424 Stemmler Hall, 36th Street and Hamilton Walk, Philadelphia, PA 19104; Translational Musculoskeletal Research Center, Corporal Michael J. Crescenz Veterans Affairs Medical Center, 3900 Woodland Avenue, Philadelphia, PA 19104;Department of Bioengineering, University of Pennsylvania, 240 Skirkanich Hall, 210 South 33rd Street, Philadelphia, PA 19104 e-mail:
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58
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Guénolé A, Legube G. A meeting at risk: Unrepaired DSBs go for broke. Nucleus 2017; 8:589-599. [PMID: 29099269 PMCID: PMC5788565 DOI: 10.1080/19491034.2017.1380138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022] Open
Abstract
Translocations are dramatic genomic rearrangements due to aberrant rejoining of distant DNA ends that can trigger cancer onset and progression. Translocations frequently occur in genes, yet the mechanisms underlying their formation remain poorly understood. One potential mechanism involves DNA Double Strand Break mobility and juxtaposition (i.e. clustering), an event that has been intensively debated over the past decade. Using Capture Hi-C, we recently found that DSBs do in fact cluster in human nuclei but only when induced in transcriptionally active genes. Notably, we found that clustering of damaged genes is regulated by cell cycle progression and coincides with damage persistency. Here, we discuss the mechanisms that could sustain clustering and speculate on the functional consequences of this seemingly double edge sword mechanism that may well stand at the heart of translocation biogenesis.
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Affiliation(s)
- Aude Guénolé
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
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59
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Fu J, Dai X, Plummer G, Suzuki K, Bautista A, Githaka JM, Senior L, Jensen M, Greitzer-Antes D, Manning Fox JE, Gaisano HY, Newgard CB, Touret N, MacDonald PE. Kv2.1 Clustering Contributes to Insulin Exocytosis and Rescues Human β-Cell Dysfunction. Diabetes 2017; 66:1890-1900. [PMID: 28607108 PMCID: PMC5482075 DOI: 10.2337/db16-1170] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 04/15/2017] [Indexed: 12/12/2022]
Abstract
Insulin exocytosis is regulated by ion channels that control excitability and Ca2+ influx. Channels also play an increasingly appreciated role in microdomain structure. In this study, we examine the mechanism by which the voltage-dependent K+ (Kv) channel Kv2.1 (KCNB1) facilitates depolarization-induced exocytosis in INS 832/13 cells and β-cells from human donors with and without type 2 diabetes (T2D). We find that Kv2.1, but not Kv2.2 (KCNB2), forms clusters of 6-12 tetrameric channels at the plasma membrane and facilitates insulin exocytosis. Knockdown of Kv2.1 expression reduces secretory granule targeting to the plasma membrane. Expression of the full-length channel (Kv2.1-wild-type) supports the glucose-dependent recruitment of secretory granules. However, a truncated channel (Kv2.1-ΔC318) that retains electrical function and syntaxin 1A binding, but lacks the ability to form clusters, does not enhance granule recruitment or exocytosis. Expression of KCNB1 appears reduced in T2D islets, and further knockdown of KCNB1 does not inhibit Kv current in T2D β-cells. Upregulation of Kv2.1-wild-type, but not Kv2.1-ΔC318, rescues the exocytotic phenotype in T2D β-cells and increases insulin secretion from T2D islets. Thus, the ability of Kv2.1 to directly facilitate insulin exocytosis depends on channel clustering. Loss of this structural role for the channel might contribute to impaired insulin secretion in diabetes.
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Affiliation(s)
- Jianyang Fu
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaoqing Dai
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Gregory Plummer
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Kunimasa Suzuki
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Austin Bautista
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - John M Githaka
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Laura Senior
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Mette Jensen
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Departments of Pharmacology & Cancer Biology and Medicine, Duke University, Durham, NC
| | - Dafna Greitzer-Antes
- Departments of Medicine and Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Jocelyn E Manning Fox
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Herbert Y Gaisano
- Departments of Medicine and Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center and Duke Molecular Physiology Institute, Departments of Pharmacology & Cancer Biology and Medicine, Duke University, Durham, NC
| | - Nicolas Touret
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Patrick E MacDonald
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
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60
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Pankert T, Jegou T, Caudron-Herger M, Rippe K. Tethering RNA to chromatin for fluorescence microscopy based analysis of nuclear organization. Methods 2017; 123:89-101. [DOI: 10.1016/j.ymeth.2017.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/23/2017] [Accepted: 01/30/2017] [Indexed: 12/22/2022] Open
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61
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Sawyer IA, Dundr M. Chromatin loops and causality loops: the influence of RNA upon spatial nuclear architecture. Chromosoma 2017; 126:541-557. [PMID: 28593374 DOI: 10.1007/s00412-017-0632-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 01/18/2023]
Abstract
An intrinsic and essential trait exhibited by cells is the properly coordinated and integrated regulation of an astoundingly large number of simultaneous molecular decisions and reactions to maintain biochemical homeostasis. This is especially true inside the cell nucleus, where the recognition of DNA and RNA by a vast range of nucleic acid-interacting proteins organizes gene expression patterns. However, this dynamic system is not regulated by simple "on" or "off" signals. Instead, transcription factor and RNA polymerase recruitment to DNA are influenced by the local chromatin and epigenetic environment, a gene's relative position within the nucleus and the action of noncoding RNAs. In addition, major phase-separated structural features of the nucleus, such as nucleoli and paraspeckles, assemble in direct response to specific transcriptional activities and, in turn, influence global genomic function. Currently, the interpretation of these data is trapped in a causality dilemma reminiscent of the "chicken and the egg" paradox as it is unclear whether changes in nuclear architecture promote RNA function or vice versa. Here, we review recent advances that suggest a complex and interdependent interaction network between gene expression, chromatin topology, and noncoding RNA function. We also discuss the functional links between these essential nuclear processes from the nanoscale (gene looping) to the macroscale (sub-nuclear gene positioning and nuclear body function) and briefly highlight some of the challenges that researchers may encounter when studying these phenomena.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Miroslav Dundr
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA.
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62
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Sawyer IA, Hager GL, Dundr M. Specific genomic cues regulate Cajal body assembly. RNA Biol 2017; 14:791-803. [PMID: 27715441 PMCID: PMC5519236 DOI: 10.1080/15476286.2016.1243648] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/06/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
The assembly of specialized sub-nuclear microenvironments known as nuclear bodies (NBs) is important for promoting efficient nuclear function. In particular, the Cajal body (CB), a prominent NB that facilitates spliceosomal snRNP biogenesis, assembles in response to genomic cues. Here, we detail the factors that regulate CB assembly and structural maintenance. These include the importance of transcription at nucleating gene loci, the grouping of these genes on human chromosomes 1, 6 and 17, as well as cell cycle and biochemical regulation of CB protein function. We also speculate on the correlation between CB formation and RNA splicing levels in neurons and cancer. The timing and location of these specific molecular events is critical to CB assembly and its contribution to genome function. However, further work is required to explore the emerging biophysical characteristics of CB assembly and the impact upon subsequent genome reorganization.
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Affiliation(s)
- Iain A. Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, Chicago Medical School, North Chicago, IL, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, Chicago Medical School, North Chicago, IL, USA
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63
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Mannen T, Yamashita S, Tomita K, Goshima N, Hirose T. The Sam68 nuclear body is composed of two RNase-sensitive substructures joined by the adaptor HNRNPL. J Cell Biol 2017; 214:45-59. [PMID: 27377249 PMCID: PMC4932371 DOI: 10.1083/jcb.201601024] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/14/2016] [Indexed: 01/21/2023] Open
Abstract
The mammalian cell nucleus contains membraneless suborganelles referred to as nuclear bodies (NBs). Some NBs are formed with an architectural RNA (arcRNA) as the structural core. Here, we searched for new NBs that are built on unidentified arcRNAs by screening for ribonuclease (RNase)-sensitive NBs using 32,651 fluorescently tagged human cDNA clones. We identified 32 tagged proteins that required RNA for their localization in distinct nuclear foci. Among them, seven RNA-binding proteins commonly localized in the Sam68 nuclear body (SNB), which was disrupted by RNase treatment. Knockdown of each SNB protein revealed that SNBs are composed of two distinct RNase-sensitive substructures. One substructure is present as a distinct NB, termed the DBC1 body, in certain conditions, and the more dynamic substructure including Sam68 joins to form the intact SNB. HNRNPL acts as the adaptor to combine the two substructures and form the intact SNB through the interaction of two sets of RNA recognition motifs with the putative arcRNAs in the respective substructures.
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Affiliation(s)
- Taro Mannen
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
| | - Seisuke Yamashita
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Kozo Tomita
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koutou 135-0064, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
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64
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Staněk D, Fox AH. Nuclear bodies: news insights into structure and function. Curr Opin Cell Biol 2017; 46:94-101. [PMID: 28577509 DOI: 10.1016/j.ceb.2017.05.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/20/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023]
Abstract
The cell nucleus contains a number of different dynamic bodies that are variously composed of proteins and generally, but not always, specific RNA molecules. Recent studies have revealed new understanding about nuclear body formation and function in different aspects of nuclear metabolism. Here, we focus on findings describing the role of nuclear bodies in the biogenesis of specific ribonucleoprotein complexes, processing of key mRNAs, and subnuclear sequestration of protein factors. We highlight how nuclear bodies are involved in stress responses, innate immunity and tumorigenesis. We further review organization of nuclear bodies and principles that govern their assembly, highlighting the pivotal role of scaffolding noncoding RNAs, and liquid-liquid phase separation, which are transforming our picture of nuclear body formation.
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Affiliation(s)
- David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Archa H Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Crawley, 6009 Western Australia, Australia.
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65
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Spichal M, Fabre E. The Emerging Role of the Cytoskeleton in Chromosome Dynamics. Front Genet 2017; 8:60. [PMID: 28580009 PMCID: PMC5437106 DOI: 10.3389/fgene.2017.00060] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/28/2017] [Indexed: 01/15/2023] Open
Abstract
Chromosomes underlie a dynamic organization that fulfills functional roles in processes like transcription, DNA repair, nuclear envelope stability, and cell division. Chromosome dynamics depend on chromosome structure and cannot freely diffuse. Furthermore, chromosomes interact closely with their surrounding nuclear environment, which further constrains chromosome dynamics. Recently, several studies enlighten that cytoskeletal proteins regulate dynamic chromosome organization. Cytoskeletal polymers that include actin filaments, microtubules and intermediate filaments can connect to the nuclear envelope via Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes and transfer forces onto chromosomes inside the nucleus. Monomers of these cytoplasmic polymers and related proteins can also enter the nucleus and play different roles in the interior of the nucleus than they do in the cytoplasm. Nuclear cytoskeletal proteins can act as chromatin remodelers alone or in complexes with other nuclear proteins. They can also act as transcription factors. Many of these mechanisms have been conserved during evolution, indicating that the cytoskeletal regulation of chromosome dynamics is an essential process. In this review, we discuss the different influences of cytoskeletal proteins on chromosome dynamics by focusing on the well-studied model organism budding yeast.
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Affiliation(s)
- Maya Spichal
- Department of Genetics, University of North Carolina, Chapel HillNC, United States
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, CNRS UMR 7212, INSERM U944, Hôpital St. Louis 1Paris, France
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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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Thanisch K, Song C, Engelkamp D, Koch J, Wang A, Hallberg E, Foisner R, Leonhardt H, Stewart CL, Joffe B, Solovei I. Nuclear envelope localization of LEMD2 is developmentally dynamic and lamin A/C dependent yet insufficient for heterochromatin tethering. Differentiation 2017; 94:58-70. [PMID: 28056360 DOI: 10.1016/j.diff.2016.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 11/28/2022]
Abstract
Peripheral heterochromatin in mammalian nuclei is tethered to the nuclear envelope by at least two mechanisms here referred to as the A- and B-tethers. The A-tether includes lamins A/C and additional unknown components presumably INM protein(s) interacting with both lamins A/C and chromatin. The B-tether includes the inner nuclear membrane (INM) protein Lamin B-receptor, which binds B-type lamins and chromatin. Generally, at least one of the tethers is always present in the nuclear envelope of mammalian cells. Deletion of both causes the loss of peripheral heterochromatin and consequently inversion of the entire nuclear architecture, with this occurring naturally in rod photoreceptors of nocturnal mammals. The tethers are differentially utilized during development, regulate gene expression in opposite manners, and play an important role during cell differentiation. Here we aimed to identify the unknown chromatin binding component(s) of the A-tether. We analyzed 10 mouse tissues by immunostaining with antibodies against 7 INM proteins and found that every cell type has specific, although differentially and developmentally regulated, sets of these proteins. In particular, we found that INM protein LEMD2 is concomitantly expressed with A-type lamins in various cell types but is lacking in inverted nuclei of rod cells. Truncation or deletion of Lmna resulted in the downregulation and mislocalization of LEMD2, suggesting that the two proteins interact and pointing at LEMD2 as a potential chromatin binding mediator of the A-tether. Using nuclei of mouse rods as an experimental model lacking peripheral heterochromatin, we expressed a LEMD2 transgene alone or in combination with lamin C in these cells and observed no restoration of peripheral heterochromatin in either case. We conclude that in contrary to the B-tether, the A-tether has a more intricate composition and consists of multiple components that presumably vary, at differing degrees of redundancy, between cell types and differentiation stages.
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Affiliation(s)
- Katharina Thanisch
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Congdi Song
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Dieter Engelkamp
- Transgenic Service Facility, BTE, Franz-Penzoldt-Centre, Friedrich-Alexander-University of Erlangen-Nürnberg, Erwin-Rommel-Str.3, D-91058 Erlangen, Germany
| | - Jeannette Koch
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Audrey Wang
- Institute of Medical Biology, 8A Biomedical Grove and Dept of Biological Sciences, NUS, 138648, Singapore
| | - Einar Hallberg
- Department of Neurochemistry, Stockholm University, Se-106 91 Stockholm, Sweden
| | - Roland Foisner
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Colin L Stewart
- Institute of Medical Biology, 8A Biomedical Grove and Dept of Biological Sciences, NUS, 138648, Singapore.
| | - Boris Joffe
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Irina Solovei
- Department of Biology II, Ludwig-Maximilians-University Munich, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany.
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Tormos AM, Rius-Pérez S, Jorques M, Rada P, Ramirez L, Valverde ÁM, Nebreda ÁR, Sastre J, Taléns-Visconti R. p38α regulates actin cytoskeleton and cytokinesis in hepatocytes during development and aging. PLoS One 2017; 12:e0171738. [PMID: 28166285 PMCID: PMC5293263 DOI: 10.1371/journal.pone.0171738] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/25/2017] [Indexed: 12/02/2022] Open
Abstract
Background Hepatocyte poliploidization is an age-dependent process, being cytokinesis failure the main mechanism of polyploid hepatocyte formation. Our aim was to study the role of p38α MAPK in the regulation of actin cytoskeleton and cytokinesis in hepatocytes during development and aging. Methods Wild type and p38α liver-specific knock out mice at different ages (after weaning, adults and old) were used. Results We show that p38α MAPK deficiency induces actin disassembly upon aging and also cytokinesis failure leading to enhanced binucleation. Although the steady state levels of cyclin D1 in wild type and p38α knock out old livers remained unaffected, cyclin B1- a marker for G2/M transition- was significantly overexpressed in p38α knock out mice. Our findings suggest that hepatocytes do enter into S phase but they do not complete cell division upon p38α deficiency leading to cytokinesis failure and binucleation. Moreover, old liver-specific p38α MAPK knock out mice exhibited reduced F-actin polymerization and a dramatic loss of actin cytoskeleton. This was associated with abnormal hyperactivation of RhoA and Cdc42 GTPases. Long-term p38α deficiency drives to inactivation of HSP27, which seems to account for the impairment in actin cytoskeleton as Hsp27-silencing decreased the number and length of actin filaments in isolated hepatocytes. Conclusions p38α MAPK is essential for actin dynamics with age in hepatocytes.
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Affiliation(s)
- Ana M. Tormos
- Department of Physiology, University of Valencia. Burjassot, Valencia, Spain
| | - Sergio Rius-Pérez
- Department of Physiology, University of Valencia. Burjassot, Valencia, Spain
| | - María Jorques
- Department of Physiology, University of Valencia. Burjassot, Valencia, Spain
| | - Patricia Rada
- Instituto de Investigaciones Biomédicas Alberto Sols (Centro Mixto CSIC-UAM), Arturo Duperier 4, Madrid, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERdem), ISCIII, Madrid, Spain
| | - Lorena Ramirez
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ángela M. Valverde
- Instituto de Investigaciones Biomédicas Alberto Sols (Centro Mixto CSIC-UAM), Arturo Duperier 4, Madrid, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERdem), ISCIII, Madrid, Spain
| | - Ángel R. Nebreda
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Juan Sastre
- Department of Physiology, University of Valencia. Burjassot, Valencia, Spain
| | - Raquel Taléns-Visconti
- Department of Pharmacy and Pharmaceutical Technology and Parasitology, University of Valencia. Burjassot, Valencia, Spain
- * E-mail:
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69
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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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70
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Marnef A, Legube G. Organizing DNA repair in the nucleus: DSBs hit the road. Curr Opin Cell Biol 2017; 46:1-8. [PMID: 28068556 DOI: 10.1016/j.ceb.2016.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/30/2016] [Accepted: 12/12/2016] [Indexed: 10/20/2022]
Abstract
In the past decade, large-scale movements of DNA double strand breaks (DSBs) have repeatedly been identified following DNA damage. These mobility events include clustering, anchoring or peripheral movement at subnuclear structures. Recent work suggests roles for motion in homology search and in break sequestration to preclude deleterious outcomes. Yet, the precise functions of these movements still remain relatively obscure, and the same holds true for the determinants. Here we review recent advances in this exciting area of research, and highlight that a recurrent characteristic of mobile DSBs may lie in their inability to undergo rapid repair. A major future challenge remains to understand how DSB mobility impacts on genome integrity.
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Affiliation(s)
- Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France.
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71
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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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72
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Abstract
Chromosomes underlie a dynamic organization that fulfills functional roles in processes like transcription, DNA repair, nuclear envelope stability, and cell division. Chromosome dynamics depend on chromosome structure and cannot freely diffuse. Furthermore, chromosomes interact closely with their surrounding nuclear environment, which further constrains chromosome dynamics. Recently, several studies enlighten that cytoskeletal proteins regulate dynamic chromosome organization. Cytoskeletal polymers that include actin filaments, microtubules and intermediate filaments can connect to the nuclear envelope via Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes and transfer forces onto chromosomes inside the nucleus. Monomers of these cytoplasmic polymers and related proteins can also enter the nucleus and play different roles in the interior of the nucleus than they do in the cytoplasm. Nuclear cytoskeletal proteins can act as chromatin remodelers alone or in complexes with other nuclear proteins. They can also act as transcription factors. Many of these mechanisms have been conserved during evolution, indicating that the cytoskeletal regulation of chromosome dynamics is an essential process. In this review, we discuss the different influences of cytoskeletal proteins on chromosome dynamics by focusing on the well-studied model organism budding yeast.
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Affiliation(s)
- Maya Spichal
- Department of Genetics, University of North Carolina, Chapel HillNC, United States
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, CNRS UMR 7212, INSERM U944, Hôpital St. Louis 1Paris, France
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73
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Sawyer IA, Sturgill D, Sung MH, Hager GL, Dundr M. Cajal body function in genome organization and transcriptome diversity. Bioessays 2016; 38:1197-1208. [PMID: 27767214 DOI: 10.1002/bies.201600144] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Nuclear bodies contribute to non-random organization of the human genome and nuclear function. Using a major prototypical nuclear body, the Cajal body, as an example, we suggest that these structures assemble at specific gene loci located across the genome as a result of high transcriptional activity. Subsequently, target genes are physically clustered in close proximity in Cajal body-containing cells. However, Cajal bodies are observed in only a limited number of human cell types, including neuronal and cancer cells. Ultimately, Cajal body depletion perturbs splicing kinetics by reducing target small nuclear RNA (snRNA) transcription and limiting the levels of spliceosomal snRNPs, including their modification and turnover following each round of RNA splicing. As such, Cajal bodies are capable of shaping the chromatin interaction landscape and the transcriptome by influencing spliceosome kinetics. Future studies should concentrate on characterizing the direct influence of Cajal bodies upon snRNA gene transcriptional dynamics. Also see the video abstract here.
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Affiliation(s)
- Iain A Sawyer
- Department of Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.,Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miroslav Dundr
- Department of Cell Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
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74
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Serebryannyy LA, Yuen M, Parilla M, Cooper ST, de Lanerolle P. The Effects of Disease Models of Nuclear Actin Polymerization on the Nucleus. Front Physiol 2016; 7:454. [PMID: 27774069 PMCID: PMC5053997 DOI: 10.3389/fphys.2016.00454] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/21/2016] [Indexed: 01/09/2023] Open
Abstract
Actin plays a crucial role in regulating multiple processes within the nucleus, including transcription and chromatin organization. However, the polymerization state of nuclear actin remains controversial, and there is no evidence for persistent actin filaments in a normal interphase nucleus. Further, several disease pathologies are characterized by polymerization of nuclear actin into stable filaments or rods. These include filaments that stain with phalloidin, resulting from point mutations in skeletal α-actin, detected in the human skeletal disease intranuclear rod myopathy, and cofilin/actin rods that form in response to cellular stressors like heatshock. To further elucidate the effects of these pathological actin structures, we examined the nucleus in both cell culture models as well as isolated human tissues. We find these actin structures alter the distribution of both RNA polymerase II and chromatin. Our data suggest that nuclear actin filaments result in disruption of nuclear organization, which may contribute to the disease pathology.
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Affiliation(s)
- Leonid A Serebryannyy
- Department of Physiology and Biophysics, University of Illinois at Chicago Chicago, IL, USA
| | - Michaela Yuen
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at WestmeadSydney, NSW, Australia; Faculty of Medicine, Discipline of Pediatrics and Child Health, University of SydneySydney, NSW, Australia
| | - Megan Parilla
- Department of Physiology and Biophysics, University of Illinois at Chicago Chicago, IL, USA
| | - Sandra T Cooper
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at WestmeadSydney, NSW, Australia; Faculty of Medicine, Discipline of Pediatrics and Child Health, University of SydneySydney, NSW, Australia
| | - Primal de Lanerolle
- Department of Physiology and Biophysics, University of Illinois at Chicago Chicago, IL, USA
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75
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Abstract
Spliceosomal snRNPs are complex particles that proceed through a fascinating maturation pathway. Several steps of this pathway are closely linked to nuclear non-membrane structures called Cajal bodies. In this review, I summarize the last 20 y of research in this field. I primarily focus on snRNP biogenesis, specifically on the steps that involve Cajal bodies. I also evaluate the contribution of the Cajal body in snRNP quality control and discuss the role of snRNPs in Cajal body formation.
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Affiliation(s)
- David Staněk
- a Institute of Molecular Genetics, Czech Academy of Sciences , Prague , Czech Republic
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76
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Martin LD, Harizanova J, Mai S, Belch AR, Pilarski LM. FGFR3 preferentially colocalizes with IGH in the interphase nucleus of multiple myeloma patient B-cells when FGFR3 is located outside of CT4. Genes Chromosomes Cancer 2016; 55:962-974. [PMID: 27509849 DOI: 10.1002/gcc.22394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 01/27/2023] Open
Abstract
Many B-cell malignancies are characterized by chromosomal translocations involving IGH and a proto-oncogene. For translocations to occur, spatial proximity of translocation-prone genes is necessary. Currently, it is not known how such genes are brought into proximity with one another. Although decondensed chromosomes occupy definitive, non-random spaces in the interphase nucleus known as chromosome territories (CTs), chromatin at the edges of CTs can intermingle, and specific genomic regions from some chromosomes have been shown to "loop out" of their respective CTs. This extra-territorial positioning of specific genomic regions may provide a mechanism whereby translocation-prone genes are brought together in the interphase nucleus. FGFR3 and MAF recurrently participate in translocations with IGH at different frequencies. Using 3D, 4-color FISH, and 3D analysis software, we show frequent extra-territorial positioning of FGFR3 and significantly less frequent extra-territorial positioning of MAF. Frequent extra-territorial positioning may be characteristic of FGFR3 in B-cells from healthy adult donors and non-malignant B-cells from patients, but not in hematopoietic stem cells from patients with translocations. The frequency of extra-territorial positioning of FGFR3 and MAF in B-cells correlates with the frequency of translocations in the patient population. Most importantly, in patient B-cells, we demonstrate a significant proportion of extra-territorial FGFR3 participating in close loci pairs and/or colocalizing with IGH. This preliminary work suggests that in patient B-cells, extra-territorial positioning of FGFR3 may provide a mechanism for forming close loci pairs and/or colocalization with IGH; indirectly facilitating translocation events involving these two genes. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lorri D Martin
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, AB, Canada
| | - Jana Harizanova
- Department of Systemic Cell Biology, Max-Planck Institute of Molecular Physiology, Dortmund, Germany.,Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, MB, Canada
| | - Sabine Mai
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, MB, Canada
| | - Andrew R Belch
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, AB, Canada
| | - Linda M Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, AB, Canada.
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77
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Venit T, Kalendová A, Petr M, Dzijak R, Pastorek L, Rohožková J, Malohlava J, Hozák P. Nuclear myosin I regulates cell membrane tension. Sci Rep 2016; 6:30864. [PMID: 27480647 PMCID: PMC4969604 DOI: 10.1038/srep30864] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 07/12/2016] [Indexed: 11/09/2022] Open
Abstract
Plasma membrane tension is an important feature that determines the cell shape and influences processes such as cell motility, spreading, endocytosis and exocytosis. Unconventional class 1 myosins are potent regulators of plasma membrane tension because they physically link the plasma membrane with adjacent cytoskeleton. We identified nuclear myosin 1 (NM1) - a putative nuclear isoform of myosin 1c (Myo1c) - as a new player in the field. Although having specific nuclear functions, NM1 localizes predominantly to the plasma membrane. Deletion of NM1 causes more than a 50% increase in the elasticity of the plasma membrane around the actin cytoskeleton as measured by atomic force microscopy. This higher elasticity of NM1 knock-out cells leads to 25% higher resistance to short-term hypotonic environment and rapid cell swelling. In contrast, overexpression of NM1 in wild type cells leads to an additional 30% reduction of their survival. We have shown that NM1 has a direct functional role in the cytoplasm as a dynamic linker between the cell membrane and the underlying cytoskeleton, regulating the degree of effective plasma membrane tension.
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Affiliation(s)
- Tomáš Venit
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics, AS CR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Albertov 6, 128 43 Prague, Czech Republic
| | - Alžběta Kalendová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics, AS CR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Martin Petr
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics, AS CR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Rastislav Dzijak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics, AS CR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Lukáš Pastorek
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics, AS CR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Jana Rohožková
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics, AS CR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Jakub Malohlava
- Department of Medical Biophysics, Faculty of Medicine and Dentistry, Palacky University in Olomouc, Hnevotinska 3, 775 15 Olomouc, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics, AS CR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
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78
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Meaburn KJ. Spatial Genome Organization and Its Emerging Role as a Potential Diagnosis Tool. Front Genet 2016; 7:134. [PMID: 27507988 PMCID: PMC4961005 DOI: 10.3389/fgene.2016.00134] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/13/2016] [Indexed: 12/12/2022] Open
Abstract
In eukaryotic cells the genome is highly spatially organized. Functional relevance of higher order genome organization is implied by the fact that specific genes, and even whole chromosomes, alter spatial position in concert with functional changes within the nucleus, for example with modifications to chromatin or transcription. The exact molecular pathways that regulate spatial genome organization and the full implication to the cell of such an organization remain to be determined. However, there is a growing realization that the spatial organization of the genome can be used as a marker of disease. While global genome organization patterns remain largely conserved in disease, some genes and chromosomes occupy distinct nuclear positions in diseased cells compared to their normal counterparts, with the patterns of reorganization differing between diseases. Importantly, mapping the spatial positioning patterns of specific genomic loci can distinguish cancerous tissue from benign with high accuracy. Genome positioning is an attractive novel biomarker since additional quantitative biomarkers are urgently required in many cancer types. Current diagnostic techniques are often subjective and generally lack the ability to identify aggressive cancer from indolent, which can lead to over- or under-treatment of patients. Proof-of-principle for the use of genome positioning as a diagnostic tool has been provided based on small scale retrospective studies. Future large-scale studies are required to assess the feasibility of bringing spatial genome organization-based diagnostics to the clinical setting and to determine if the positioning patterns of specific loci can be useful biomarkers for cancer prognosis. Since spatial reorganization of the genome has been identified in multiple human diseases, it is likely that spatial genome positioning patterns as a diagnostic biomarker may be applied to many diseases.
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Affiliation(s)
- Karen J. Meaburn
- Cell Biology of Genomes Group, National Cancer Institute, National Institutes of HealthBethesda, MD, USA
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79
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A novel single cell method to identify the genetic composition at a single nuclear body. Sci Rep 2016; 6:29191. [PMID: 27389808 PMCID: PMC4937434 DOI: 10.1038/srep29191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/14/2016] [Indexed: 11/24/2022] Open
Abstract
Gene loci make specific associations with compartments of the nucleus (e.g. the nuclear envelope, nucleolus, and transcription factories) and this association may determine or reflect a mechanism of genetic control. With current methods, it is not possible to identify sets of genes that converge to form a “gene hub” as there is a reliance on loci-specific probes, or immunoprecipitation of a particular protein from bulk cells. We introduce a method that will allow for the identification of loci contained within the vicinity of a single nuclear body in a single cell. For the first time, we demonstrate that the DNA sequences originating from a single sub-nuclear structure in a single cell targeted by two-photon irradiation can be determined, and mapped to a particular locus. Its application to single PML nuclear bodies reveals ontologically related loci that frequently associate with each other and with PML bodies in a population of cells, and a possible nuclear body targeting role for specific transcription factor binding sites.
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80
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Kulashreshtha M, Mehta IS, Kumar P, Rao BJ. Chromosome territory relocation during DNA repair requires nuclear myosin 1 recruitment to chromatin mediated by ϒ-H2AX signaling. Nucleic Acids Res 2016; 44:8272-91. [PMID: 27365048 PMCID: PMC5041470 DOI: 10.1093/nar/gkw573] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 06/03/2016] [Indexed: 11/22/2022] Open
Abstract
During DNA damage response (DDR), certain gene rich chromosome territories (CTs) relocate to newer positions within interphase nuclei and revert to their native locations following repair. Such dynamic relocation of CTs has been observed under various cellular conditions, however, the underlying mechanistic basis of the same has remained largely elusive. In this study, we aim to understand the temporal and molecular details of such crosstalk between DDR signaling and CT relocation dynamics. We demonstrate that signaling at DNA double strand breaks (DSBs) by the phosphorylated histone variant (ϒ-H2AX) is a pre-requisite for damage induced CT relocation, as cells deficient in ϒ-H2AX signaling fail to exhibit such a response. Inhibition of Rad51 or DNA Ligase IV mediated late steps of double strand break repair does not seem to abrogate CT relocation completely. Upon DNA damage, an increase in the levels of chromatin bound motor protein nuclear myosin 1 (NM1) ensues, which appears to be functionally linked to ϒ-H2AX signaling. Importantly, the motor function of NM1 is essential for its recruitment to chromatin and CT relocation following damage. Taking these observations together, we propose that early DDR sensing and signaling result in NM1 recruitment to chromosomes which in turn guides DNA damage induced CT relocation.
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Affiliation(s)
- Mugdha Kulashreshtha
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Ishita S Mehta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India UM-DAE Centre for Excellence in Basic Sciences, Biological Sciences, Kalina Campus, Santacruz (E), Mumbai, Maharashtra 400098, India
| | - Pradeep Kumar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India UM-DAE Centre for Excellence in Basic Sciences, Biological Sciences, Kalina Campus, Santacruz (E), Mumbai, Maharashtra 400098, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
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81
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Knockleby J, Kim BJ, Mehta A, Lee H. Cdk1-mediated phosphorylation of Cdc7 suppresses DNA re-replication. Cell Cycle 2016; 15:1494-505. [PMID: 27105124 PMCID: PMC4934051 DOI: 10.1080/15384101.2016.1176658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 03/23/2016] [Accepted: 04/06/2016] [Indexed: 12/18/2022] Open
Abstract
To maintain genetic stability, the entire mammalian genome must replicate only once per cell cycle. This is largely achieved by strictly regulating the stepwise formation of the pre-replication complex (pre-RC), followed by the activation of individual origins of DNA replication by Cdc7/Dbf4 kinase. However, the mechanism how Cdc7 itself is regulated in the context of cell cycle progression is poorly understood. Here we report that Cdc7 is phosphorylated by a Cdk1-dependent manner during prometaphase on multiple sites, resulting in its dissociation from origins. In contrast, Dbf4 is not removed from origins in prometaphase, nor is it degraded as cells exit mitosis. Our data thus demonstrates that constitutive phosphorylation of Cdc7 at Cdk1 recognition sites, but not the regulation of Dbf4, prevents the initiation of DNA replication in normally cycling cells and under conditions that promote re-replication in G2/M. As cells exit mitosis, PP1α associates with and dephosphorylates Cdc7. Together, our data support a model where Cdc7 (de)phosphorylation is the molecular switch for the activation and inactivation of DNA replication in mitosis, directly connecting Cdc7 and PP1α/Cdk1 to the regulation of once-per-cell cycle DNA replication in mammalian cells.
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Affiliation(s)
- James Knockleby
- Tumour Biology Group, Advanced Medical Research Institute of Canada, Health Sciences North, Sudbury, Ontario, Canada
| | - Byung Ju Kim
- Tumour Biology Group, Advanced Medical Research Institute of Canada, Health Sciences North, Sudbury, Ontario, Canada
| | - Avani Mehta
- Tumour Biology Group, Advanced Medical Research Institute of Canada, Health Sciences North, Sudbury, Ontario, Canada
| | - Hoyun Lee
- Tumour Biology Group, Advanced Medical Research Institute of Canada, Health Sciences North, Sudbury, Ontario, Canada
- Departments of Medicine, the Faculty of Medicine, the University of Ottawa, Ottawa, Ontario, Canada
- Northern Ontario School of Medicine, Sudbury, Ontario, Canada
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82
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Abstract
A concern in the field of genomics is the proper interpretation of large, high-throughput sequencing datasets. The use of DNA FISH followed by high-content microscopy is a valuable tool for validation and contextualization of frequently occurring gene pairing events at the single-cell level identified by deep sequencing. However, these techniques possess certain limitations. Firstly, they do not permit the study of colocalization of many gene loci simultaneously. Secondly, the direct assessment of the relative position of many clustered gene loci within their respective chromosome territories is impossible. Thus, methods are required to advance the study of higher-order nuclear and cellular organization. Here, we describe a multiplexed DNA FISH technique combined with indirect immunofluorescence to study the relative position of 6 distinct genomic or cellular structures. This can be achieved in a single hybridization step using spectral imaging during image acquisition and linear unmixing. Here, we detail the use of this method to quantify gene pairing between highly expressed spliceosomal genes and compare these data to randomly positioned in silico simulated gene clusters. This is a potentially universally applicable approach for the validation of 3C-based technologies, deep imaging of spatial organization within the nucleus and global cellular organization.
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Affiliation(s)
- Iain A Sawyer
- a Department of Cell Biology , Rosalind Franklin University of Medicine & Science, Chicago Medical School , North Chicago , IL , USA.,b Laboratory of Receptor Biology and Gene Expression , National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
| | - Sergei P Shevtsov
- a Department of Cell Biology , Rosalind Franklin University of Medicine & Science, Chicago Medical School , North Chicago , IL , USA
| | - Miroslav Dundr
- a Department of Cell Biology , Rosalind Franklin University of Medicine & Science, Chicago Medical School , North Chicago , IL , USA
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83
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Verboon JM, Sugumar B, Parkhurst SM. Wiskott-Aldrich syndrome proteins in the nucleus: aWASH with possibilities. Nucleus 2016; 6:349-59. [PMID: 26305109 PMCID: PMC4915506 DOI: 10.1080/19491034.2015.1086051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Actin and proteins that regulate its dynamics or interactions have well-established roles in the cytoplasm where they function as key components of the cytoskeleton to control diverse processes, including cellular infrastructure, cellular motility, cell signaling, and vesicle transport. Recent work has also uncovered roles for actin and its regulatory proteins in the nucleus, primarily in mechanisms governing gene expression. The Wiskott Aldrich Syndrome (WAS) family of proteins, comprising the WASP/N-WASP, SCAR/WAVE, WHAMM/JMY/WHAMY, and WASH subfamilies, function in the cytoplasm where they activate the Arp2/3 complex to form branched actin filaments. WAS proteins are present in the nucleus and have been implicated as transcriptional regulators. We found that Drosophila Wash, in addition to transcriptional effects, is involved in global nuclear architecture. Here we summarize the regulation and function of nuclear WAS proteins, and highlight how our work with Wash expands the possibilities for the functions of these proteins in the nucleus.
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Affiliation(s)
- Jeffrey M Verboon
- a Division of Basic Sciences; Fred Hutchinson Cancer Research Center ; Seattle , WA USA
| | - Bina Sugumar
- a Division of Basic Sciences; Fred Hutchinson Cancer Research Center ; Seattle , WA USA
| | - Susan M Parkhurst
- a Division of Basic Sciences; Fred Hutchinson Cancer Research Center ; Seattle , WA USA
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84
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Hervé B, Coussement A, Gilbert T, Dumont F, Jacques S, Cuisset L, Chicard M, Hizem S, Bourdoncle P, Letourneur F, Dupont C, Vialard F, Choiset A, Dupont JM. Aneuploidy: the impact of chromosome imbalance on nuclear organization and overall genome expression. Clin Genet 2016; 90:35-48. [PMID: 27283765 DOI: 10.1111/cge.12731] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/05/2016] [Accepted: 01/05/2016] [Indexed: 12/19/2022]
Abstract
The organization and dynamics of chromatin within the interphase nucleus as chromosome territories (CTs) and the relationship with transcriptional regulation are not fully understood. We studied a natural example of chromosomal disorganization: aneuploidy due to trisomies 13, 18 and 21. We hypothesized that the presence of an extra copy of one chromosome alters the CT distribution, which perturbs transcriptional activity. We used 3D-FISH to study the position of the chromosomes of interest (18 and 21) in cultured amniocytes and chorionic villus cells from pregnancies with a normal or aneuploid karyotype. We studied the volumes of nuclei and CTs in both conditions and performed a compared transcriptome analysis. We did not observe any differences between euploid and aneuploid cells in terms of the radial and relative CT positions, suggesting that the same rules govern nuclear organization in cases of trisomy. We observed lower volumes for CTs 18 and 21. Overall genome expression profiles highlighted changes in the expression of a subset of genes in trisomic chromosomes, while the majority of transcriptional changes concerned genes located on euploid chromosomes. Our results suggest that a dosage imbalance of the genes on trisomic chromosomes is associated with a disturbance of overall genomic expression.
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Affiliation(s)
- B Hervé
- UFR des Sciences de la Santé Simone Veil, GIG, EA7404, Montigny le Bretonneux, France.,Génomique, Epigénétique et Physiopathologie de la Reproduction, U1016 INSERM-UMR 8104 CNRS, Institut Cochin, Université Paris Descartes, Paris, France.,Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France.,Service de Cytogénétique, Centre Hospitalier Intercommunal de Poissy Saint-Germain-en-Laye, Poissy, France
| | - A Coussement
- Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France
| | - T Gilbert
- Plate-Forme Cochin Imagerie, Université Paris Descartes, Institut Cochin, Paris, France
| | - F Dumont
- Genom'ic, Université Paris Descartes, Institut Cochin, Paris, France
| | - S Jacques
- Genom'ic, Université Paris Descartes, Institut Cochin, Paris, France
| | - L Cuisset
- Génomique, Epigénétique et Physiopathologie de la Reproduction, U1016 INSERM-UMR 8104 CNRS, Institut Cochin, Université Paris Descartes, Paris, France.,Service de Biochimie et Génétique Moléculaire, APHP - Hôpital Cochin, Paris, France
| | - M Chicard
- Genom'ic, Université Paris Descartes, Institut Cochin, Paris, France
| | - S Hizem
- Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France
| | - P Bourdoncle
- Plate-Forme Cochin Imagerie, Université Paris Descartes, Institut Cochin, Paris, France
| | - F Letourneur
- Genom'ic, Université Paris Descartes, Institut Cochin, Paris, France
| | - C Dupont
- Unité fonctionnelle de Cytogénétique-Département de Génétique- APHP, Hôpital Robert Debré, Paris, France
| | - F Vialard
- UFR des Sciences de la Santé Simone Veil, GIG, EA7404, Montigny le Bretonneux, France.,Service de Cytogénétique, Centre Hospitalier Intercommunal de Poissy Saint-Germain-en-Laye, Poissy, France
| | - A Choiset
- Génomique, Epigénétique et Physiopathologie de la Reproduction, U1016 INSERM-UMR 8104 CNRS, Institut Cochin, Université Paris Descartes, Paris, France.,Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France
| | - J-M Dupont
- Génomique, Epigénétique et Physiopathologie de la Reproduction, U1016 INSERM-UMR 8104 CNRS, Institut Cochin, Université Paris Descartes, Paris, France.,Service de Cytogénétique, APHP - Hôpital Cochin, Paris, France
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85
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Wang Q, Sawyer IA, Sung MH, Sturgill D, Shevtsov SP, Pegoraro G, Hakim O, Baek S, Hager GL, Dundr M. Cajal bodies are linked to genome conformation. Nat Commun 2016; 7:10966. [PMID: 26997247 PMCID: PMC4802181 DOI: 10.1038/ncomms10966] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/07/2016] [Indexed: 12/12/2022] Open
Abstract
The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. Here we examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromosome conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear or nucleolar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. In particular, we observed a number of CB-dependent gene-positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production results in increased splicing noise, even in CB-distal regions. Therefore, we conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity. Nuclear bodies can nucleate at sites of active transcription and are beneficial for efficient gene expression. Here, the authors show that Cajal bodies, a prominent type of nuclear body, contribute to genome organization with global effects on gene expression and RNA splicing fidelity.
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Affiliation(s)
- Qiuyan Wang
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA.,Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Iain A Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA.,Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Sergey P Shevtsov
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA.,High-Throughput Imaging Facility (HiTIF), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Ofir Hakim
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA
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86
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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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87
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García-Morales L, González-González L, Querol E, Piñol J. A minimized motile machinery forMycoplasma genitalium. Mol Microbiol 2016; 100:125-38. [DOI: 10.1111/mmi.13305] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2015] [Indexed: 01/29/2023]
Affiliation(s)
- Luis García-Morales
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular; Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Luis González-González
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular; Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | | | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular; Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
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88
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Spichal M, Brion A, Herbert S, Cournac A, Marbouty M, Zimmer C, Koszul R, Fabre E. Evidence for a dual role of actin in regulating chromosome organization and dynamics in yeast. J Cell Sci 2016; 129:681-92. [PMID: 26763908 DOI: 10.1242/jcs.175745] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/05/2016] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic chromosomes undergo movements that are involved in the regulation of functional processes such as DNA repair. To better understand the origin of these movements, we used fluorescence microscopy, image analysis and chromosome conformation capture to quantify the actin contribution to chromosome movements and interactions in budding yeast. We show that both the cytoskeletal and nuclear actin drive local chromosome movements, independently of Csm4, a putative LINC protein. Inhibition of actin polymerization reduces subtelomere dynamics, resulting in more confined territories and enrichment in subtelomeric contacts. Artificial tethering of actin to nuclear pores increased both nuclear pore complex (NPC) and subtelomere motion. Chromosome loci that were positioned away from telomeres exhibited reduced motion in the presence of an actin polymerization inhibitor but were unaffected by the lack of Csm4. We further show that actin was required for locus mobility that was induced by targeting the chromatin-remodeling protein Ino80. Correlated with this, DNA repair by homologous recombination was less efficient. Overall, interphase chromosome dynamics are modulated by the additive effects of cytoskeletal actin through forces mediated by the nuclear envelope and nuclear actin, probably through the function of actin in chromatin-remodeling complexes.
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Affiliation(s)
- Maya Spichal
- INSERM UMR 944, Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis 1, Avenue Claude Vellefaux, Paris 75010, France CNRS, UMR 7212, Paris 75010, France Université Paris Diderot, Sorbonne Paris Cité, Paris 75010, France Institut Pasteur, Groupe Régulation Spatiale des Génomes, Paris 75015, France CNRS, UMR 3525, Paris 75015, France Sorbonne Universités, UPMC Université Paris 6, Paris 75005, France
| | - Alice Brion
- INSERM UMR 944, Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis 1, Avenue Claude Vellefaux, Paris 75010, France CNRS, UMR 7212, Paris 75010, France Université Paris Diderot, Sorbonne Paris Cité, Paris 75010, France
| | - Sébastien Herbert
- Institut Pasteur, Unité Imagerie et Modélisation, Paris 75015, France CNRS, URA 2582, Paris 75015, France
| | - Axel Cournac
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Paris 75015, France CNRS, UMR 3525, Paris 75015, France
| | - Martial Marbouty
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Paris 75015, France CNRS, UMR 3525, Paris 75015, France
| | - Christophe Zimmer
- Institut Pasteur, Unité Imagerie et Modélisation, Paris 75015, France CNRS, URA 2582, Paris 75015, France
| | - Romain Koszul
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Paris 75015, France CNRS, UMR 3525, Paris 75015, France
| | - Emmanuelle Fabre
- INSERM UMR 944, Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis 1, Avenue Claude Vellefaux, Paris 75010, France CNRS, UMR 7212, Paris 75010, France Université Paris Diderot, Sorbonne Paris Cité, Paris 75010, France Institut Pasteur, Groupe Régulation Spatiale des Génomes, Paris 75015, France CNRS, UMR 3525, Paris 75015, France
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89
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Migocka-Patrzałek M, Makowiecka A, Nowak D, Mazur AJ, Hofmann WA, Malicka-Błaszkiewicz M. β- and γ-Actins in the nucleus of human melanoma A375 cells. Histochem Cell Biol 2015; 144:417-28. [PMID: 26239425 PMCID: PMC4628621 DOI: 10.1007/s00418-015-1349-8] [Citation(s) in RCA: 9] [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] [Accepted: 06/14/2015] [Indexed: 11/13/2022]
Abstract
Actin is a highly conserved protein that is expressed in all eukaryotic cells and has essential functions in the cytoplasm and the nucleus. Nuclear actin is involved in transcription by all three RNA polymerases, chromatin remodelling, RNA processing, intranuclear transport, nuclear export and in maintenance of the nuclear architecture. The nuclear actin level and polymerization state are important factors regulating nuclear processes such as transcription. Our study shows that, in contrast to the cytoplasm, the majority of endogenous nuclear actin is unpolymerized in human melanoma A375 cells. Most mammalian cells express the two non-muscle β- and γ-actin isoforms that differ in only four amino acids. Despite their sequence similarity, studies analysing the cytoplasmic functions of these isoforms demonstrated that β- and γ-actins show differences in localization and function. However, little is known about the involvement of the individual actin isoforms in nuclear processes. Here, we used the human melanoma A375 cell line to analyse actin isoforms in regard to their nuclear localization. We show that both β- and γ-non-muscle actin isoforms are present in nuclei of these cells. Immunolocalization studies demonstrate that both isoforms co-localize with RNA polymerase II and hnRNP U. However, we observe differences in the ratio of cytoplasmic to nuclear actin distribution between the isoforms. We show that β-actin has a significantly higher nucleus-to-cytoplasm ratio than γ-actin.
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Affiliation(s)
- Marta Migocka-Patrzałek
- Department of Animal Developmental Biology, Institute of Experimental Biology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335, Wroclaw, Poland.
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland.
- Department of Physiology and Biophysics, University at Buffalo State University of New York, Buffalo, NY, USA.
| | - Aleksandra Makowiecka
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dorota Nowak
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Antonina J Mazur
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Wilma A Hofmann
- Department of Physiology and Biophysics, University at Buffalo State University of New York, Buffalo, NY, USA
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90
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Abstract
Initially identified as a marker of coiled bodies (now Cajal bodies or CBs), the protein coilin was discovered a quarter of century ago. Coilin is now known to scaffold the CB, but its structure and function are poorly understood. Nearly devoid of predicted structural motifs, coilin has numerous reported molecular interactions that must underlie its role in the formation and function of CBs. In this review, we summarize what we have learned in the past 25 years about coilin's structure, post-transcriptional modifications, and interactions with RNA and proteins. We show that genes with homology to human coilin are found in primitive metazoans and comment on differences among model organisms. Coilin's function in Cajal body formation and RNP metabolism will be discussed in the light of these developments.
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Affiliation(s)
- Martin Machyna
- a Department of Molecular Biophysics & Biochemistry ; Yale University ; New Haven , CT USA
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91
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Oh I, Choi S, Jung Y, Kim JS. Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes. SOFT MATTER 2015; 11:6450-6459. [PMID: 26179211 DOI: 10.1039/c5sm01096a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.
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Affiliation(s)
- Inrok Oh
- Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
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92
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Abstract
Chromatin, once thought to serve only as a means to package DNA, is now recognized as a major regulator of gene activity. As a result of the wide range of methods used to describe the numerous levels of chromatin organization, the terminology that has emerged to describe these organizational states is often imprecise and sometimes misleading. In this review, we discuss our current understanding of chromatin architecture and propose terms to describe the various biochemical and structural states of chromatin.
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Affiliation(s)
- Liron Even-Faitelson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | | | - Zahra Baghestani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada
| | - David P Bazett-Jones
- Program in Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada.
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93
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Nuclear actin and myosins in adenovirus infection. Exp Cell Res 2015; 338:170-82. [PMID: 26226218 DOI: 10.1016/j.yexcr.2015.07.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 11/21/2022]
Abstract
Adenovirus serotypes have been shown to cause drastic changes in nuclear organization, including the transcription machinery, during infection. This ability of adenovirus to subvert transcription in the host cell facilitates viral replication. Because nuclear actin and nuclear myosin I, myosin V and myosin VI have been implicated as direct regulators of transcription and important factors in the replication of other viruses, we sought to determine how nuclear actin and myosins are involved in adenovirus infection. We first confirmed reorganization of the host's transcription machinery to viral replication centers. We found that nuclear actin also reorganizes to sites of transcription through the intermediate but not the advanced late phase of viral infection. Furthermore, nuclear myosin I localized with nuclear actin and sites of transcription in viral replication centers. Intriguingly, nuclear myosins V and VI, which also reorganized to viral replication centers, exhibited different localization patterns, suggesting specialized roles for these nuclear myosins. Finally, we assessed the role of actin in adenovirus infection and found both cytoplasmic and nuclear actin likely play roles in adenovirus infection and replication. Together our data suggest the involvement of actin and multiple myosins in the nuclear replication and late viral gene expression of adenovirus.
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94
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Myosin VI regulates gene pairing and transcriptional pause release in T cells. Proc Natl Acad Sci U S A 2015; 112:E1587-93. [PMID: 25770220 DOI: 10.1073/pnas.1502461112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Naive CD4 T cells differentiate into several effector lineages, which generate a stronger and more rapid response to previously encountered immunological challenges. Although effector function is a key feature of adaptive immunity, the molecular basis of this process is poorly understood. Here, we investigated the spatiotemporal regulation of cytokine gene expression in resting and restimulated effector T helper 1 (Th1) cells. We found that the Lymphotoxin (LT)/TNF alleles, which encode TNF-α, were closely juxtaposed shortly after T-cell receptor (TCR) engagement, when transcription factors are limiting. Allelic pairing required a nuclear myosin, myosin VI, which is rapidly recruited to the LT/TNF locus upon restimulation. Furthermore, transcription was paused at the TNF locus and other related genes in resting Th1 cells and released in a myosin VI-dependent manner following activation. We propose that homologous pairing and myosin VI-mediated transcriptional pause release account for the rapid and efficient expression of genes induced by an external stimulus.
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95
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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96
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SART3-Dependent Accumulation of Incomplete Spliceosomal snRNPs in Cajal Bodies. Cell Rep 2015; 10:429-440. [PMID: 25600876 DOI: 10.1016/j.celrep.2014.12.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/18/2014] [Accepted: 12/13/2014] [Indexed: 12/16/2022] Open
Abstract
Cajal bodies (CBs) are evolutionarily conserved nuclear structures involved in the metabolism of spliceosomal small nuclear ribonucleoprotein particles (snRNPs). CBs are not present in all cell types, and the trigger for their formation is not yet known. Here, we depleted cells of factors required for the final steps of snRNP assembly and assayed for the presence of stalled intermediates in CBs. We show that depletion induces formation of CBs in cells that normally lack these nuclear compartments, suggesting that CB nucleation is triggered by an imbalance in snRNP assembly. Accumulation of stalled intermediates in CBs depends on the di-snRNP assembly factor SART3. SART3 is required for both the induction of CB formation as well as the tethering of incomplete snRNPs to coilin, the CB scaffolding protein. We propose a model wherein SART3 monitors tri-snRNP assembly and sequesters incomplete particles in CBs, thereby allowing cells to maintain a homeostatic balance of mature snRNPs in the nucleoplasm.
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97
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Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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98
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100
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Simon DN, Zastrow MS, Wilson KL. Direct actin binding to A- and B-type lamin tails and actin filament bundling by the lamin A tail. Nucleus 2014. [DOI: 10.4161/nucl.11799] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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