1
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Ovejero S, Soulet C, Kumanski S, Moriel-Carretero M. Coordination between phospholipid pools and DNA damage sensing. Biol Cell 2022; 114:211-219. [PMID: 35524759 DOI: 10.1111/boc.202200007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 11/27/2022]
Abstract
Both phospholipid synthesis and the detection of DNA damage are coupled to cell cycle progression, yet whether these two aspects crosstalk to each other remains unassessed. We postulate here that shortage of phospholipids, which negatively affects proliferation, may reduce the need for checkpoint activation in response to DNA damage. By exploring the DDR activation in response to seven different genotoxins, in three distinct cell types, and manipulating phospholipid synthesis both pharmacologically and genetically, we point at the DNA damage response kinase ATR as responsible for the coordination between phospholipid levels and DNA damage sensing. Further, our analysis reveals the functional significance of this crosstalk to keep genome homeostasis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sara Ovejero
- Institut de Génétique Humaine (IGH), Université de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France.,Department of Biological Hematology, CHU Montpellier, Montpellier, 34295, France
| | - Caroline Soulet
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France
| | - Sylvain Kumanski
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier-Centre National de la Recherche Scientifique, Montpellier, France
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2
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Pentzold C, Kokal M, Pentzold S, Weise A. Sites of chromosomal instability in the context of nuclear architecture and function. Cell Mol Life Sci 2020; 78:2095-2103. [PMID: 33219838 PMCID: PMC7966619 DOI: 10.1007/s00018-020-03698-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/02/2020] [Accepted: 10/31/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal fragile sites are described as areas within the tightly packed mitotic chromatin that appear as breaks or gaps mostly tracing back to a loosened structure and not a real nicked break within the DNA molecule. Most facts about fragile sites result from studies in mitotic cells, mainly during metaphase and mainly in lymphocytes. Here, we synthesize facts about the genomic regions that are prone to form gaps and breaks on metaphase chromosomes in the context of interphase. We conclude that nuclear architecture shapes the activity profile of the cell, i.e. replication timing and transcriptional activity, thereby influencing genomic integrity during interphase with the potential to cause fragility in mitosis. We further propose fragile sites as examples of regions specifically positioned in the interphase nucleus with putative anchoring points at the nuclear lamina to enable a tightly regulated replication–transcription profile and diverse signalling functions in the cell. Consequently, fragility starts before the actual display as chromosomal breakage in metaphase to balance the initial contradiction of cellular overgrowth or malfunctioning and maintaining diversity in molecular evolution.
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Affiliation(s)
- Constanze Pentzold
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany.
| | - Miriam Kokal
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Stefan Pentzold
- Research Center Lobeda, Jena University Hospital, 07747, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
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3
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Nusbaumer D, Marques da Cunha L, Wedekind C. Sperm cryopreservation reduces offspring growth. Proc Biol Sci 2019; 286:20191644. [PMID: 31551057 PMCID: PMC6784727 DOI: 10.1098/rspb.2019.1644] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Abstract
Sperm cryopreservation is routinely used in reproductive medicine, livestock production and wildlife management. Its effect on offspring performance is often assumed to be negligible, but this still remains to be confirmed in well-controlled within-subject experiments. We use a vertebrate model that allows us to experimentally separate parental and environmental effects to test whether sperm cryopreservation influences offspring phenotype under stress and non-stress conditions, and whether such effects are male-specific. Wild brown trout (Salmo trutta) were stripped for their gametes, and a portion of each male's milt was cryopreserved. Then, 960 eggs were simultaneously fertilized with either non-cryopreserved or frozen-thawed semen and raised singly in the presence or absence of a pathogen. We found no significant effects of cryopreservation on fertilization rates, and no effects on growth, survival nor pathogen resistance during the embryo stage. However, fertilization by cryopreserved sperm led to significantly reduced larval growth after hatching. Males varied in genetic quality as determined from offspring performance, but effects of cryopreservation on larval growth were not male-specific. We conclude that cryopreservation causes a reduction in offspring growth that is easily overlooked because it only manifests itself at later developmental stages, when many other factors affect growth and survival too.
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Affiliation(s)
| | | | - Claus Wedekind
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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4
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Irwin NAT, Keeling PJ. Extensive Reduction of the Nuclear Pore Complex in Nucleomorphs. Genome Biol Evol 2019; 11:678-687. [PMID: 30715330 PMCID: PMC6411479 DOI: 10.1093/gbe/evz029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2019] [Indexed: 12/17/2022] Open
Abstract
The nuclear pore complex (NPC) is a large macromolecular assembly situated within the pores of the nuclear envelope. Through interactions between its subcomplexes and import proteins, the NPC mediates the transport of molecules into and out of the nucleus and facilitates dynamic chromatin regulation and gene expression. Accordingly, the NPC constitutes a highly integrated nuclear component that is ubiquitous and conserved among eukaryotes. Potential exceptions to this are nucleomorphs: Highly reduced, relict nuclei that were derived from green and red algae following their endosymbiotic integration into two lineages, the chlorarachniophytes and the cryptophyceans. A previous investigation failed to identify NPC genes in nucleomorph genomes suggesting that these genes have either been relocated to the host nucleus or lost. Here, we sought to investigate the composition of the NPC in nucleomorphs by using genomic and transcriptomic data to identify and phylogenetically classify NPC proteins in nucleomorph-containing algae. Although we found NPC proteins in all examined lineages, most of those found in chlorarachniophytes and cryptophyceans were single copy, host-related proteins that lacked signal peptides. Two exceptions were Nup98 and Rae1, which had clear nucleomorph-derived homologs. However, these proteins alone are likely insufficient to structure a canonical NPC and previous reports revealed that Nup98 and Rae1 have other nuclear functions. Ultimately, these data indicate that nucleomorphs represent eukaryotic nuclei without a canonical NPC, raising fundamental questions about their structure and function.
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Affiliation(s)
- Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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5
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Birendra Kc, May DG, Benson BV, Kim DI, Shivega WG, Ali MH, Faustino RS, Campos AR, Roux KJ. VRK2A is an A-type lamin-dependent nuclear envelope kinase that phosphorylates BAF. Mol Biol Cell 2017. [PMID: 28637768 PMCID: PMC5555652 DOI: 10.1091/mbc.e17-03-0138] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
By the use of comparative BioID of nuclear envelope (NE) proteins lamin A and Sun2, as well as a minimal inner nuclear membrane targeting motif, VRK2 is identified as a novel constituent of the NE. A-type lamins retain the transmembrane kinase VRK2 at the NE, where it phosphorylates and regulates the nuclear mobility of BAF. The nuclear envelope (NE) is critical for numerous fundamental cellular functions, and mutations in several NE constituents can lead to a heterogeneous spectrum of diseases. We used proximity biotinylation to uncover new constituents of the inner nuclear membrane (INM) by comparative BioID analysis of lamin A, Sun2 and a minimal INM-targeting motif. These studies identify vaccinia-related kinase-2 (VRK2) as a candidate constituent of the INM. The transmembrane VRK2A isoform is retained at the NE by association with A-type lamins. Furthermore, VRK2A physically interacts with A-type, but not B-type, lamins. Finally, we show that VRK2 phosphorylates barrier to autointegration factor (BAF), a small and highly dynamic chromatin-binding protein, which has roles including NE reassembly, cell cycle, and chromatin organization in cells, and subtly alters its nuclear mobility. Together these findings support the value of using BioID to identify unrecognized constituents of distinct subcellular compartments refractory to biochemical isolation and reveal VRK2A as a transmembrane kinase in the NE that regulates BAF.
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Affiliation(s)
- Birendra Kc
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Danielle G May
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Benjamin V Benson
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Dae In Kim
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Winnie G Shivega
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Manaal H Ali
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Randolph S Faustino
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104.,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
| | - Alexandre R Campos
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Kyle J Roux
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104 .,Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
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6
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Rai U, Najm F, Tartakoff AM. Nucleolar asymmetry and the importance of septin integrity upon cell cycle arrest. PLoS One 2017; 12:e0174306. [PMID: 28339487 PMCID: PMC5365125 DOI: 10.1371/journal.pone.0174306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/07/2017] [Indexed: 12/31/2022] Open
Abstract
Cell cycle arrest can be imposed by inactivating the anaphase promoting complex (APC). In S. cerevisiae this arrest has been reported to stabilize a metaphase-like intermediate in which the nuclear envelope spans the bud neck, while chromatin repeatedly translocates between the mother and bud domains. The present investigation was undertaken to learn how other features of nuclear organization are affected upon depletion of the APC activator, Cdc20. We observe that the spindle pole bodies and the spindle repeatedly translocate across the narrow orifice at the level of the neck. Nevertheless, we find that the nucleolus (organized around rDNA repeats on the long right arm of chromosome XII) remains in the mother domain, marking the polarity of the nucleus. Accordingly, chromosome XII is polarized: TelXIIR remains in the mother domain and its centromere is predominantly located in the bud domain. In order to learn why the nucleolus remains in the mother domain, we studied the impact of inhibiting rRNA synthesis in arrested cells. We observed that this fragments the nucleolus and that these fragments entered the bud domain. Taken together with earlier observations, the restriction of the nucleolus to the mother domain therefore can be attributed to its massive structure. We also observed that inactivation of septins allowed arrested cells to complete the cell cycle, that the alternative APC activator, Cdh1, was required for completion of the cell cycle and that induction of Cdh1 itself caused arrested cells to progress to the end of the cell cycle.
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Affiliation(s)
- Urvashi Rai
- Cell Biology Program/Department of Molecular and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Fadi Najm
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alan M. Tartakoff
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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7
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The Intra-S Checkpoint Responses to DNA Damage. Genes (Basel) 2017; 8:genes8020074. [PMID: 28218681 PMCID: PMC5333063 DOI: 10.3390/genes8020074] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 02/03/2023] Open
Abstract
Faithful duplication of the genome is a challenge because DNA is susceptible to damage by a number of intrinsic and extrinsic genotoxins, such as free radicals and UV light. Cells activate the intra-S checkpoint in response to damage during S phase to protect genomic integrity and ensure replication fidelity. The checkpoint prevents genomic instability mainly by regulating origin firing, fork progression, and transcription of G1/S genes in response to DNA damage. Several studies hint that regulation of forks is perhaps the most critical function of the intra-S checkpoint. However, the exact role of the checkpoint at replication forks has remained elusive and controversial. Is the checkpoint required for fork stability, or fork restart, or to prevent fork reversal or fork collapse, or activate repair at replication forks? What are the factors that the checkpoint targets at stalled replication forks? In this review, we will discuss the various pathways activated by the intra-S checkpoint in response to damage to prevent genomic instability.
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8
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Labade AS, Karmodiya K, Sengupta K. HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205. Epigenetics Chromatin 2016; 9:54. [PMID: 27980680 PMCID: PMC5135769 DOI: 10.1186/s13072-016-0106-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022] Open
Abstract
Background The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes. However, the functional consequences of the association of Nup93 with HOXA is unknown. Results Here, we examined the association of Nup93 with the HOXA gene cluster and its consequences on HOXA gene expression in diploid colorectal cancer cells (DLD1). Nup93 showed a specific enrichment ~1 Kb upstream of the transcription start site of each of the HOXA1, HOXA3 and HOXA5 promoters, respectively. Furthermore, the association of Nup93 with HOXA was assisted by its interacting partners Nup188 and Nup205. The depletion of the Nup93 sub-complex significantly upregulated HOXA gene expression levels. However, expression levels of a control gene locus (GLCCI1) on human chromosome 7 were unaffected. Three-dimensional fluorescence in situ hybridization (3D-FISH) analyses revealed that the depletion of the Nup93 sub-complex (but not Nup98) disengages the HOXA gene locus from the nuclear periphery, suggesting a potential role for Nup93 in tethering and repressing the HOXA gene cluster. Consistently, Nup93 knockdown increased active histone marks (H3K9ac), decreased repressive histone marks (H3K27me3) on the HOXA1 promoter and increased transcription elongation marks (H3K36me3) within the HOXA1 gene. Moreover, the combined depletion of Nup93 and CTCF (a known organizer of HOXA gene cluster) but not Nup93 alone, significantly increased GLCCI1 gene expression levels. Taken together, this suggests a novel role for Nup93 and its interactors in repressing the HOXA gene cluster. Conclusions This study reveals that the nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 mediates the repression of HOXA gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0106-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ajay S Labade
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
| | - Krishanpal Karmodiya
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
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9
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Methods to Study the Atypical Roles of DNA Repair and SMC Proteins in Gene Silencing. Methods Mol Biol 2016. [PMID: 27797079 DOI: 10.1007/978-1-4939-6545-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Silenced heterochromatin influences all nuclear processes including chromosome structure, nuclear organization, transcription, replication, and repair. Proteins that mediate silencing affect all of these nuclear processes. Similarly proteins involved in replication, repair, and chromosome structure play a role in the formation and maintenance of silenced heterochromatin. In this chapter we describe a handful of simple tools and methods that can be used to study the atypical role of proteins in gene silencing.
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10
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Abstract
ATR (Ataxia Telangiectasia and Rad3-related) is a member of the Phosphatidylinositol 3-kinase-related kinases (PIKKs) family, amongst six other vertebrate proteins known so far. ATR is indispensable for cell survival and its essential role is in sensing DNA damage and initiating appropriate repair responses. In this review we highlight emerging and recent observations connecting ATR to alternative roles in controlling the nuclear envelope, nucleolus, centrosome and other organelles in response to both internal and external stress conditions. We propose that ATR functions control cell plasticity by sensing structural deformations of different cellular components, including DNA and initiating appropriate repair responses, most of which are yet to be understood completely.
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Affiliation(s)
- Gururaj Rao Kidiyoor
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy
| | - Amit Kumar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Marco Foiani
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy.
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11
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Closing a gap in the nuclear envelope. Curr Opin Cell Biol 2016; 40:90-97. [PMID: 27016712 DOI: 10.1016/j.ceb.2016.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/13/2016] [Accepted: 03/05/2016] [Indexed: 11/22/2022]
Abstract
The nuclear envelope (NE) ensures nucleo-cytoplasmic compartmentalization, with trafficking of macromolecules across this double membrane controlled by embedded nuclear pore complexes (NPCs). The NE and associated proteins are dismantled during open mitosis and reestablishment of this barrier during mitotic exit requires dynamic remodeling of endoplasmic reticulum (ER) membranes and coordination with NPC reformation, with NPC deposition continuing during subsequent interphase. In this review, we discuss recent progress in our understanding of NE reformation and nuclear pore complex generation, with special focus on work implicating the endosomal sorting complex required for transport (ESCRT) membrane remodeling machinery in these events.
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12
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Tsai SYA, Chuang JY, Tsai MS, Wang XF, Xi ZX, Hung JJ, Chang WC, Bonci A, Su TP. Sigma-1 receptor mediates cocaine-induced transcriptional regulation by recruiting chromatin-remodeling factors at the nuclear envelope. Proc Natl Acad Sci U S A 2015; 112:E6562-70. [PMID: 26554014 PMCID: PMC4664336 DOI: 10.1073/pnas.1518894112] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The sigma-1 receptor (Sig-1R) chaperone at the endoplasmic reticulum (ER) plays important roles in cellular regulation. Here we found a new function of Sig-1R, in that it translocates from the ER to the nuclear envelope (NE) to recruit chromatin-remodeling molecules and regulate the gene transcription thereof. Sig-1Rs mainly reside at the ER-mitochondrion interface. However, on stimulation by agonists such as cocaine, Sig-1Rs translocate from ER to the NE, where Sig-1Rs bind NE protein emerin and recruit chromatin-remodeling molecules, including lamin A/C, barrier-to-autointegration factor (BAF), and histone deacetylase (HDAC), to form a complex with the gene repressor specific protein 3 (Sp3). Knockdown of Sig-1Rs attenuates the complex formation. Cocaine was found to suppress the gene expression of monoamine oxidase B (MAOB) in the brain of wild-type but not Sig-1R knockout mouse. A single dose of cocaine (20 mg/kg) in rats suppresses the level of MAOB at nuclear accumbens without affecting the level of dopamine transporter. Daily injections of cocaine in rats caused behavioral sensitization. Withdrawal from cocaine in cocaine-sensitized rats induced an apparent time-dependent rebound of the MAOB protein level to about 200% over control on day 14 after withdrawal. Treatment of cocaine-withdrawn rats with the MAOB inhibitor deprenyl completely alleviated the behavioral sensitization to cocaine. Our results demonstrate a role of Sig-1R in transcriptional regulation and suggest cocaine may work through this newly discovered genomic action to achieve its addictive action. Results also suggest the MAOB inhibitor deprenyl as a therapeutic agent to block certain actions of cocaine during withdrawal.
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Affiliation(s)
- Shang-Yi A Tsai
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, Baltimore, MD 21224
| | - Jian-Ying Chuang
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, Baltimore, MD 21224; The Ph.D. Program for Neural Regenerative Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Meng-Shan Tsai
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, Baltimore, MD 21224
| | - Xiao-Fei Wang
- Molecular Targets and Medication Discovery Branch, National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, Baltimore, MD 21224
| | - Zheng-Xiong Xi
- Molecular Targets and Medication Discovery Branch, National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, Baltimore, MD 21224
| | - Jan-Jong Hung
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wen-Chang Chang
- Graduate Institute of Medical Science, Taipei Medical University, Taipei 11031, Taiwan
| | - Antonello Bonci
- Cellular Neurobiology Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, Baltimore, MD 21224; Department of Neurology, University of California, San Francisco, CA 94608; Solomon H. Snyder Neuroscience Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Tsung-Ping Su
- Cellular Pathobiology Section, Integrative Neuroscience Research Branch, National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, Baltimore, MD 21224;
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13
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Abstract
Recombination is a central process to stably maintain and transmit a genome through somatic cell divisions and to new generations. Hence, recombination needs to be coordinated with other events occurring on the DNA template, such as DNA replication, transcription, and the specialized chromosomal functions at centromeres and telomeres. Moreover, regulation with respect to the cell-cycle stage is required as much as spatiotemporal coordination within the nuclear volume. These regulatory mechanisms impinge on the DNA substrate through modifications of the chromatin and directly on recombination proteins through a myriad of posttranslational modifications (PTMs) and additional mechanisms. Although recombination is primarily appreciated to maintain genomic stability, the process also contributes to gross chromosomal arrangements and copy-number changes. Hence, the recombination process itself requires quality control to ensure high fidelity and avoid genomic instability. Evidently, recombination and its regulatory processes have significant impact on human disease, specifically cancer and, possibly, neurodegenerative diseases.
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Affiliation(s)
- Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616-8665 Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665
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14
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Krefman NI, Drubin DG, Barnes G. Control of the spindle checkpoint by lateral kinetochore attachment and limited Mad1 recruitment. Mol Biol Cell 2015; 26:2620-39. [PMID: 26023090 PMCID: PMC4501360 DOI: 10.1091/mbc.e15-05-0276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 05/18/2015] [Indexed: 01/06/2023] Open
Abstract
The spindle checkpoint proteins Mad1 and Bub1 are dynamically recruited after induced de novo kinetochore assembly. Detached kinetochores compete with alternate binding sites in the nucleus to recruit Mad1 and Bub1 from very limited pools. Lateral kinetochore attachment to microtubules licenses Mad1 removal from kinetochores. We observed the dynamic recruitment of spindle checkpoint proteins Mad1 and Bub1 to detached kinetochores in budding yeast using real-time live-cell imaging and quantified recruitment in fixed cells. After induced de novo kinetochore assembly at one pair of sister centromeres, Mad1 appeared after the kinetochore protein Mtw1. Detached kinetochores were not associated with the nuclear envelope, so Mad1 does not anchor them to nuclear pore complexes (NPCs). Disrupting Mad1's NPC localization increased Mad1 recruitment to detached sister kinetochores. Conversely, increasing the number of detached kinetochores reduced the amount of Mad1 per detached kinetochore. Bub1 also relocalized completely from the spindle to detached sister centromeres after kinetochore assembly. After their capture by microtubules, Mad1 and Bub1 progressively disappeared from kinetochores. Sister chromatids that arrested with a lateral attachment to one microtubule exhibited half the Mad1 of fully detached sisters. We propose that detached kinetochores compete with alternate binding sites in the nucleus to recruit Mad1 and Bub1 from available pools that are small enough to be fully depleted by just one pair of detached kinetochores and that lateral attachment licenses Mad1 removal from kinetochores after a kinetic delay.
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Affiliation(s)
- Nathaniel I Krefman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Georjana Barnes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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15
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Abstract
Billions of base pairs of DNA must be replicated trillions of times in a human lifetime. Complete and accurate replication once and only once per cell division cycle is essential to maintain genome integrity and prevent disease. Impediments to replication fork progression including difficult to replicate DNA sequences, conflicts with transcription, and DNA damage further add to the genome maintenance challenge. These obstacles frequently cause fork stalling, but only rarely cause a failure to complete replication. Robust mechanisms ensure that stalled forks remain stable and capable of either resuming DNA synthesis or being rescued by converging forks. However, when failures do happen the fork collapses leading to genome rearrangements, cell death and disease. Despite intense interest, the mechanisms to repair damaged replication forks, stabilize them, and ensure successful replication remain only partly understood. Different models of fork collapse have been proposed with varying descriptions of what happens to the DNA and replisome. Here, I will define fork collapse and describe what is known about how the replication checkpoint prevents it to maintain genome stability.
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16
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Steglich B, Strålfors A, Khorosjutina O, Persson J, Smialowska A, Javerzat JP, Ekwall K. The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast. PLoS Genet 2015; 11:e1005101. [PMID: 25798942 PMCID: PMC4370569 DOI: 10.1371/journal.pgen.1005101] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 02/25/2015] [Indexed: 12/21/2022] Open
Abstract
In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3∆ cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and the nuclear envelope. In the genome of eukaryotic cells, domains of active and repressive chromatin alternate along the chromosome arms. Insulator elements are necessary to shield these different environments from each other. In the fission yeast Schizosaccharomyces pombe, the chromatin remodeler Fft3 is required to maintain the repressed subtelomeric chromatin. Here we show that Fft3 maintains nucleosome structure of insulator elements at the subtelomeric borders. We also observe that subtelomeres and insulator elements move away from the nuclear envelope in cells lacking Fft3. The nuclear periphery is known to harbor repressive chromatin in many eukaryotes and has been implied in insulator function. Our results suggest that chromatin remodeling through Fft3 is required to maintain proper chromatin structure and nuclear organization of insulator elements.
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Affiliation(s)
- Babett Steglich
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Annelie Strålfors
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Olga Khorosjutina
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Jenna Persson
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Agata Smialowska
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Jean-Paul Javerzat
- Univ. Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, Bordeaux, France
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, Bordeaux, France
| | - Karl Ekwall
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
- * E-mail:
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17
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Kumar A, Mazzanti M, Mistrik M, Kosar M, Beznoussenko GV, Mironov AA, Garrè M, Parazzoli D, Shivashankar GV, Scita G, Bartek J, Foiani M. ATR mediates a checkpoint at the nuclear envelope in response to mechanical stress. Cell 2015; 158:633-46. [PMID: 25083873 PMCID: PMC4121522 DOI: 10.1016/j.cell.2014.05.046] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 04/14/2014] [Accepted: 05/28/2014] [Indexed: 11/16/2022]
Abstract
ATR controls chromosome integrity and chromatin dynamics. We have previously shown that yeast Mec1/ATR promotes chromatin detachment from the nuclear envelope to counteract aberrant topological transitions during DNA replication. Here, we provide evidence that ATR activity at the nuclear envelope responds to mechanical stress. Human ATR associates with the nuclear envelope during S phase and prophase, and both osmotic stress and mechanical stretching relocalize ATR to nuclear membranes throughout the cell cycle. The ATR-mediated mechanical response occurs within the range of physiological forces, is reversible, and is independent of DNA damage signaling. ATR-defective cells exhibit aberrant chromatin condensation and nuclear envelope breakdown. We propose that mechanical forces derived from chromosome dynamics and torsional stress on nuclear membranes activate ATR to modulate nuclear envelope plasticity and chromatin association to the nuclear envelope, thus enabling cells to cope with the mechanical strain imposed by these molecular processes. ATR localizes at the nuclear envelope in S phase and prophase ATR responds to mechanical stress by relocalizing to the nuclear envelope The ATR mechanical response is fast and reversible ATR coordinates chromatin condensation and nuclear envelope breakdown
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Affiliation(s)
- Amit Kumar
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | | | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 77115 Olomouc, Czech Republic
| | - Martin Kosar
- Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic
| | - Galina V Beznoussenko
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Alexandre A Mironov
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Massimiliano Garrè
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Dario Parazzoli
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Giorgio Scita
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, 20122 Milan, Italy
| | - Jiri Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 77115 Olomouc, Czech Republic; Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic.
| | - Marco Foiani
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, 20122 Milan, Italy.
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18
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Abstract
Telomeres form protective caps at the ends of linear chromosomes to prevent nucleolytic degradation, end-to-end fusion, irregular recombination, and chromosomal instability. Telomeres are composed of repetitive DNA sequences (TTAGGG)n in humans, that are bound by specialized telomere binding proteins. Telomeres lose capping function in response to telomere shortening, which occurs during each division of cells that lack telomerase activity-the enzyme that can synthesize telomeres de novo. Telomeres have a dual role in cancer: telomere shortening can lead to induction of chromosomal instability and to the initiation of tumors, however, initiated tumors need to reactivate telomerase in order to stabilize chromosomes and to gain immortal growth capacity. In this review, we summarize current knowledge on the role of telomeres in the maintenance of chromosomal stability and carcinogenesis.
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Felipe-Abrio I, Lafuente-Barquero J, García-Rubio ML, Aguilera A. RNA polymerase II contributes to preventing transcription-mediated replication fork stalls. EMBO J 2014; 34:236-50. [PMID: 25452497 DOI: 10.15252/embj.201488544] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transcription is a major contributor to genome instability. A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. However, we know little of the possible role, if any, of the RNA polymerase (RNAP) in this process. Here, we analyzed 4 specific yeast RNAPII mutants that show different phenotypes of genetic instability including hyper-recombination, DNA damage sensitivity and/or a strong dependency on double-strand break repair functions for viability. Three specific alleles of the RNAPII core, rpb1-1, rpb1-S751F and rpb9∆, cause a defect in replication fork progression, compensated for by additional origin firing, as the main action responsible for instability. The transcription elongation defects of rpb1-S751F and rpb9∆ plus our observation that rpb1-1 causes RNAPII retention on chromatin suggest that RNAPII could participate in facilitating fork progression upon a transcription-replication encounter. Our results imply that the RNAPII or ancillary factors actively help prevent transcription-associated genome instability.
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Affiliation(s)
- Irene Felipe-Abrio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - Juan Lafuente-Barquero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Seville, Spain
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20
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Abstract
Cell-cycle checkpoints are generally global in nature: one unattached kinetochore prevents the segregation of all chromosomes; stalled replication forks inhibit late origin firing throughout the genome. A potential exception to this rule is the regulation of replication fork progression by the S-phase DNA damage checkpoint. In this case, it is possible that the checkpoint is global, and it slows all replication forks in the genome. However, it is also possible that the checkpoint acts locally at sites of DNA damage, and only slows those forks that encounter DNA damage. Whether the checkpoint regulates forks globally or locally has important mechanistic implications for how replication forks deal with damaged DNA during S-phase.
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Hamperl S, Cimprich KA. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst) 2014; 19:84-94. [PMID: 24746923 PMCID: PMC4051866 DOI: 10.1016/j.dnarep.2014.03.023] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate DNA replication and DNA repair are crucial for the maintenance of genome stability, and it is generally accepted that failure of these processes is a major source of DNA damage in cells. Intriguingly, recent evidence suggests that DNA damage is more likely to occur at genomic loci with high transcriptional activity. Furthermore, loss of certain RNA processing factors in eukaryotic cells is associated with increased formation of co-transcriptional RNA:DNA hybrid structures known as R-loops, resulting in double-strand breaks (DSBs) and DNA damage. However, the molecular mechanisms by which R-loop structures ultimately lead to DNA breaks and genome instability is not well understood. In this review, we summarize the current knowledge about the formation, recognition and processing of RNA:DNA hybrids, and discuss possible mechanisms by which these structures contribute to DNA damage and genome instability in the cell.
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Affiliation(s)
- Stephan Hamperl
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Karlene A Cimprich
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
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22
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Unexpected function of the glucanosyltransferase Gas1 in the DNA damage response linked to histone H3 acetyltransferases in Saccharomyces cerevisiae. Genetics 2014; 196:1029-39. [PMID: 24532730 DOI: 10.1534/genetics.113.158824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromatin organization and structure are crucial for transcriptional regulation, DNA replication, and damage repair. Although initially characterized in remodeling cell wall glucans, the β-1,3-glucanosyltransferase Gas1 was recently discovered to regulate transcriptional silencing in a manner separable from its activity at the cell wall. However, the function of Gas1 in modulating chromatin remains largely unexplored. Our genetic characterization revealed that GAS1 had critical interactions with genes encoding the histone H3 lysine acetyltransferases Gcn5 and Sas3. Specifically, whereas the gas1 gcn5 double mutant was synthetically lethal, deletion of both GAS1 and SAS3 restored silencing in Saccharomyces cerevisiae. The loss of GAS1 also led to broad DNA damage sensitivity with reduced Rad53 phosphorylation and defective cell cycle checkpoint activation following exposure to select genotoxins. Deletion of SAS3 in the gas1 background restored both Rad53 phosphorylation and checkpoint activation following exposure to genotoxins that trigger the DNA replication checkpoint. Our analysis thus uncovers previously unsuspected functions for both Gas1 and Sas3 in DNA damage response and cell cycle regulation.
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23
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Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans. Genome Biol 2014; 15:R21. [PMID: 24490688 PMCID: PMC4053756 DOI: 10.1186/gb-2014-15-2-r21] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 02/03/2014] [Indexed: 01/01/2023] Open
Abstract
Background Laminopathies are diseases characterized by defects in nuclear envelope structure. A well-known example is Emery-Dreifuss muscular dystrophy, which is caused by mutations in the human lamin A/C and emerin genes. While most nuclear envelope proteins are ubiquitously expressed, laminopathies often affect only a subset of tissues. The molecular mechanisms underlying these tissue-specific manifestations remain elusive. We hypothesize that different functional subclasses of genes might be differentially affected by defects in specific nuclear envelope components. Results Here we determine genome-wide DNA association profiles of two nuclear envelope components, lamin/LMN-1 and emerin/EMR-1 in adult Caenorhabditis elegans. Although both proteins bind to transcriptionally inactive regions of the genome, EMR-1 is enriched at genes involved in muscle and neuronal function. Deletion of either EMR-1 or LEM-2, another integral envelope protein, causes local changes in nuclear architecture as evidenced by altered association between DNA and LMN-1. Transcriptome analyses reveal that EMR-1 and LEM-2 are associated with gene repression, particularly of genes implicated in muscle and nervous system function. We demonstrate that emr-1, but not lem-2, mutants are sensitive to the cholinesterase inhibitor aldicarb, indicating altered activity at neuromuscular junctions. Conclusions We identify a class of elements that bind EMR-1 but do not associate with LMN-1, and these are enriched for muscle and neuronal genes. Our data support a redundant function of EMR-1 and LEM-2 in chromatin anchoring to the nuclear envelope and gene repression. We demonstrate a specific role of EMR-1 in neuromuscular junction activity that may contribute to Emery-Dreifuss muscular dystrophy in humans.
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Niepel M, Molloy KR, Williams R, Farr JC, Meinema AC, Vecchietti N, Cristea IM, Chait BT, Rout MP, Strambio-De-Castillia C. The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome. Mol Biol Cell 2013; 24:3920-38. [PMID: 24152732 PMCID: PMC3861087 DOI: 10.1091/mbc.e13-07-0412] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mlp1p and Mlp2p form the basket of the yeast nuclear pore complex (NPC) and contribute to NPC positioning, nuclear stability, and nuclear envelope morphology. The Mlps also embed the NPC within an extended interactome, which includes protein complexes involved in mRNP biogenesis, silencing, spindle organization, and protein degradation. The basket of the nuclear pore complex (NPC) is generally depicted as a discrete structure of eight protein filaments that protrude into the nucleoplasm and converge in a ring distal to the NPC. We show that the yeast proteins Mlp1p and Mlp2p are necessary components of the nuclear basket and that they also embed the NPC within a dynamic protein network, whose extended interactome includes the spindle organizer, silencing factors, the proteasome, and key components of messenger ribonucleoproteins (mRNPs). Ultrastructural observations indicate that the basket reduces chromatin crowding around the central transporter of the NPC and might function as a docking site for mRNP during nuclear export. In addition, we show that the Mlps contribute to NPC positioning, nuclear stability, and nuclear envelope morphology. Our results suggest that the Mlps are multifunctional proteins linking the nuclear transport channel to multiple macromolecular complexes involved in the regulation of gene expression and chromatin maintenance.
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Affiliation(s)
- Mario Niepel
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115 Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, New York, NY 10065 Laboratory of Cellular and Structural Biology, Rockefeller University, New York, NY 10065 Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland Istituto Cantonale di Microbiologia, 6500 Bellinzona, Switzerland Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
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25
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Ferrández-Ayela A, Alonso-Peral MM, Sánchez-García AB, Micol-Ponce R, Pérez-Pérez JM, Micol JL, Ponce MR. Arabidopsis TRANSCURVATA1 encodes NUP58, a component of the nucleopore central channel. PLoS One 2013; 8:e67661. [PMID: 23840761 PMCID: PMC3695937 DOI: 10.1371/journal.pone.0067661] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/20/2013] [Indexed: 01/20/2023] Open
Abstract
The selective trafficking of proteins and RNAs through the nuclear envelope regulates nuclear-cytoplasmic segregation of macromolecules and is mediated by nucleopore complexes (NPCs), which consist of about 400 nucleoporins (Nups) of about 30 types. Extensive studies of nucleoporin function in yeast and vertebrates showed that Nups function in nucleocytoplasmic trafficking and other processes. However, limited studies of plant Nups have identified only a few mutations, which cause pleiotropic phenotypes including reduced growth and early flowering. Here, we describe loss-of-function alleles of Arabidopsis TRANSCURVATA1 (TCU1); these mutations cause increased hypocotyl and petiole length, reticulate and asymmetrically epinastic leaf laminae of reduced size, and early flowering. TCU1 is transcribed in all of the organs and tissues examined, and encodes the putative ortholog of yeast and vertebrate Nup58, a nucleoporin of the Nup62 subcomplex. Nup58 forms the central channel of the NPC and acts directly in translocation of proteins through the nuclear envelope in yeast and vertebrates. Yeast two-hybrid (Y2H) assays identified physical interactions between TCU1/NUP58 and 34 proteins, including nucleoporins, SCF (Skp1/Cul1/F-box) ubiquitin ligase complex components and other nucleoplasm proteins. Genetic interactions were also found between TCU1 and genes encoding nucleoporins, soluble nuclear transport receptors and components of the ubiquitin-proteasome and auxin signaling pathways. These genetic and physical interactions indicate that TCU1/NUP58 is a member of the Nup62 subcomplex of the Arabidopsis NPC. Our findings also suggest regulatory roles for TCU1/NUP58 beyond its function in nucleocytoplasmic trafficking, a hypothesis that is supported by the Y2H and genetic interactions that we observed.
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Affiliation(s)
| | | | | | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Spain
| | | | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, Spain
- * E-mail:
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26
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Cryopreservation Causes Genetic and Epigenetic Changes in Zebrafish Genital Ridges. PLoS One 2013; 8:e67614. [PMID: 23805321 PMCID: PMC3689738 DOI: 10.1371/journal.pone.0067614] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 05/21/2013] [Indexed: 12/17/2022] Open
Abstract
Cryopreservation is an important tool routinely employed in Assisted Reproduction Technologies (ARTs) and germplasm banking. For several years, the assessment of global DNA fragmentation seemed to be enough to ensure the integrity of genetic material. However, cryopreservation can produce molecular alterations in key genes and transcripts undetectable by traditional assays, such modifications could interfere with normal embryo development. We used zebrafish as a model to study the effect of cryopreservation on key transcripts and genes. We employed an optimized cryopreservation protocol for genital ridges (GRs) containing primordial germ cells (PGCs) considered one of the best cell sources for gene banking. Our results indicated that cryopreservation produced a decrease in most of the zebrafish studied transcripts (cxcr4b, pou5f1, vasa and sox2) and upregulation of heat shock proteins (hsp70, hsp90). The observed downregulation could not always be explained by promoter hypermethylation (only the vasa promoter underwent clear hypermethylation). To corroborate this, we used human spermatozoa (transcriptionally inactive cells) obtaining a reduction in some transcripts (eIF2S1, and LHCGR). Our results also demonstrated that this effect was caused by freezing/thawing rather than exposure to cryoprotectants (CPAs). Finally, we employed real-time PCR (qPCR) technology to quantify the number of lesions produced by cryopreservation in the studied zebrafish genes, observing very different vulnerability to damage among them. All these data suggest that molecular alterations caused by cryopreservation should be studied in detail in order to ensure the total safety of the technique.
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27
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Agromayor M, Martin-Serrano J. Knowing when to cut and run: mechanisms that control cytokinetic abscission. Trends Cell Biol 2013; 23:433-41. [PMID: 23706391 DOI: 10.1016/j.tcb.2013.04.006] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/07/2013] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
Abscission, the final step of cytokinesis, mediates the severing of the membrane tether, or midbody, that connects two daughter cells. It is now recognized that abscission is a complex process requiring tight spatiotemporal regulation of its machinery to ensure equal chromosome segregation and cytoplasm content distribution between daughter cells. Failure to coordinate these events results in genetic damage. Here, we review recent evidence suggesting that proper abscission timing is coordinated by cytoskeletal rearrangements and recruitment of regulators of the Endosomal Sorting Complex Required for Transport (ESCRT) machinery such as CEP55 and MIT-domain-containing protein 1 (MITD1) to the abscission site. Additionally, we discuss the surveillance mechanism known as the Aurora B-mediated abscission checkpoint (NoCut), which prevents genetic damage by ensuring proper abscission delay when chromatin is trapped at the midbody.
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Affiliation(s)
- Monica Agromayor
- Department of Infectious Diseases, King's College London School of Medicine, London SE1 9RT, UK
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28
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Culjkovic-Kraljacic B, Borden KLB. Aiding and abetting cancer: mRNA export and the nuclear pore. Trends Cell Biol 2013; 23:328-35. [PMID: 23582887 DOI: 10.1016/j.tcb.2013.03.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 12/21/2022]
Abstract
mRNA export is a critical step in gene expression. Export of transcripts can be modulated in response to cellular signaling or stress. Consistently, mRNA export is dysregulated in primary human specimens derived from many different forms of cancer. Aberrant expression of export factors can alter the export of specific transcripts encoding proteins involved in proliferation, survival, and oncogenesis. These specific factors, which are not used for bulk mRNA export, are obvious therapeutic targets. Indeed, given the emerging role of mRNA export in cancer, it is not surprising that efforts to target different aspects of this pathway have reached the clinical trial stage. Thus, like transcription and translation, mRNA export may also play a critical role in cancer genesis and maintenance.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer (IRIC), Department of Pathology and Cell Biology, Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montréal, Québec H3T 1J4, Canada
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29
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Jossen R, Bermejo R. The DNA damage checkpoint response to replication stress: A Game of Forks. Front Genet 2013; 4:26. [PMID: 23493417 PMCID: PMC3595514 DOI: 10.3389/fgene.2013.00026] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/18/2013] [Indexed: 12/23/2022] Open
Abstract
Conditions challenging replication fork progression, collectively referred to as replication stress, represent a major source of genomic instability and are associated to cancer onset. The replication checkpoint, a specialized branch of the DNA damage checkpoint, monitors fork problems, and triggers a cellular response aimed at preserving genome integrity. Here, we review the mechanisms by which the replication checkpoint monitors and responds to replication stress, focusing on the checkpoint-mediated pathways contributing to protect replication fork integrity. We discuss how cells achieve checkpoint signaling inactivation once replication stress is overcome and how a failure to timely revert checkpoint-mediated changes in cellular physiology might impact on replication dynamics and genome integrity. We also highlight the checkpoint function as an anti-cancer barrier preventing cells malignant transformation following oncogene-induced replication stress.
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Affiliation(s)
- Rachel Jossen
- Instituto de Biología Funcional y Genómica, CSIC/USAL Salamanca, Spain
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30
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Abstract
The nuclear envelope forms a cocoon that surrounds the cellular genome keeping it out of harm’s way and can be utilized by the cell as a means of functionally regulating chromatin structure and gene expression. At the same time, this double-layered membrane system constitutes a formidable obstacle to the unimpeded flow of genetic information between the genome and the rest of the cell. The nuclear pore has been long considered the sole passageway between nucleus and cytoplasm. A new report1 challenges this view and proposes a novel mechanism by which RNA transcripts destined for localized translation in highly polarized cell types, cross both inner and outer nuclear envelope membranes and reach the cytoplasm without utilizing the nuclear pore route.
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