1
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Osterli E, Ellenbecker M, Wang X, Terzo M, Jacobson K, Cuello D, Voronina E. COP9 signalosome component CSN-5 stabilizes PUF proteins FBF-1 and FBF-2 in Caenorhabditis elegans germline stem and progenitor cells. Genetics 2024; 227:iyae033. [PMID: 38427913 PMCID: PMC11075551 DOI: 10.1093/genetics/iyae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 03/03/2024] Open
Abstract
RNA-binding proteins FBF-1 and FBF-2 (FBFs) are required for germline stem cell maintenance and the sperm/oocyte switch in Caenorhabditis elegans, although the mechanisms controlling FBF protein levels remain unknown. We identified an interaction between both FBFs and CSN-5), a component of the constitutive photomorphogenesis 9 (COP9) signalosome best known for its role in regulating protein degradation. Here, we find that the Mpr1/Pad1 N-terminal metalloprotease domain of CSN-5 interacts with the Pumilio and FBF RNA-binding domain of FBFs and the interaction is conserved for human homologs CSN5 and PUM1. The interaction between FBF-2 and CSN-5 can be detected in vivo by proximity ligation. csn-5 mutation results in the destabilization of FBF proteins, which may explain previously observed decrease in the numbers of germline stem and progenitor cells, and disruption of oogenesis. The loss of csn-5 does not decrease the levels of a related PUF protein PUF-3, and csn-5(lf) phenotype is not enhanced by fbf-1/2 knockdown, suggesting that the effect is specific to FBFs. The effect of csn-5 on oogenesis is largely independent of the COP9 signalosome and is cell autonomous. Surprisingly, the regulation of FBF protein levels involves a combination of COP9-dependent and COP9-independent mechanisms differentially affecting FBF-1 and FBF-2. This work supports a previously unappreciated role for CSN-5 in the stabilization of germline stem cell regulatory proteins FBF-1 and FBF-2.
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Affiliation(s)
- Emily Osterli
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Mary Ellenbecker
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Mikaya Terzo
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Ketch Jacobson
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - DeAnna Cuello
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
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2
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Demchenko A, Belova L, Balyasin M, Kochergin-Nikitsky K, Kondrateva E, Voronina E, Pozhitnova V, Tabakov V, Salikhova D, Bukharova T, Goldshtein D, Kondratyeva E, Kyian T, Amelina E, Zubkova O, Popova O, Ozharovskaia T, Lavrov A, Smirnikhina S. Airway basal cells from human-induced pluripotent stem cells: a new frontier in cystic fibrosis research. Front Cell Dev Biol 2024; 12:1336392. [PMID: 38737127 PMCID: PMC11082282 DOI: 10.3389/fcell.2024.1336392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/08/2024] [Indexed: 05/14/2024] Open
Abstract
Human-induced airway basal cells (hiBCs) derived from human-induced pluripotent stem cells (hiPSCs) offer a promising cell model for studying lung diseases, regenerative medicine, and developing new gene therapy methods. We analyzed existing differentiation protocols and proposed our own protocol for obtaining hiBCs, which involves step-by-step differentiation of hiPSCs into definitive endoderm, anterior foregut endoderm, NKX2.1+ lung progenitors, and cultivation on basal cell medium with subsequent cell sorting using the surface marker CD271 (NGFR). We derived hiBCs from two healthy cell lines and three cell lines with cystic fibrosis (CF). The obtained hiBCs, expressing basal cell markers (NGFR, KRT5, and TP63), could differentiate into lung organoids (LOs). We demonstrated that LOs derived from hiBCs can assess cystic fibrosis transmembrane conductance regulator (CFTR) channel function using the forskolin-induced swelling (FIS) assay. We also carried out non-viral (electroporation) and viral (recombinant adeno-associated virus (rAAV)) serotypes 6 and 9 and recombinant adenovirus (rAdV) serotype 5 transgene delivery to hiBCs and showed that rAAV serotype 6 is most effective against hiBCs, potentially applicable for gene therapy research.
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Affiliation(s)
- Anna Demchenko
- Laboratory of Genome Editing, Research Centre for Medical Genetics, Moscow, Russia
| | - Lyubava Belova
- Laboratory of Genome Editing, Research Centre for Medical Genetics, Moscow, Russia
| | - Maxim Balyasin
- Scientific and Educational Resource Center, Peoples’ Friendship University of Russia, Moscow, Russia
- Department of Cell Technology, Endocrinology Research Center, Moscow, Russia
| | | | - Ekaterina Kondrateva
- Laboratory of Genome Editing, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina Voronina
- Laboratory of Mutagenesis, Research Centre for Medical Genetics, Moscow, Russia
| | - Victoria Pozhitnova
- Laboratory of Mutagenesis, Research Centre for Medical Genetics, Moscow, Russia
| | - Vyacheslav Tabakov
- Moscow Branch of the Biobank “All-Russian Collection of Biological Samples of Hereditary Diseases”, Research Centre for Medical Genetics, Moscow, Russia
| | - Diana Salikhova
- Stem Cell Genetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Tatiana Bukharova
- Stem Cell Genetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Dmitry Goldshtein
- Stem Cell Genetics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - Elena Kondratyeva
- Scientific and Clinical Department of Cystic Fibrosis, Research Centre for Medical Genetics, Moscow, Russia
| | - Tatiana Kyian
- Scientific and Clinical Department of Cystic Fibrosis, Research Centre for Medical Genetics, Moscow, Russia
| | - Elena Amelina
- Laboratory of Cystic Fibrosis, Research Institute of Pulmonology, Moscow, Russia
| | - Olga Zubkova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named After Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Olga Popova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named After Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Tatiana Ozharovskaia
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named After Honorary Academician N F Gamaleya” of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander Lavrov
- Laboratory of Genome Editing, Research Centre for Medical Genetics, Moscow, Russia
| | - Svetlana Smirnikhina
- Laboratory of Genome Editing, Research Centre for Medical Genetics, Moscow, Russia
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3
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Kurnikov IV, Pereyaslavets L, Kamath G, Sakipov SN, Voronina E, Butin O, Illarionov A, Leontyev I, Nawrocki G, Darkhovskiy M, Olevanov M, Ivahnenko I, Chen Y, Lock CB, Levitt M, Kornberg RD, Fain B. Neural Network Corrections to Intermolecular Interaction Terms of a Molecular Force Field Capture Nuclear Quantum Effects in Calculations of Liquid Thermodynamic Properties. J Chem Theory Comput 2024; 20:1347-1357. [PMID: 38240485 PMCID: PMC11042917 DOI: 10.1021/acs.jctc.3c00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We incorporate nuclear quantum effects (NQE) in condensed matter simulations by introducing short-range neural network (NN) corrections to the ab initio fitted molecular force field ARROW. Force field NN corrections are fitted to average interaction energies and forces of molecular dimers, which are simulated using the Path Integral Molecular Dynamics (PIMD) technique with restrained centroid positions. The NN-corrected force field allows reproduction of the NQE for computed liquid water and methane properties such as density, radial distribution function (RDF), heat of evaporation (HVAP), and solvation free energy. Accounting for NQE through molecular force field corrections circumvents the need for explicit computationally expensive PIMD simulations in accurate calculations of the properties of chemical and biological systems. The accuracy and locality of pairwise NN NQE corrections indicate that this approach could be applicable to complex heterogeneous systems, such as proteins.
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Affiliation(s)
- Igor V Kurnikov
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Leonid Pereyaslavets
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ganesh Kamath
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Serzhan N Sakipov
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ekaterina Voronina
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Oleg Butin
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Alexey Illarionov
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor Leontyev
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Grzegorz Nawrocki
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Mikhail Darkhovskiy
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Michael Olevanov
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ilya Ivahnenko
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - YuChun Chen
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Christopher B Lock
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Boris Fain
- InterX Inc., (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
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4
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Kamath G, Illarionov A, Sakipov S, Pereyaslavets L, Kurnikov IV, Butin O, Voronina E, Ivahnenko I, Leontyev I, Nawrocki G, Darkhovskiy M, Olevanov M, Cherniavskyi YK, Lock C, Greenslade S, Chen Y, Kornberg RD, Levitt M, Fain B. Combining Force Fields and Neural Networks for an Accurate Representation of Bonded Interactions. J Phys Chem A 2024; 128:807-812. [PMID: 38232765 PMCID: PMC11008955 DOI: 10.1021/acs.jpca.3c07598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
We present a formalism of a neural network encoding bonded interactions in molecules. This intramolecular encoding is consistent with the models of intermolecular interactions previously designed by this group. Variants of the encoding fed into a corresponding neural network may be used to economically improve the representation of torsional degrees of freedom in any force field. We test the accuracy of the reproduction of the ab initio potential energy surface on a set of conformations of two dipeptides, methyl-capped ALA and ASP, in several scenarios. The encoding, either alone or in conjunction with an analytical potential, improves agreement with ab initio energies that are on par with those of other neural network-based potentials. Using the encoding and neural nets in tandem with an analytical model places the agreements firmly within "chemical accuracy" of ±0.5 kcal/mol.
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Affiliation(s)
- Ganesh Kamath
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Alexey Illarionov
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Serzhan Sakipov
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Leonid Pereyaslavets
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor V Kurnikov
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Oleg Butin
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Ekaterina Voronina
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
- Lomonosov MSU, Skobeltsyn Institute of Nuclear Physics, Moscow 119991, Russia
| | - Ilya Ivahnenko
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor Leontyev
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Grzegorz Nawrocki
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Mikhail Darkhovskiy
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Michael Olevanov
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
- Department of Physics, Lomonosov MSU, Moscow 119991, Russia
| | - Yevhen K Cherniavskyi
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Christopher Lock
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Sean Greenslade
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - YuChun Chen
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Boris Fain
- InterX Inc. (a subsidiary of NeoTX Therapeutics LTD), 805 Allston Way, Berkeley, California 94710, United States
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5
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Kondrateva E, Grigorieva O, Panchuk I, Bychkov I, Zakharova E, Tabakov V, Pozhitnova V, Voronina E, Shchagina O, Lavrov A, Smirnikhina S, Kutsev S. Generation of induced pluripotent stem cell line (RCMGi012-A) from fibroblasts of patient with mucopolysaccharidosis type VI. Stem Cell Res 2023; 73:103259. [PMID: 38006675 DOI: 10.1016/j.scr.2023.103259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023] Open
Abstract
Skin fibroblasts obtained from a 5-year-old girl with genetically proven (two heterozygous mutations in ARSB gene) and clinically manifested mucopolysaccharidosis type VI were successfully transformed into induced pluripotent stem cells by using Sendai virus-based reprogramming vectors including the four Yamanaka factors namely SOX2, OCT3/4, KLF4, and c-MYC. These iPSCs expressed pluripotency markers, had a normal karyotype and the potential to differentiate into three germ layers in spontaneous differentiation assay. The line may be used for cell differentiation and pharmacological investigations, and also may provide a model for development of a personalized treatment including drug screening and genome editing.
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Affiliation(s)
| | - Olga Grigorieva
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Irina Panchuk
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Igor Bychkov
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | | | | | | | | | - Olga Shchagina
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Alexander Lavrov
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | | | - Sergey Kutsev
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
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6
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Illarionov A, Sakipov S, Pereyaslavets L, Kurnikov IV, Kamath G, Butin O, Voronina E, Ivahnenko I, Leontyev I, Nawrocki G, Darkhovskiy M, Olevanov M, Cherniavskyi YK, Lock C, Greenslade S, Sankaranarayanan SKRS, Kurnikova MG, Potoff J, Kornberg RD, Levitt M, Fain B. Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions. J Am Chem Soc 2023; 145:23620-23629. [PMID: 37856313 PMCID: PMC10623557 DOI: 10.1021/jacs.3c07628] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Indexed: 10/21/2023]
Abstract
A key goal of molecular modeling is the accurate reproduction of the true quantum mechanical potential energy of arbitrary molecular ensembles with a tractable classical approximation. The challenges are that analytical expressions found in general purpose force fields struggle to faithfully represent the intermolecular quantum potential energy surface at close distances and in strong interaction regimes; that the more accurate neural network approximations do not capture crucial physics concepts, e.g., nonadditive inductive contributions and application of electric fields; and that the ultra-accurate narrowly targeted models have difficulty generalizing to the entire chemical space. We therefore designed a hybrid wide-coverage intermolecular interaction model consisting of an analytically polarizable force field combined with a short-range neural network correction for the total intermolecular interaction energy. Here, we describe the methodology and apply the model to accurately determine the properties of water, the free energy of solvation of neutral and charged molecules, and the binding free energy of ligands to proteins. The correction is subtyped for distinct chemical species to match the underlying force field, to segment and reduce the amount of quantum training data, and to increase accuracy and computational speed. For the systems considered, the hybrid ab initio parametrized Hamiltonian reproduces the two-body dimer quantum mechanics (QM) energies to within 0.03 kcal/mol and the nonadditive many-molecule contributions to within 2%. Simulations of molecular systems using this interaction model run at speeds of several nanoseconds per day.
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Affiliation(s)
- Alexey Illarionov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Serzhan Sakipov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Leonid Pereyaslavets
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor V. Kurnikov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ganesh Kamath
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Oleg Butin
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Ekaterina Voronina
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Lomonosov
MSU, Skobeltsyn Institute of Nuclear Physics, Moscow, 119991, Russia
| | - Ilya Ivahnenko
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Igor Leontyev
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Grzegorz Nawrocki
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Mikhail Darkhovskiy
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Michael Olevanov
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Lomonosov
MSU, Dept. of Physics, Moscow, 119991, Russia
| | - Yevhen K. Cherniavskyi
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Christopher Lock
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
- Department
of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Sean Greenslade
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
| | - Subramanian KRS Sankaranarayanan
- Center
for Nanoscale Materials, Argonne National
Lab, Argonne, Illinois 604391, United States
- Department
of Mechanical and Industrial Engineering, University of Illinois, Chicago, Illinois 60607, United States
| | - Maria G. Kurnikova
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jeffrey Potoff
- Department
of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, United States
| | - Roger D. Kornberg
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94304, United States
| | - Michael Levitt
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94304, United States
| | - Boris Fain
- InterX
Inc. (a Subsidiary of NeoTX Therapeutics Ltd.), 805 Allston Way, Berkeley, California 94710, United States
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7
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Kondrateva E, Grigorieva O, Kurshakova E, Panchuk I, Pozhitnova V, Voronina E, Tabakov V, Orlova M, Lavrov A, Smirnikhina S, Kutsev S. Generation of induced pluripotent stem cell line (RCMGi009-A) from urine cells of patient with fibrodysplasia ossificans progressiva. Stem Cell Res 2023; 70:103133. [PMID: 37307755 DOI: 10.1016/j.scr.2023.103133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/23/2023] [Accepted: 06/02/2023] [Indexed: 06/14/2023] Open
Abstract
Urine cells obtained from a 14-year-old man with genetically proven (ACVR1: c.6176G > A) and clinically manifested fibrodysplasia ossificans progressiva were successfully transformed into induced pluripotent stem cells by using Sendai virus-based reprogramming vectors including the four Yamanaka factors such as OCT3/4, SOX2, KLF4, and c-MYC. These iPSCs expressed pluripotency markers, exhibited the potential to differentiate into three germ layers in spontaneous differentiation assay and had a normal karyotype. The iPSC line may provide a model for development of a personalized treatment including genome editing and drug screening, may be used for disease modelling, cell differentiation and pharmacological investigations. .
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Affiliation(s)
| | - Olga Grigorieva
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | | | - Irina Panchuk
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | | | | | | | - Maria Orlova
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Alexander Lavrov
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | | | - Sergey Kutsev
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
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8
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Schwartzkopf CM, Robinson AJ, Ellenbecker M, Faith DR, Schmidt AK, Brooks DM, Lewerke L, Voronina E, Dandekar AA, Secor PR. Tripartite interactions between filamentous Pf4 bacteriophage, Pseudomonas aeruginosa, and bacterivorous nematodes. PLoS Pathog 2023; 19:e1010925. [PMID: 36800381 PMCID: PMC9980816 DOI: 10.1371/journal.ppat.1010925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/02/2023] [Accepted: 02/08/2023] [Indexed: 02/18/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa PAO1 is infected by the filamentous bacteriophage Pf4. Pf4 virions promote biofilm formation, protect bacteria from antibiotics, and modulate animal immune responses in ways that promote infection. Furthermore, strains cured of their Pf4 infection (ΔPf4) are less virulent in animal models of infection. Consistently, we find that strain ΔPf4 is less virulent in a Caenorhabditis elegans nematode infection model. However, our data indicate that PQS quorum sensing is activated and production of the pigment pyocyanin, a potent virulence factor, is enhanced in strain ΔPf4. The reduced virulence of ΔPf4 despite high levels of pyocyanin production may be explained by our finding that C. elegans mutants unable to sense bacterial pigments through the aryl hydrocarbon receptor are more susceptible to ΔPf4 infection compared to wild-type C. elegans. Collectively, our data support a model where suppression of quorum-regulated virulence factors by Pf4 allows P. aeruginosa to evade detection by innate host immune responses.
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Affiliation(s)
- Caleb M. Schwartzkopf
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Autumn J. Robinson
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Mary Ellenbecker
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Dominick R. Faith
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Amelia K. Schmidt
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Diane M. Brooks
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Lincoln Lewerke
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Ajai A. Dandekar
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Patrick R. Secor
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- * E-mail:
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9
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Ellenbecker M, Voronina E. Disruption of C. elegans embryonic P granules upon dlc-1(RNAi) is not associated with P granule component loss. MicroPubl Biol 2022; 2022:10.17912/micropub.biology.000700. [PMID: 36568482 PMCID: PMC9772925 DOI: 10.17912/micropub.biology.000700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/21/2022] [Accepted: 12/03/2022] [Indexed: 12/27/2022]
Abstract
Dynein light chain (DLC-1) is a light chain component of the dynein motor complex, it functions as an allosteric regulator of multi-subunit protein complexes and promotes P granule integrity in the C. elegans embryo. P granules are RNA-protein complexes located in the C. elegans germline that are important for RNA regulation and fertility. To further study the role of DLC-1 during C. elegans embryogenesis we performed quantitative tandem mass tag mass spectrometry on embryos after dlc-1 knock down. The amount of core P granule components and nucleoporin proteins did not change after dlc-1(RNAi). These results show that DLC-1 does not help regulate P granule protein levels and support the model that DLC-1 facilitates phase separation of P granule components in vivo .
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10
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Nawrocki G, Leontyev I, Sakipov S, Darkhovskiy M, Kurnikov I, Pereyaslavets L, Kamath G, Voronina E, Butin O, Illarionov A, Olevanov M, Kostikov A, Ivahnenko I, Patel DS, Sankaranarayanan SKRS, Kurnikova MG, Lock C, Crooks GE, Levitt M, Kornberg RD, Fain B. Protein-Ligand Binding Free-Energy Calculations with ARROW─A Purely First-Principles Parameterized Polarizable Force Field. J Chem Theory Comput 2022; 18:7751-7763. [PMID: 36459593 PMCID: PMC9753910 DOI: 10.1021/acs.jctc.2c00930] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Indexed: 12/03/2022]
Abstract
Protein-ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we present results obtained with the ARROW force field (FF)─a multipolar polarizable and physics-based model with all parameters fitted entirely to high-level ab initio quantum mechanical (QM) calculations. ARROW has already proven its ability to determine solvation free energy of arbitrary neutral compounds with unprecedented accuracy. The ARROW FF parameterization is now extended to include coverage of all amino acids including charged groups, allowing molecular simulations of a series of protein-ligand systems and prediction of their relative binding free energies. We ensure adequate sampling by applying a novel technique that is based on coupling the Hamiltonian Replica exchange (HREX) with a conformation reservoir generated via potential softening and nonequilibrium MD. ARROW provides predictions with near chemical accuracy (mean absolute error of ∼0.5 kcal/mol) for two of the three protein systems studied here (MCL1 and Thrombin). The third protein system (CDK2) reveals the difficulty in accurately describing dimer interaction energies involving polar and charged species. Overall, for all of the three protein systems studied here, ARROW FF predicts relative binding free energies of ligands with a similar accuracy level as leading nonpolarizable force fields.
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Affiliation(s)
- Grzegorz Nawrocki
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Igor Leontyev
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Serzhan Sakipov
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | | | - Igor Kurnikov
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | | | - Ganesh Kamath
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Ekaterina Voronina
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
- Faculty
of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Oleg Butin
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Alexey Illarionov
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Michael Olevanov
- Faculty
of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
| | | | - Ilya Ivahnenko
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Dhilon S. Patel
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Subramanian K. R. S. Sankaranarayanan
- Center
for Nanoscale Materials, Argonne National
Lab, Lemont, Illinois 60439, United States
- Department
of Mechanical and Industrial Engineering, University of Illinois, Chicago, Illinois 60607, United States
| | - Maria G. Kurnikova
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Christopher Lock
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
- Department
of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, California 94304, United States
| | - Gavin E. Crooks
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
| | - Michael Levitt
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Roger D. Kornberg
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Boris Fain
- InterX
Inc., 805 Allston Way, Berkeley California, 94710, United States
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11
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Panchuk I, Kondrateva E, Demchenko A, Grigorieva O, Erofeeva A, Amelina E, Tabakov V, Orlova M, Voronina E, Pozhitnova V, Lavrov A, Smirnikhina S, Kutsev S. Generation of two induced pluripotent stem cell lines (RCMGi005-A/B) from human skin fibroblasts of a cystic fibrosis patient with homozygous F508del mutation in CFTR gene. Stem Cell Res 2022; 64:102896. [DOI: 10.1016/j.scr.2022.102896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/25/2022] Open
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12
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Day NJ, Ellenbecker M, Wang X, Voronina E. DLC-1 facilitates germ granule assembly in C. elegans embryo. Mol Biol Cell 2022; 33:ar41. [PMID: 35274966 PMCID: PMC9282019 DOI: 10.1091/mbc.e21-05-0275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Germ granules are cytoplasmic assemblies of RNA-binding proteins (RBPs) required for germ cell development and fertility. During the first four cell divisions of the Caenorhabditis elegans zygote, regulated assembly of germ (P) granules leads to their selective segregation to the future germ cell. Here we investigate the role of DLC-1, a hub protein implicated in stabilization and function of diverse protein complexes, in maintaining P granule integrity. We find that DLC-1 directly interacts with several core P granule proteins, predominantly during embryogenesis. The loss of dlc-1 disrupts assembly of P granule components into phase-separated organelles in the embryos, regardless of whether or not DLC-1 directly interacts with these proteins. Finally, we infer that P granule dispersal in the absence of dlc-1 is likely independent of DLC-1’s function as a subunit of the dynein motor and does not result from a loss of cell polarity.
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Affiliation(s)
- Nicholas J Day
- Division of Biological Sciences, University of Montana, Missoula, MT 59812
| | - Mary Ellenbecker
- Division of Biological Sciences, University of Montana, Missoula, MT 59812
| | - Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, MT 59812
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT 59812
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13
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Pereyaslavets L, Kamath G, Butin O, Illarionov A, Olevanov M, Kurnikov I, Sakipov S, Leontyev I, Voronina E, Gannon T, Nawrocki G, Darkhovskiy M, Ivahnenko I, Kostikov A, Scaranto J, Kurnikova MG, Banik S, Chan H, Sternberg MG, Sankaranarayanan SKRS, Crawford B, Potoff J, Levitt M, Kornberg RD, Fain B. Accurate determination of solvation free energies of neutral organic compounds from first principles. Nat Commun 2022; 13:414. [PMID: 35058472 PMCID: PMC8776904 DOI: 10.1038/s41467-022-28041-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 01/03/2022] [Indexed: 12/28/2022] Open
Abstract
The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools' computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.
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Affiliation(s)
| | - Ganesh Kamath
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | - Oleg Butin
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | | | - Michael Olevanov
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
- Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Igor Kurnikov
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | | | - Igor Leontyev
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | - Ekaterina Voronina
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
- Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tyler Gannon
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA
| | | | | | | | | | - Jessica Scaranto
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Maria G Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Suvo Banik
- Center for Nanoscale Materials, Argonne National Lab, Argonne, IL, 60439, USA
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, 60607, USA
| | - Henry Chan
- Center for Nanoscale Materials, Argonne National Lab, Argonne, IL, 60439, USA
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, 60607, USA
| | - Michael G Sternberg
- Center for Nanoscale Materials, Argonne National Lab, Argonne, IL, 60439, USA
| | - Subramanian K R S Sankaranarayanan
- Center for Nanoscale Materials, Argonne National Lab, Argonne, IL, 60439, USA
- Department of Mechanical and Industrial Engineering, University of Illinois, Chicago, IL, 60607, USA
| | - Brad Crawford
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI, 48202, USA
| | - Jeffrey Potoff
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI, 48202, USA
| | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Boris Fain
- InterX Inc, 805 Allston Way, Berkeley, CA, 94710, USA.
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14
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Iakunchykova O, Schirmer H, Leong D, Malyutina S, Ryabikov A, Averina M, Kudryavtsev A, Kornev M, Voronina E, Paramonov A, Wilsgaard T, Leon D. Heavy alcohol drinking and subclinical echocardiographic abnormalities of structure and function. Open Heart 2021; 8:openhrt-2020-001457. [PMID: 34083387 PMCID: PMC8174503 DOI: 10.1136/openhrt-2020-001457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/14/2021] [Indexed: 11/12/2022] Open
Abstract
Objective The aim of the study is to assess changes in heart structure and function associated with heavy alcohol use by comparing echocardiographic indices in a population-based sample to those in patients admitted to an inpatient facility with severe alcohol problems. Methods and results We used data from the Know Your Heart study (2015–2017) which is a cross-sectional study that recruited 2479 participants aged 35–69 years from the general population of the city of Arkhangelsk in Northwest Russia and 278 patients from the Arkhangelsk Regional Psychiatric Hospital with a primary diagnosis related to chronic alcohol use (narcology clinic subsample). The drinking patterns of the population-based sample were characterised in detail. We used regression models controlling for age, sex, smoking, education and waist to hip ratio to evaluate the differences in echocardiographic indices in participants with different drinking patterns. The means of left ventricular end-diastolic diameter and indexed left atrial systolic diameter were increased among heavy drinkers (narcology clinic subsample), while mean left ventricular ejection fraction was decreased in this group compared with the population-based sample. In contrast, the harmful and hazardous drinkers in the population-based sample did not differ from non-problem drinkers with respect to echocardiographic indices of systolic and diastolic function. Conclusions Extremely heavy drinking is associated with a specific set of structural and functional abnormalities of the heart that may be regarded as precursors of alcohol-related dilated cardiomyopathy.
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Affiliation(s)
- Olena Iakunchykova
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Henrik Schirmer
- Department of Cardiology, Akershus University Hospital, Lorenskog, Norway.,Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway.,Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Darryl Leong
- Population Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Sofia Malyutina
- Branch of Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Research Institute of Internal and Preventive Medicine, Novosibirsk, Russian Federation.,Novosibirsk State Medical University, Novosibirsk, Russian Federation
| | - Andrew Ryabikov
- Branch of Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Research Institute of Internal and Preventive Medicine, Novosibirsk, Russian Federation.,Novosibirsk State Medical University, Novosibirsk, Russian Federation
| | - Maria Averina
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Laboratory Medicine, University Hospital of North Norway, Tromsø, Norway
| | - Alexander Kudryavtsev
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Innovative Programs, Northern State Medical University, Arkhangelsk, Russia
| | - Mikhail Kornev
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ekaterina Voronina
- Branch of Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Research Institute of Internal and Preventive Medicine, Novosibirsk, Russian Federation
| | - Andrey Paramonov
- Central Scientific Research Laboratory, Northern State Medical University, Arkhangelsk, Russian Federation
| | - Tom Wilsgaard
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - David Leon
- Department of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Non-Communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.,International Laboratory For Population and Health, National Research University Higher School of Economics, Moscow, Russia
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15
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Kondrateva E, Demchenko A, Slesarenko Y, Yasinovsky M, Amelina E, Tabakov V, Voronina E, Lavrov A, Smirnikhina S. Derivation of iPSC line (RCMGi002-A) from dermal fibroblasts of a cystic fibrosis female patient with homozygous F508del mutation. Stem Cell Res 2021; 53:102251. [PMID: 33684631 DOI: 10.1016/j.scr.2021.102251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/13/2021] [Accepted: 02/11/2021] [Indexed: 11/25/2022] Open
Abstract
Cystic fibrosis is one of the most common inherited diseases caused by mutations in CFTR gene, of which F508del is the most frequent. Currently, the possibility of cell therapy including genome editing is widely discussed. We generated induced pluripotent stem cells from fibroblasts obtained from a 22-year-old woman with clinically manifested and genetically proven disease by using non-viral, non-integrating RNA reprogramming vector that contains five reprogramming factors: OCT4, KLF4, SOX2, GLIS1, and c-MYC. The established cell line can express endogenous pluripotency markers, possesses a normal karyotype, and has the ability to differentiate into three germ layers in spontaneous differentiation assay.
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Affiliation(s)
| | - Anna Demchenko
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Yana Slesarenko
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Matvey Yasinovsky
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Elena Amelina
- The Research Institute of Pulmonology, Moscow 115682, Russian Federation
| | | | | | - Alexander Lavrov
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
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16
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Andropova U, Serenko O, Tebeneva N, Tarasenkov A, Askadskii A, Afanasyev E, Novikov L, Chernik V, Voronina E, Muzafarov A. New oligomeric metallosiloxane - polyimide nanocomposites for anti-atomic-oxygen erosion. Polym Degrad Stab 2021. [DOI: 10.1016/j.polymdegradstab.2020.109424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Wang X, Ellenbecker M, Hickey B, Day NJ, Osterli E, Terzo M, Voronina E. Antagonistic control of Caenorhabditis elegans germline stem cell proliferation and differentiation by PUF proteins FBF-1 and FBF-2. eLife 2020; 9:52788. [PMID: 32804074 PMCID: PMC7467723 DOI: 10.7554/elife.52788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
Stem cells support tissue maintenance, but the mechanisms that coordinate the rate of stem cell self-renewal with differentiation at a population level remain uncharacterized. We find that two PUF family RNA-binding proteins FBF-1 and FBF-2 have opposite effects on Caenorhabditis elegans germline stem cell dynamics: FBF-1 restricts the rate of meiotic entry, while FBF-2 promotes both cell division and meiotic entry rates. Antagonistic effects of FBFs are mediated by their distinct activities toward the shared set of target mRNAs, where FBF-1-mediated post-transcriptional control requires the activity of CCR4-NOT deadenylase, while FBF-2 is deadenylase-independent and might protect the targets from deadenylation. These regulatory differences depend on protein sequences outside of the conserved PUF family RNA-binding domain. We propose that the opposing FBF-1 and FBF-2 activities serve to modulate stem cell division rate simultaneously with the rate of meiotic entry.
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Affiliation(s)
- Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Mary Ellenbecker
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Benjamin Hickey
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Nicholas J Day
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Emily Osterli
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Mikaya Terzo
- Division of Biological Sciences, University of Montana, Missoula, United States
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, United States
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18
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Kondrateva E, Adilgereeva E, Amelina E, Tabakov V, Demchenko A, Ustinov K, Yasinovsky M, Voronina E, Lavrov A, Smirnikhina S. Generation of induced pluripotent stem cell line (RCMGi001-A) from human skin fibroblasts of a cystic fibrosis patient with p.F508del mutation. Stem Cell Res 2020; 48:101933. [PMID: 32777768 DOI: 10.1016/j.scr.2020.101933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 01/08/2023] Open
Abstract
Skin fibroblasts obtained from a 27-year-old man with clinically manifested and genetically proven (F508del/F508del) cystic fibrosis were successfully transformed into induced pluripotent stem cells (iPSCs) by using Sendai virus-based reprogramming vectors including the four Yamanaka factors, OCT3/4, SOX2, KLF4, and c-MYC. The iPSCs showed a normal karyotype, expressed pluripotency markers and exhibited the potential to differentiate into three germ layers in spontaneous differentiation assay. This iPSC line may be subsequently used for development of a personalized etiotropic treatment including genome editing, and for disease modelling and drug screening.
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Affiliation(s)
| | | | - Elena Amelina
- The Research Institute of Pulmonology, Moscow 115682, Russian Federation
| | | | - Anna Demchenko
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Kirill Ustinov
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | - Matvey Yasinovsky
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
| | | | - Alexander Lavrov
- Research Centre for Medical Genetics, Moscow 115522, Russian Federation
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19
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Serenko O, Andropova U, Tebeneva N, Buzin M, Afanasyev E, Tarasenkov A, Bukalov S, Leites L, Aysin R, Novikov L, Chernik V, Voronina E, Muzafarov A. Influence of the Composition of the Hybrid Filler on the Atomic Oxygen Erosion Resistance of Polyimide Nanocomposites. Materials (Basel) 2020; 13:E3204. [PMID: 32708441 PMCID: PMC7411669 DOI: 10.3390/ma13143204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
Abstract
The structure and properties of nanocomposites based on organosoluble polyimide (PI) and branched functional metallosiloxane oligomers with different types of central metal atoms (Al, Cr, Fe, Zr, Hf and Nb) were investigated. Under the same weight content of the filler, the geometric parameters of the nanoparticles and thermal properties of the nanocomposites did not exhibit a direct relationship with the ability of the materials to withstand the incident flow of oxygen plasma. The atomic oxygenerosion resistance of the filled PI films was influenced by the composition of the hybrid fillerand the type of metal atom in the hybrid filler in the base metallosiloxane oligomer. To determine the effectiveness of the nanoparticles as protective elements of the polymer surface, the nanocomposite erosion yields pertaining to the concentration of the crosslinked organo-inorganic polymer forming the dispersed phase were determined and expressed in mmol per gram PI. The filler concentration in the polymer, expressed in these units, allows for comparison of the efficiency of different nanosize fillers for use in fabricating space survivable coatings. This can be important in the pursuit of new precursors, fillers for fabricating space survivable polymer composites.
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Affiliation(s)
- Olga Serenko
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 28 Vavilova St., GSP-1, V-334, 119991 Moscow, Russia; (U.A.); (M.B.); (E.A.); (S.B.); (L.L.); (R.A.); (A.M.)
| | - Ulyana Andropova
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 28 Vavilova St., GSP-1, V-334, 119991 Moscow, Russia; (U.A.); (M.B.); (E.A.); (S.B.); (L.L.); (R.A.); (A.M.)
- N.S. Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, 70 Profsoyuznaya St., 117393 Moscow, Russia; (N.T.); (A.T.)
| | - Nadezhda Tebeneva
- N.S. Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, 70 Profsoyuznaya St., 117393 Moscow, Russia; (N.T.); (A.T.)
| | - Mihail Buzin
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 28 Vavilova St., GSP-1, V-334, 119991 Moscow, Russia; (U.A.); (M.B.); (E.A.); (S.B.); (L.L.); (R.A.); (A.M.)
| | - Egor Afanasyev
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 28 Vavilova St., GSP-1, V-334, 119991 Moscow, Russia; (U.A.); (M.B.); (E.A.); (S.B.); (L.L.); (R.A.); (A.M.)
| | - Aleksander Tarasenkov
- N.S. Enikolopov Institute of Synthetic Polymeric Materials of Russian Academy of Sciences, 70 Profsoyuznaya St., 117393 Moscow, Russia; (N.T.); (A.T.)
| | - Sergey Bukalov
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 28 Vavilova St., GSP-1, V-334, 119991 Moscow, Russia; (U.A.); (M.B.); (E.A.); (S.B.); (L.L.); (R.A.); (A.M.)
| | - Larisa Leites
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 28 Vavilova St., GSP-1, V-334, 119991 Moscow, Russia; (U.A.); (M.B.); (E.A.); (S.B.); (L.L.); (R.A.); (A.M.)
| | - Rinat Aysin
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 28 Vavilova St., GSP-1, V-334, 119991 Moscow, Russia; (U.A.); (M.B.); (E.A.); (S.B.); (L.L.); (R.A.); (A.M.)
| | - Lev Novikov
- D.V. Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.N.); (V.C.); (E.V.)
| | - Vladimir Chernik
- D.V. Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.N.); (V.C.); (E.V.)
| | - Ekaterina Voronina
- D.V. Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, 119991 Moscow, Russia; (L.N.); (V.C.); (E.V.)
| | - Aziz Muzafarov
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, 28 Vavilova St., GSP-1, V-334, 119991 Moscow, Russia; (U.A.); (M.B.); (E.A.); (S.B.); (L.L.); (R.A.); (A.M.)
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20
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Day NJ, Wang X, Voronina E. In Situ Detection of Ribonucleoprotein Complex Assembly in the C. elegans Germline using Proximity Ligation Assay. J Vis Exp 2020. [PMID: 32449701 DOI: 10.3791/60982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Understanding when and where protein-protein interactions (PPIs) occur is critical to understanding protein function in the cell and how broader processes such as development are affected. The Caenorhabditis elegans germline is a great model system for studying PPIs that are related to the regulation of stem cells, meiosis, and development. There are a variety of well-developed techniques that allow proteins of interest to be tagged for recognition by standard antibodies, making this system advantageous for proximity ligation assay (PLA) reactions. As a result, the PLA is able to show where PPIs occur in a spatial and temporal manner in germlines more effectively than alternative approaches. Described here is a protocol for the application and quantification of this technology to probe PPIs in the C. elegans germline.
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Affiliation(s)
| | - Xiaobo Wang
- Division of Biological Sciences, University of Montana
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21
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Wang X, Voronina E. Diverse Roles of PUF Proteins in Germline Stem and Progenitor Cell Development in C. elegans. Front Cell Dev Biol 2020; 8:29. [PMID: 32117964 PMCID: PMC7015873 DOI: 10.3389/fcell.2020.00029] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/14/2020] [Indexed: 01/05/2023] Open
Abstract
Stem cell development depends on post-transcriptional regulation mediated by RNA-binding proteins (RBPs) (Zhang et al., 1997; Forbes and Lehmann, 1998; Okano et al., 2005; Ratti et al., 2006; Kwon et al., 2013). Pumilio and FBF (PUF) family RBPs are highly conserved post-transcriptional regulators that are critical for stem cell maintenance (Wickens et al., 2002; Quenault et al., 2011). The RNA-binding domains of PUF proteins recognize a family of related sequence motifs in the target mRNAs, yet individual PUF proteins have clearly distinct biological functions (Lu et al., 2009; Wang et al., 2018). The C. elegans germline is a simple and powerful model system for analyzing regulation of stem cell development. Studies in C. elegans uncovered specific physiological roles for PUFs expressed in the germline stem cells ranging from control of proliferation and differentiation to regulation of the sperm/oocyte decision. Importantly, recent studies started to illuminate the mechanisms behind PUF functional divergence. This review summarizes the many roles of PUF-8, FBF-1, and FBF-2 in germline stem and progenitor cells (SPCs) and discusses the factors accounting for their distinct biological functions. PUF proteins are conserved in evolution, and insights into PUF-mediated regulation provided by the C. elegans model system are likely relevant for other organisms.
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Affiliation(s)
- Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
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22
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Zyulkov I, Madhiwala V, Voronina E, Snelgrove M, Bogan J, O'Connor R, De Gendt S, Armini S. Area-Selective ALD of Ru on Nanometer-Scale Cu Lines through Dimerization of Amino-Functionalized Alkoxy Silane Passivation Films. ACS Appl Mater Interfaces 2020; 12:4678-4688. [PMID: 31913003 DOI: 10.1021/acsami.9b14596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The selective deposition of materials on predefined areas on a substrate is of crucial importance for various applications, such as energy harvesting, microelectronic device fabrication, and catalysis. A representative example of area-confined deposition is the selective deposition of a metal film as the interconnect material in multilevel metallization schemes for CMOS technology. This allows the formation of multilevel structures with standard lithographical techniques while minimizing pattern misalignment and overlay and improving the uniformity of the structures across the wafer. In this work, area-selective deposition of Ru by atomic layer deposition (ALD) is investigated using alkoxy siloxane dielectric passivation layers. In this work, a comparison of several silane organic SAM precursors in terms of Ru ALD ASD performance is reported. The importance of the surface areal concentration of the passivation molecules is demonstrated. According to the in situ X-ray photoelectron spectroscopy film characterization, the ALD blocking layers derived from a (3-trimethoxysilylpropyl) diethylenetriamine (DETA) precursor have the ability to polymerize under ALD-compatible temperatures, such as 250 °C, which leads to a significant inhibition of Ru growth up to 400 ALD cycles. At the same time, the DETA layer can be selectively removed from the oxidized Cu surface by rinsing in acetic acid, which allows selective deposition of ca. 14 nm of Ru on Cu with no Ru detected on the DETA-coated surface by RBS. The approach is successfully tested on 50 nm half-pitch patterned SiO2/Cu lines.
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Affiliation(s)
- Ivan Zyulkov
- Department of Chemistry, Faculty of Science , KU Leuven , B-3001 Leuven , Belgium
- Imec , Kapeldreef 75 , B-3001 Leuven , Belgium
| | - Viraj Madhiwala
- Faculty of Electrical Engineering and Information Technology , TU Chemnitz , 09107 Chemnitz , Germany
| | - Ekaterina Voronina
- Faculty of Physics , Lomonosov Moscow State University , Leninskie Gory, GSP-1 , Moscow 119991 , Russian Federation
| | | | | | | | - Stefan De Gendt
- Department of Chemistry, Faculty of Science , KU Leuven , B-3001 Leuven , Belgium
- Imec , Kapeldreef 75 , B-3001 Leuven , Belgium
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23
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Day NJ, Ellenbecker M, Voronina E. Caenorhabditis elegans DLC-1 associates with ribonucleoprotein complexes to promote mRNA regulation. FEBS Lett 2018; 592:3683-3695. [PMID: 30264890 PMCID: PMC6263831 DOI: 10.1002/1873-3468.13259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/07/2018] [Accepted: 09/14/2018] [Indexed: 12/21/2022]
Abstract
Ribonucleoprotein complexes, which contain mRNAs and their regulator proteins, carry out post-transcriptional control of gene expression. The function of many RNA-binding proteins depends on their association with cofactors. Here, we use a genomic approach to identify transcripts associated with DLC-1, a protein previously identified as a cofactor of two unrelated RNA-binding proteins that act in the Caenorhabditis elegans germline. Among the 2732 potential DLC-1 targets, most are germline mRNAs associated with oogenesis. Removal of DLC-1 affects expression of its targets expressed in the oocytes, meg-1 and meg-3. We propose that DLC-1 acts as a cofactor for multiple ribonucleoprotein complexes, including the ones regulating gene expression during oogenesis.
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Affiliation(s)
- Nicholas J Day
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Mary Ellenbecker
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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24
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Shadrina A, Tsepilov Y, Smetanina M, Voronina E, Seliverstov E, Ilyukhin E, Kirienko A, Zolotukhin I, Filipenko M. Correction to: Polymorphisms of genes involved in inflammation and blood vessel development influence the risk of varicose veins. Clin Genet 2018; 94:491. [PMID: 30295924 DOI: 10.1111/cge.13445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A Shadrina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Theoretical and Applied Functional Genomics Laboratory, Novosibirsk State University, Novosibirsk, Russia
| | - Y Tsepilov
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Theoretical and Applied Functional Genomics Laboratory, Novosibirsk State University, Novosibirsk, Russia
| | - M Smetanina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Fundamental Medicine, Novosibirsk State University, Novosibirsk, Russia
| | - E Voronina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - E Seliverstov
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Moscow, Russia
| | - E Ilyukhin
- Private Surgery Center "Medalp", Saint Petersburg, Russia
| | - A Kirienko
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Moscow, Russia
| | - I Zolotukhin
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - M Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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25
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Shadrina A, Tsepilov Y, Smetanina M, Voronina E, Seliverstov E, Ilyukhin E, Kirienko A, Zolotukhin I, Filipenko M. Polymorphisms of genes involved in inflammation and blood vessel development influence the risk of varicose veins. Clin Genet 2018; 94:191-199. [PMID: 29660117 DOI: 10.1111/cge.13362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 12/29/2022]
Abstract
Heredity plays an important role in the etiology of varicose veins (VVs). However, the genetic basis underlying this condition remains poorly understood. Our aim was to replicate top association signals from genome-wide association studies (GWASs) for VVs of lower extremities using 2 independent datasets-our sample of ethnic Russian individuals (709 cases and 278 controls) and a large cohort of British residents from UK Biobank (10 861 cases and 397 594 controls). Associations of polymorphisms rs11121615, rs6712038, rs507666, rs966562, rs7111987, rs6062618, and rs6905288 were validated in the UK Biobank individuals at a Bonferroni-corrected significance level. In Russian cohort, only rs11121615 reached a nominal significance level of P < .05. Results of original GWAS and replication studies were combined by a meta-analysis, and polymorphisms listed above as well as rs111434909 and rs4463578 passed a genome-wide significant threshold. Notably, the majority of these polymorphisms were located within or near genes involved in vascular development and remodeling, and regulation of inflammatory response. Our results confirm the role of these polymorphisms in genetic susceptibility to VVs and indicate the revealed genomic regions as good candidates for further fine-mapping studies and functional analysis. Moreover, our findings implicate inflammation and abnormal vascular architecture in VVs pathogenesis.
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Affiliation(s)
- A Shadrina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Theoretical and Applied Functional Genomics Laboratory, Novosibirsk State University, Novosibirsk, Russia
| | - Y Tsepilov
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Theoretical and Applied Functional Genomics Laboratory, Novosibirsk State University, Novosibirsk, Russia
| | - M Smetanina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Fundamental Medicine, Novosibirsk State University, Novosibirsk, Russia
| | - E Voronina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Natural Sciences, Novosibirsk State University, Moscow, Russia
| | - E Seliverstov
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Moscow, Russia
| | - E Ilyukhin
- Private Surgery Center "Medalp", Saint Petersburg, Russia
| | - A Kirienko
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Moscow, Russia
| | - I Zolotukhin
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - M Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Department of Natural Sciences, Novosibirsk State University, Moscow, Russia
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26
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Battisti JM, Watson LA, Naung MT, Drobish AM, Voronina E, Minnick MF. Analysis of the Caenorhabditis elegans innate immune response to Coxiella burnetii. Innate Immun 2016; 23:111-127. [PMID: 27884946 DOI: 10.1177/1753425916679255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The nematode Caenorhabditis elegans is well established as a system for characterization and discovery of molecular mechanisms mediating microbe-specific inducible innate immune responses to human pathogens. Coxiella burnetii is an obligate intracellular bacterium that causes a flu-like syndrome in humans (Q fever), as well as abortions in domesticated livestock, worldwide. Initially, when wild type C. elegans (N2 strain) was exposed to mCherry-expressing C. burnetii (CCB) a number of overt pathological manifestations resulted, including intestinal distension, deformed anal region and a decreased lifespan. However, nematodes fed autoclave-killed CCB did not exhibit these symptoms. Although vertebrates detect C. burnetii via TLRs, pathologies in tol-1(-) mutant nematodes were indistinguishable from N2, and indicate nematodes do not employ this orthologue for detection of C. burnetii. sek-1(-) MAP kinase mutant nematodes succumbed to infection faster, suggesting that this signaling pathway plays a role in immune activation, as previously shown for orthologues in vertebrates during a C. burnetii infection. C. elegans daf-2(-) mutants are hyper-immune and exhibited significantly reduced pathological consequences during challenge. Collectively, these results demonstrate the utility of C. elegans for studying the innate immune response against C. burnetii and could lead to discovery of novel methods for prevention and treatment of disease in humans and livestock.
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Affiliation(s)
- James M Battisti
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Lance A Watson
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Myo T Naung
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Adam M Drobish
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Ekaterina Voronina
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Michael F Minnick
- Program in Cellular, Molecular and Microbial Biology, Division of Biological Sciences, University of Montana, Missoula, MT, USA
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27
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Wang X, Olson JR, Rasoloson D, Ellenbecker M, Bailey J, Voronina E. Dynein light chain DLC-1 promotes localization and function of the PUF protein FBF-2 in germline progenitor cells. Development 2016; 143:4643-4653. [PMID: 27864381 DOI: 10.1242/dev.140921] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/04/2016] [Indexed: 11/20/2022]
Abstract
PUF family translational repressors are conserved developmental regulators, but the molecular function provided by the regions flanking the PUF RNA-binding domain is unknown. In C. elegans, the PUF proteins FBF-1 and FBF-2 support germline progenitor maintenance by repressing production of meiotic proteins and use distinct mechanisms to repress their target mRNAs. We identify dynein light chain DLC-1 as an important regulator of FBF-2 function. DLC-1 directly binds to FBF-2 outside of the RNA-binding domain and promotes FBF-2 localization and function. By contrast, DLC-1 does not interact with FBF-1 and does not contribute to FBF-1 activity. Surprisingly, we find that the contribution of DLC-1 to FBF-2 activity is independent of the dynein motor. Our findings suggest that PUF protein localization and activity are mediated by sequences flanking the RNA-binding domain that bind specific molecular partners. Furthermore, these results identify a new role for DLC-1 in post-transcriptional regulation of gene expression.
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Affiliation(s)
- Xiaobo Wang
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jenessa R Olson
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Dominique Rasoloson
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, HHMI, Baltimore, MD 21205, USA
| | - Mary Ellenbecker
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Jessica Bailey
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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28
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Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN, Denu JM. Reader domain specificity and lysine demethylase-4 family function. Nat Commun 2016; 7:13387. [PMID: 27841353 PMCID: PMC5114558 DOI: 10.1038/ncomms13387] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 09/28/2016] [Indexed: 12/14/2022] Open
Abstract
The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.
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Affiliation(s)
- Zhangli Su
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
| | - Jin-Hee Lee
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Kimberly E. Stephens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Kimberly A. Krautkramer
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Ana Raman
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy J. Thorpe
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Melissa D. Boersma
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Vyacheslav I. Kuznetsov
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | | | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - George N. Phillips
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
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29
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Abstract
Drosophila germ cell specification depends on localization of mRNAs required for patterning to the posterior of the oocyte during oogenesis. In a recent issue of Nature, Vourekas et al. (2016) suggest that Aubergine in complex with piRNAs may provide a low-specificity anchoring mechanism for posterior mRNAs.
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Affiliation(s)
- Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.
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30
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Sergeeva A, Kirillov B, Voronina E. Analyzing the PVCs Documents: A Multimodal Rate-based Approach to Understand Community’s Goals and Values. Proc Doc Acad 2016. [DOI: 10.35492/docam/2/1/15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
A significant amount of modern professional communication takes place in the so-called Virtual Communities of Practice or Professional Virtual Communities (PVCs): social systems of individuals who use Information Technologies to mediate their relationships and facilitate knowledge exchange and generation. In current research we analyze one of the biggest Russian IT-PVCs, Habrahabr.ru. The community’s official goal is connecting the IT-specialists; communication takes form of users articles and comments; users can rate the articles, the comments and the other users themselves. Using the number of SNA instruments, community’s metadata, linguistics statistics and discourse analysis we show the structure of the community, main topics within the professional field, and find the core ideas and values which “paste together” the communities members.
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Papazyan R, Voronina E, Chapman JR, Luperchio TR, Gilbert TM, Meier E, Mackintosh SG, Shabanowitz J, Tackett AJ, Reddy KL, Coyne RS, Hunt DF, Liu Y, Taverna SD. Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during meiosis. eLife 2014; 3:e02996. [PMID: 25161194 PMCID: PMC4141274 DOI: 10.7554/elife.02996] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite the well-established role of heterochromatin in protecting chromosomal integrity during meiosis and mitosis, the contribution and extent of heterochromatic histone posttranslational modifications (PTMs) remain poorly defined. Here, we gained novel functional insight about heterochromatic PTMs by analyzing histone H3 purified from the heterochromatic germline micronucleus of the model organism Tetrahymena thermophila. Mass spectrometric sequencing of micronuclear H3 identified H3K23 trimethylation (H3K23me3), a previously uncharacterized PTM. H3K23me3 became particularly enriched during meiotic leptotene and zygotene in germline chromatin of Tetrahymena and C. elegans. Loss of H3K23me3 in Tetrahymena through deletion of the methyltransferase Ezl3p caused mislocalization of meiosis-induced DNA double-strand breaks (DSBs) to heterochromatin, and a decrease in progeny viability. These results show that an evolutionarily conserved developmental pathway regulates H3K23me3 during meiosis, and our studies in Tetrahymena suggest this pathway may function to protect heterochromatin from DSBs. DOI:http://dx.doi.org/10.7554/eLife.02996.001 Inside the nucleus of a cell, the DNA is wound around histone proteins. This forms a structure called chromatin that allows the long DNA strands to fit inside the cell. Variations in chromatin structure also help the cell to control the functional properties of DNA. For example, a large proportion of chromatin in the cell is in the form of heterochromatin, which is very densely packed, and is associated with many roles such as gene silencing and keeping DNA intact during reproduction. Many animals and plants have two copies of each DNA molecule: one inherited from the mother, and one from the father of the organism. Reproductive cells undergo a process called recombination when they form, where the matching copies of each DNA molecule break in a number of places and rejoin to form a new ‘blend’ of their mother's and their father's DNA, which is passed on to their own offspring. In contrast, most heterochromatin is inherited without recombining, preserving it in an unaltered form. This is important since recombination in heterochromatin can create genetic abnormalities. Adding small chemical modifications—such as methyl groups—to the histone proteins at the core of the chromatin can change how the DNA is packed. However, the histone modifications that yield different chromatin structures, and the effect of these modifications, are not very well understood. Papazyan et al. have taken advantage of a distinct feature of the protozoan Tetrahymena thermophila: a single-celled organism that divides its chromatin into two different nuclei. The smaller micronuclei contain only heterochromatin, and Papazyan et al. discovered that the histone H3 protein in the micronuclei is modified by methyl groups at a specific site that had not been studied before. Furthermore, this protozoan makes more of these modifications when it reproduces. An enzyme called Ezl3p adds these methyl groups, and without this enzyme T. thermophila reproduces more slowly and has offspring that are less likely to survive and more likely to be infertile. Papazyan et al. provide evidence that these characteristics arise because the cells without the histone modification are unable to prevent DNA breaks from occurring in heterochromatin during recombination. The same histone modification also occurs when the microscopic worm Caenorhabditis elegans reproduces, suggesting that this method of DNA protection has been conserved throughout evolution. Papazyan et al. propose that the histone modification may prevent another enzyme that induces DNA breaks from accessing the heterochromatin in reproductive cells; but more work is required to support this hypothesis. These findings reveal the importance of a new histone modification during reproduction, and could provide new directions for infertility research. DOI:http://dx.doi.org/10.7554/eLife.02996.002
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Affiliation(s)
- Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ekaterina Voronina
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Balitmore, United States Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jessica R Chapman
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - Teresa R Luperchio
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Tonya M Gilbert
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Elizabeth Meier
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, United States
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, United States
| | - Karen L Reddy
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, United States
| | - Robert S Coyne
- Department of Genomic Medicine, J. Craig Venter Institute, Rockville, United States
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, United States Department of Pathology, University of Virginia, Charlottesville, United States
| | - Yifan Liu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, United States Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, United States
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Sirotkina A, Khokhlov A, Voronina E. PP155—Prevalence of Gene Polymorphism SLCO1B1 in Patients with Dyslipidemia and Systemic Atherosclerosis in Russian Population. Clin Ther 2013. [DOI: 10.1016/j.clinthera.2013.07.196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Papazvan R, Voronina E, Chapman JR, Gilbert TM, Meier E, Shabanowitz J, Hunt DF, Liu Y, Taverna SD. Methylation of histone H3 at lysine 23 in meiotic heterochromatin. Epigenetics Chromatin 2013. [PMCID: PMC3600677 DOI: 10.1186/1756-8935-6-s1-o13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Voronina E. The diverse functions of germline P-granules in Caenorhabditis elegans. Mol Reprod Dev 2012; 80:624-31. [PMID: 23150384 DOI: 10.1002/mrd.22136] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/05/2012] [Indexed: 12/14/2022]
Abstract
P-granules are conserved cytoplasmic organelles, similar to nuage, that are present in Caenorhabditis elegans germ cells. Based on the prevailing sterility phenotype of the component mutants, P-granules have been seen as regulators of germ cell development and function. Yet, specific germline defects resulting from P-granule failure vary, depending on which component(s) are inactivated, at which stage of development, as well as on the presence of stress factors during animal culture. This review discusses the unifying themes in many P-granule functions, with the main focus on their role as organizing centers nucleating RNA regulation in the germ cell cytoplasm.
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Affiliation(s)
- Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA.
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Voronina E, Paix A, Seydoux G. The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells. Development 2012; 139:3732-40. [PMID: 22991439 DOI: 10.1242/dev.083980] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In the C. elegans germline, maintenance of undifferentiated stem cells depends on the PUF family RNA-binding proteins FBF-1 and FBF-2. FBF-1 and FBF-2 are 89% identical and are required redundantly to silence the expression of mRNAs that promote meiosis. Here we show that, despite their extensive sequence similarity, FBF-1 and FBF-2 have different effects on target mRNAs. FBF-1 promotes the degradation and/or transport of meiotic mRNAs out of the stem cell region, whereas FBF-2 prevents translation. FBF-2 activity depends on the P granule component PGL-1. PGL-1 is required to localize FBF-2 to perinuclear P granules and for efficient binding of FBF-2 to its mRNA targets. We conclude that multiple regulatory mechanisms converge on meiotic RNAs to ensure silencing in germline stem cells. Our findings also support the view that P granules facilitate mRNA silencing by providing an environment in which translational repressors can encounter their mRNA targets immediately upon exit from the nucleus.
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Affiliation(s)
- Ekaterina Voronina
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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36
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Joseph-Strauss D, Gorjánácz M, Santarella-Mellwig R, Voronina E, Audhya A, Cohen-Fix O. Sm protein down-regulation leads to defects in nuclear pore complex disassembly and distribution in C. elegans embryos. Dev Biol 2012; 365:445-57. [PMID: 22426005 DOI: 10.1016/j.ydbio.2012.02.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/24/2012] [Accepted: 02/29/2012] [Indexed: 10/28/2022]
Abstract
Nuclear pore complexes (NPCs) are large macromolecular structures embedded in the nuclear envelope (NE), where they facilitate exchange of molecules between the cytoplasm and the nucleoplasm. In most cell types, NPCs are evenly distributed around the NE. However, the mechanisms dictating NPC distribution are largely unknown. Here, we used the model organism Caenorhabditis elegans to identify genes that affect NPC distribution during early embryonic divisions. We found that down-regulation of the Sm proteins, which are core components of the spliceosome, but not down-regulation of other splicing factors, led to clustering of NPCs. Down-regulation of Sm proteins also led to incomplete disassembly of NPCs during mitosis, but had no effect on lamina disassembly, suggesting that the defect in NPC disassembly was not due to a general defect in nuclear envelope breakdown. We further found that these mitotic NPC remnants persisted on an ER membrane that juxtaposes the mitotic spindle. At the end of mitosis, the remnant NPCs moved toward the chromatin and the reforming NE, where they ultimately clustered by forming membrane stacks perforated by NPCs. Our results suggest a novel, splicing-independent, role for Sm proteins in NPC disassembly, and point to a possible link between NPC disassembly in mitosis and NPC distribution in the subsequent interphase.
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Affiliation(s)
- Daphna Joseph-Strauss
- The Laboratory of Molecular and Cellular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda MD 20892, USA
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Abstract
"Germ granules" are cytoplasmic, nonmembrane-bound organelles unique to germline. Germ granules share components with the P bodies and stress granules of somatic cells, but also contain proteins and RNAs uniquely required for germ cell development. In this review, we focus on recent advances in our understanding of germ granule assembly, dynamics, and function. One hypothesis is that germ granules operate as hubs for the posttranscriptional control of gene expression, a function at the core of the germ cell differentiation program.
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Affiliation(s)
- Ekaterina Voronina
- Department of Molecular Biology and Genetics and Howard Hughes Medical Institute, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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38
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Ermolenko Kostrykina NA, Boyarskih UA, Voronina E, Sushko AG, Selezneva IA, Lazarev AF, Petrova VD, Filipenko ML, Boyarskikh UA. Associations of polymorphisms in genes antioxidant enzymes and detoxification enzymes and breast cancer risk in residents of the west Siberian region. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.e12023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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39
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Voronina E, Seydoux G. The C. elegans homolog of nucleoporin Nup98 is required for the integrity and function of germline P granules. J Cell Sci 2010. [DOI: 10.1242/jcs.073148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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40
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Voronina E, Seydoux G. The C. elegans homolog of nucleoporin Nup98 is required for the integrity and function of germline P granules. Development 2010; 137:1441-50. [PMID: 20335358 DOI: 10.1242/dev.047654] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
C. elegans P granules are conserved cytoplasmic ribonucleoprotein complexes that are unique to the germline and essential for fertility. During most of germline development, P granules are perinuclear and associate with clusters of nuclear pores. In an RNAi screen against nucleoporins, we have identified a specific nucleoporin essential for P granule integrity and function. The C. elegans homolog of vertebrate Nup98 (CeNup98) is enriched in P granules and associates with the translationally repressed, P granule-enriched mRNA nos-2 (nanos homolog). Loss of CeNup98 causes P granules to disperse in the cytoplasm and to release nos-2 mRNA. Embryos depleted for CeNup98 express a nos-2 3'UTR reporter prematurely. In the mouse, Nup98 immunoprecipitates with the germ granule component MVH. Our findings suggest that, in germ cells, the function of Nup98 extends beyond transport at the nuclear pore to include mRNA regulation in the cytoplasm.
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Affiliation(s)
- Ekaterina Voronina
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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41
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Voronina E, Lopez M, Juliano CE, Gustafson E, Song JL, Extavour C, George S, Oliveri P, McClay D, Wessel G. Vasa protein expression is restricted to the small micromeres of the sea urchin, but is inducible in other lineages early in development. Dev Biol 2008; 314:276-86. [PMID: 18191830 PMCID: PMC2692673 DOI: 10.1016/j.ydbio.2007.11.039] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 11/06/2007] [Accepted: 11/20/2007] [Indexed: 11/18/2022]
Abstract
Vasa is a DEAD-box RNA helicase that functions in translational regulation of specific mRNAs. In many animals it is essential for germ line development and may have a more general stem cell role. Here we identify vasa in two sea urchin species and analyze the regulation of its expression. We find that vasa protein accumulates in only a subset of cells containing vasa mRNA. In contrast to vasa mRNA, which is present uniformly throughout all cells of the early embryo, vasa protein accumulates selectively in the 16-cell stage micromeres, and then is restricted to the small micromeres through gastrulation to larval development. Manipulating early embryonic fate specification by blastomere separations, exposure to lithium, and dominant-negative cadherin each suggest that, although vasa protein accumulation in the small micromeres is fixed, accumulation in other cells of the embryo is inducible. Indeed, we find that embryos in which micromeres are removed respond by significant up-regulation of vasa protein translation, followed by spatial restriction of the protein late in gastrulation. Overall, these results support the contention that sea urchins do not have obligate primordial germ cells determined in early development, that vasa may function in an early stem cell population of the embryo, and that vasa expression in this embryo is restricted early by translational regulation to the small micromere lineage.
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Affiliation(s)
- Ekaterina Voronina
- Providence Institute of Molecular Oogenesis, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI 02912
| | - Manuel Lopez
- Department of Biology, LSRC Building, Duke University, Durham, NC 27708
| | - Celina E. Juliano
- Providence Institute of Molecular Oogenesis, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI 02912
| | - Eric Gustafson
- Providence Institute of Molecular Oogenesis, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI 02912
| | - Jia L. Song
- Providence Institute of Molecular Oogenesis, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI 02912
| | - Cassandra Extavour
- Laboratory for Development and Evolution, University Museum of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, England
| | - Sophie George
- Department of Biology, Georgia Southern University, Statesboro, Georgia 30460
| | - Paola Oliveri
- Division of Biology 156-29, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125
| | - David McClay
- Department of Biology, LSRC Building, Duke University, Durham, NC 27708
| | - Gary Wessel
- Providence Institute of Molecular Oogenesis, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI 02912
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Voronina E, Lovasco LA, Gyuris A, Baumgartner RA, Parlow AF, Freiman RN. Ovarian granulosa cell survival and proliferation requires the gonad-selective TFIID subunit TAF4b. Dev Biol 2006; 303:715-26. [PMID: 17207475 PMCID: PMC1950739 DOI: 10.1016/j.ydbio.2006.12.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 11/27/2006] [Accepted: 12/06/2006] [Indexed: 01/29/2023]
Abstract
Oocyte development in the mammalian ovary requires productive interactions with somatic granulosa cells of the ovarian follicle. Proliferating granulosa cells support the progression of follicular growth and maturation, multiplying dramatically as it unfolds. The cell cycle recruitment of granulosa cells is regulated at least in part by hormones such as follicle-stimulating hormone (FSH) and estrogen. Follicles recruited into the growth phase following formation of multiple layers of granulosa cells have two major fates: either to continue proliferation followed by differentiation, or to die by programmed cell death, or atresia. While many of the signaling pathways orchestrating ovarian follicle development are known, the downstream transcriptional regulators that integrate such signals in the mammalian ovary remain to be defined. Recent experiments in diverse organisms have revealed multiple instances of gonad-selective components of the basal transcriptional machinery. One such protein, TAF4b, is a gonadal-enriched coactivator subunit of the TFIID complex required for normal female fertility in the mouse. To determine the etiology of female infertility of the TAF4b-deficient mice, we have determined multiple functions of TAF4b during postnatal ovarian follicle development. Here we demonstrate that the TAF4b protein is expressed in the granulosa cell compartment of the mammalian ovarian follicle. Furthermore, TAF4b-deficient mouse ovaries contain reduced numbers of primordial as well as growing follicles and a concomitant increased proportion of apoptotic follicles in comparison to wild type counterparts. Importantly, TAF4b-null follicles are largely resistant to induction of proliferation in response to multiple hormonal stimuli including estrogen and FSH and demonstrate compromised granulosa cell survival. Together, these data suggest that TAF4b integrates a program of granulosa cell gene expression required for normal ovarian follicle survival and proliferation in response to diverse ovarian signaling events.
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Affiliation(s)
- Ekaterina Voronina
- Brown University, Department of Molecular and Cell Biology and Biochemistry, 69 Brown St., Box G-J115, Providence, RI 02912 USA
| | - Lindsay A. Lovasco
- Brown University, Department of Molecular and Cell Biology and Biochemistry, 69 Brown St., Box G-J115, Providence, RI 02912 USA
| | - Aron Gyuris
- Brown University, Department of Molecular and Cell Biology and Biochemistry, 69 Brown St., Box G-J115, Providence, RI 02912 USA
| | - Robert A. Baumgartner
- Brown University, Department of Molecular and Cell Biology and Biochemistry, 69 Brown St., Box G-J115, Providence, RI 02912 USA
| | - Albert F. Parlow
- National Hormone & Peptide Program, Harbor-UCLA Medical Center, 1000 W. Carson. St., Torrance, CA 90509 USA
| | - Richard N. Freiman
- Brown University, Department of Molecular and Cell Biology and Biochemistry, 69 Brown St., Box G-J115, Providence, RI 02912 USA
- Corresponding author EMAIL: Phone: (401)-863-9633, FAX: (401) 863-2421
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Abstract
An asymmetric fourth cell division in the sea urchin embryo results in formation of daughter cells, macromeres and micromeres, with distinct sizes and fates. Several lines of functional evidence presented here, including pharmacological interference and dominant negative protein expression, indicate that heterotrimeric G protein Gi and its interaction partner, activator of G-protein signaling (AGS), are necessary for this asymmetric cell division. Inhibition of Gi signaling by pertussis toxin interferes with micromere formation and leads to defects in embryogenesis. AGS was isolated in a yeast two-hybrid screen with G alpha i as bait and was expressed in embryos localized to the cell cortex at the time of asymmetric divisions. Introduction of exogenous dominant-negative AGS protein, containing only G-protein regulatory (GPR) domains, selectively prevented the asymmetric division in normal micromere formation. These results support the growing evidence that AGS is a universal regulator of asymmetric cell divisions in embryos.
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Affiliation(s)
- Ekaterina Voronina
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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44
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Robertson AJ, Croce J, Carbonneau S, Voronina E, Miranda E, McClay DR, Coffman JA. The genomic underpinnings of apoptosis in Strongylocentrotus purpuratus. Dev Biol 2006; 300:321-34. [PMID: 17010332 DOI: 10.1016/j.ydbio.2006.08.053] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 08/21/2006] [Accepted: 08/22/2006] [Indexed: 11/30/2022]
Abstract
Programmed cell death through apoptosis is a pan-metazoan character involving intermolecular signaling networks that have undergone substantial lineage-specific evolution. A survey of apoptosis-related proteins encoded in the sea urchin genome provides insight into this evolution while revealing some interesting novelties, which we highlight here. First, in addition to a typical CARD-carrying Apaf-1 homologue, sea urchins have at least two novel Apaf-1-like proteins that are each linked to a death domain, suggesting that echinoderms have evolved unique apoptotic signaling pathways. Second, sea urchins have an unusually large number of caspases. While the set of effector caspases (caspases-3/7 and caspase-6) in sea urchins is similar to that found in other basal deuterostomes, signal-responsive initiator caspase subfamilies (caspases-8/10 and 9, which are respectively linked to DED and CARD adaptor domains) have undergone echinoderm-specific expansions. In addition, there are two groups of divergent caspases, one distantly related to the vertebrate interleukin converting enzyme (ICE)-like subfamily, and a large clan that does not cluster with any of the vertebrate caspases. Third, the complexity of proteins containing an anti-apoptotic BIR domain and of Bcl-2 family members approaches that of vertebrates, and is greater than that found in protostome model systems such as Drosophila or Caenorhabditis elegans. Finally, the presence of Death receptor homologues, previously known only in vertebrates, in both Strongylocentrotus purpuratus and Nematostella vectensis suggests that this family of apoptotic signaling proteins evolved early in animals and was subsequently lost in the nematode and arthropod lineage(s). Our results suggest that cell survival is contingent upon a diverse array of signals in sea urchins, more comparable in complexity to vertebrates than to arthropods or nematodes, but also with unique features that may relate to specific requirements imposed by the biphasic life cycle and/or immunological idiosyncrasies of this organism.
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Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006; 314:941-52. [PMID: 17095691 PMCID: PMC3159423 DOI: 10.1126/science.1133609] [Citation(s) in RCA: 798] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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Beane WS, Voronina E, Wessel GM, McClay DR. Lineage-specific expansions provide genomic complexity among sea urchin GTPases. Dev Biol 2006; 300:165-79. [PMID: 17014838 DOI: 10.1016/j.ydbio.2006.08.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 08/18/2006] [Accepted: 08/19/2006] [Indexed: 12/30/2022]
Abstract
In every organism, GTP-binding proteins control many aspects of cell signaling. Here, we examine in silico several GTPase families from the Strongylocentrotus purpuratus genome: the monomeric Ras superfamily, the heterotrimeric G proteins, the dynamin superfamily, the SRP/SR family, and the "protein biosynthesis" translational GTPases. Identified were 174 GTPases, of which over 90% are expressed in the embryo as shown by tiling array and expressed sequence tag data. Phylogenomic comparisons restricted to Drosophila, Ciona, and humans (protostomes, urochordates, and vertebrates, respectively) revealed both common and unique elements in the expected composition of these families. Galpha and dynamin families contain vertebrate expansions, consistent with whole genome duplications, whereas SRP/SR and translational GTPases are highly conserved. Unexpectedly, Ras superfamily analyses revealed several large (5+) lineage-specific expansions in the sea urchin. For Rho, Rab, Arf, and Ras subfamilies, comparing total human gene numbers to the number of sea urchin genes with vertebrate orthologs suggests reduced genomic complexity in the sea urchin. However, gene duplications in the sea urchin increase overall numbers such that total sea urchin gene numbers approximate vertebrate gene numbers for each monomeric GTPase family. These findings suggest that lineage-specific expansions may be an important component of genomic evolution in signal transduction.
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Affiliation(s)
- Wendy S Beane
- Department of Biology, Developmental, Cell and Molecular Group, Duke University, Box 91000, Durham, NC 27708, USA.
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Juliano CE, Voronina E, Stack C, Aldrich M, Cameron AR, Wessel GM. Germ line determinants are not localized early in sea urchin development, but do accumulate in the small micromere lineage. Dev Biol 2006; 300:406-15. [PMID: 16970939 DOI: 10.1016/j.ydbio.2006.07.035] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Revised: 07/20/2006] [Accepted: 07/27/2006] [Indexed: 11/26/2022]
Abstract
Two distinct modes of germ line determination are used throughout the animal kingdom: conditional-an inductive mechanism, and autonomous-an inheritance of maternal factors in early development. This study identifies homologs of germ line determinants in the sea urchin Strongylocentrotus purpuratus to examine its mechanism of germ line determination. A list of conserved germ-line associated genes from diverse organisms was assembled to search the S. purpuratus genome for homologs, and the expression patterns of these genes were examined during embryogenesis by whole mount in situ RNA hybridization and QPCR. Of the 14 genes tested, all transcripts accumulate uniformly during oogenesis and Sp-pumilio, Sp-tudor, Sp-MSY, and Sp-CPEB1 transcripts are also uniformly distributed during embryonic development. Sp-nanos2, Sp-seawi, and Sp-ovo transcripts, however, are enriched in the vegetal plate of the mesenchyme blastula stage and Sp-vasa, Sp-nanos2, Sp-seawi, and Sp-SoxE transcripts are localized in small micromere descendents at the tip of the archenteron during gastrulation and are then enriched in the left coelomic pouch of larvae. The results of this screen suggest that sea urchins conditionally specify their germ line, and support the hypothesis that this mechanism is the basal mode of germ line determination amongst deuterostomes. Furthermore, accumulation of germ line determinants selectively in small micromere descendents supports the hypothesis that these cells contribute to the germ line.
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Affiliation(s)
- Celina E Juliano
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 69 Brown Street, Providence, RI 02912, USA
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Geles KG, Freiman RN, Liu WL, Zheng S, Voronina E, Tjian R. Cell-type-selective induction of c-jun by TAF4b directs ovarian-specific transcription networks. Proc Natl Acad Sci U S A 2006; 103:2594-9. [PMID: 16473943 PMCID: PMC1413803 DOI: 10.1073/pnas.0510764103] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell-type-selective expression of the TFIID subunit TAF(II)105 (renamed TAF4b) in the ovary is essential for proper follicle development. Although a multitude of signaling pathways required for folliculogenesis have been identified, downstream transcriptional integrators of these signals remain largely unknown. Here, we show that TAF4b controls the granulosa-cell-specific expression of the proto-oncogene c-jun, and together they regulate transcription of ovary-selective promoters. Instead of using cell-type-specific activators, our findings suggest that the coactivator TAF4b regulates the expression of tissue-specific genes, at least in part, through the cell-type-specific induction of c-jun, a ubiquitous activator. Importantly, the loss of TAF4b in ovarian granulosa cells disrupts cellular morphologies and interactions during follicle growth that likely contribute to the infertility observed in TAF4b-null female mice. These data highlight a mechanism for potentiating tissue-selective functions of the basal transcription machinery and reveal intricate networks of gene expression that orchestrate ovarian-specific functions and cell morphology.
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Affiliation(s)
- Kenneth G. Geles
- *Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, 16 Barker Hall, #3204, Berkeley, CA 94720; and
| | - Richard N. Freiman
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 69 Brown Street, Box G-J115, Providence, RI 02912
| | - Wei-Li Liu
- *Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, 16 Barker Hall, #3204, Berkeley, CA 94720; and
| | - Shuang Zheng
- *Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, 16 Barker Hall, #3204, Berkeley, CA 94720; and
| | - Ekaterina Voronina
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 69 Brown Street, Box G-J115, Providence, RI 02912
| | - Robert Tjian
- *Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, 16 Barker Hall, #3204, Berkeley, CA 94720; and
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Abstract
A cytoplasmic Ca2+ transient is required for egg activation at fertilization in all animals. The pathway leading to release of Ca2+ from the endoplasmic reticulum in echinoderms includes activation of a SRC homolog, followed by phospholipase Cγ activation, and formation of inositol trisphosphate. However, the upstream activators or modulators of this signaling pathway are not known. We recently identified four Gα subunits of heterotrimeric G-proteins present in the sea urchin egg, and here we find that activation of G-proteins of the Gαs and Gαq type, but not Gαi or Gα12 type, is required for normal Ca2+ dynamics at fertilization. The effects of these G-proteins are mediated by the Gβγ subunits, occur upstream of the cytoplasmic Ca2+ release, and influence both the amplitude of Ca2+ release and the duration of the lag phase. We propose integration of the G-protein input into the framework of signaling at sea urchin fertilization.
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Affiliation(s)
- Ekaterina Voronina
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 69 Brown Street, Providence, RI 02912, USA
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Covián-Nares F, Martínez-Cadena G, López-Godínez J, Voronina E, Wessel GM, García-Soto J. A Rho-signaling pathway mediates cortical granule translocation in the sea urchin oocyte. Mech Dev 2004; 121:225-35. [PMID: 15003626 DOI: 10.1016/j.mod.2004.01.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Revised: 01/13/2004] [Accepted: 01/23/2004] [Indexed: 11/27/2022]
Abstract
Cortical granules are secretory vesicles of the egg that play a fundamental role in preventing polyspermy at fertilization. In the sea urchin egg, they localize directly beneath the plasma membrane forming a compact monolayer and, upon fertilization, undergo a Ca(2+)-dependent exocytosis. Cortical granules form during early oogenesis and, during maturation, translocate from the cytosol to the oocyte cortex in a microfilament-mediated process. We tested the hypothesis that these cortical granule dynamics were regulated by Rho, a GTPase of the Ras superfamily. We observed that Rho is synthesized early in oogenesis, mainly in a soluble form. At the end of maturation, however, Rho associates with cortical granules. Inhibition of Rho with the C3 transferase from C. botulinum blocks cortical granule translocation and microfilaments undergo a significant disorganization. A similar effect is observed by GGTI-286, a geranylgeranyl transferase inhibitor, suggesting that the association of Rho with the cortical granules is indispensable for its function. In contrast, the anchorage of the cortical granules in the cortex, as well as their fusion at fertilization, are Rho-independent processes. We conclude that Rho association with the cortical granules is a critical regulatory step in their translocation to the egg cortex.
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Affiliation(s)
- Fernando Covián-Nares
- Instituto de Investigación en Biología Experimental, Facultad de Química, Universidad de Guanajuato, Col. Noria Alta, Guanajuato, Gto 3600, A.P. 187, Mexico
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