A unified phylogeny-based nomenclature for histone variants Public Deposited

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Creator
  • Ladurner, Andreas G
    • Other Affiliation: Department of Physiological Chemistry, Butenandt Institute and Biomedical Center, Ludwig Maximilians University of Munich, Munich, 81377, Germany
  • Cross, George A M
    • Other Affiliation: Laboratory of Molecular Parasitology, The Rockefeller University, New York, NY 10065, USA
  • Waterborg, Jakob
    • Other Affiliation: Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
  • Cui, Liwang
    • Other Affiliation: Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
  • Berger, Frederic
    • Other Affiliation: Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
  • Henikoff, Steven
    • Other Affiliation: Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle,, WA 98109, USA
  • Tremethick, David
    • Other Affiliation: The John Curtin School of Medical Research, Genome Biology Department, The Australian National University, Canberra, ACT 2601, Australia
  • Doenecke, Detlef
    • Other Affiliation: Department of Biochemistry, University of Goettingen, Goettingen, D- 37073, Germany
  • Malik, Harmit S
    • Other Affiliation: Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle,, WA 98109, USA
  • Gorovsky, Martin A
    • Other Affiliation: Department of Biology, University of Rochester, Rochester, NY 14627, USA
  • Thompson, Eric
    • Other Affiliation: Sars International Center for Marine Molecular Biology and Department of Biology, University of Bergen, Bergen, N-5008, Norway
  • Landsman, David
    • Other Affiliation: National Center for Biotechnology Information, National institutes of Health, Bethesda, MD 20894, USA
  • Almouzni, Geneviève
    • Other Affiliation: CNRS, UMR 218, Institut Curie, Centre de Recherche, Paris, F-75248 cx 05, France
  • Turner, Bryan M
    • Other Affiliation: College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
  • Eirin-López, José M
    • Other Affiliation: Department of Cellular and Molecular Biology, University of A Coruna, A Coruna, E15071, Spain
  • Cande, W
    • Other Affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA
  • Holec, Sarah
    • Other Affiliation: Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
  • Singh, Mohan B
    • Other Affiliation: Plant Molecular Biology and Biotechnology Group, Melbourne School of Land and Environment, The University of Melbourne, Parkville, VIC 3010, Australia
  • Latham, John A
    • Other Affiliation: Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle,, WA 98109, USA
  • Yelagandula, Ramesh
    • Other Affiliation: Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
  • Wollmann, Heike
    • Other Affiliation: Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
  • Loppin, Benjamin
    • Other Affiliation: CGphiMC - CNRS UMR5534, Claude Bernard University Lyon1 - University of Lyon, Villeurbanne, 69622 Cedex, France
  • Schneider, Robert
    • Other Affiliation: Max Planck Institute for Immunbiology and Epigenetics, Freiburg, 79108, Germany; Institut de Genetique et Biologie Moleculaire et Cellulaire, Illkirch, 67404, France
  • Hamkalo, Barbara A
    • Other Affiliation: Department of Molecular Biology and Biochemistry, University of CA, Irvine, CA 92697, USA
  • Talbert, Paul B
    • Other Affiliation: Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle,, WA 98109, USA
  • Hake, Sandra B
    • Other Affiliation: Center for Integrated Protein Science Munich at the Adolf-Butenandt Institute, Department for Molecular Biology, Ludwig-Maximilians-University Munich, Munich, 80336, Germany
  • Bhalla, Prem L
    • Other Affiliation: Plant Molecular Biology and Biotechnology Group, Melbourne School of Land and Environment, The University of Melbourne, Parkville, VIC 3010, Australia
  • Chan, Simon W L
    • Other Affiliation: Department of Plant Biology, UC Davis / HHMI, Davis, CA 95616, USA
  • Khochbin, Saadi
    • Other Affiliation: INSERM, U823; Université Joseph Fourier - Grenoble 1, La Tronche, F-38706, France
  • Torres-Padilla, Maria-Elena
    • Other Affiliation: Stem Cells and Developmental Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Universite de Strasbourg, Illkirch, CU de Strasbourg F-67404, France
  • Jacobsen, Steven E
    • Other Affiliation: Howard Hughes Medical Institute, Department of Molecular Cellular and Developmental Biology, University of California, Los Angeles, CA 9009, USA
  • Postberg, Jan
    • Other Affiliation: HELIOS Medical Centre Wuppertal, Paediatrics Centre, Witten/Herdecke University, Wuppertal, D-42283, Germany
  • Bonner, William M
    • Other Affiliation: Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, MD 20892, USA
  • Dimitrov, Stefan I
    • Other Affiliation: Laboratoire de Biologie Moléculaire et Cellulaire de la Différenciation, Institut Albert Bonniot, INSERM/UJF U821, Grenoble, France
  • Ahmad, Kami
    • Other Affiliation: Department of BCMP, Harvard Medical School, Boston, MA 02115, USA
  • Pehrson, John R
    • Other Affiliation: Department of Animal Biology, University of Pennsylvania, Philadelphia, PA 19104-6046, USA
  • Zhu, Bing
    • Other Affiliation: Chromatin Lab, National Institute of Biological Sciences, Beijing, Beijing 102206, China
  • Ausió, Juan
    • Other Affiliation: Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada
  • Chadwick, Brian P
    • Other Affiliation: Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA
  • Kamieniarz, Kinga
    • Other Affiliation: Max Planck Institute for Immunbiology and Epigenetics, Freiburg, 79108, Germany
  • Marzluff, William
    • Affiliation: School of Medicine, Integrative Program for Biological and Genome Sciences
  • Smith, M
    • Other Affiliation: Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
Abstract
  • Abstract Histone variants are non-allelic protein isoforms that play key roles in diversifying chromatin structure. The known number of such variants has greatly increased in recent years, but the lack of naming conventions for them has led to a variety of naming styles, multiple synonyms and misleading homographs that obscure variant relationships and complicate database searches. We propose here a unified nomenclature for variants of all five classes of histones that uses consistent but flexible naming conventions to produce names that are informative and readily searchable. The nomenclature builds on historical usage and incorporates phylogenetic relationships, which are strong predictors of structure and function. A key feature is the consistent use of punctuation to represent phylogenetic divergence, making explicit the relationships among variant subtypes that have previously been implicit or unclear. We recommend that by default new histone variants be named with organism-specific paralog-number suffixes that lack phylogenetic implication, while letter suffixes be reserved for structurally distinct clades of variants. For clarity and searchability, we encourage the use of descriptors that are separate from the phylogeny-based variant name to indicate developmental and other properties of variants that may be independent of structure.
Date of publication
Identifier
  • 22650316
  • doi:10.1186/1756-8935-5-7
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Paul B Talbert et al.; licensee BioMed Central Ltd.
License
Journal title
  • Epigenetics & Chromatin
Journal volume
  • 5
Journal issue
  • 1
Page start
  • 7
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1756-8935
Bibliographic citation
  • Epigenetics & Chromatin. 2012 May 31;5(1):7
Access
  • Open Access
Publisher
  • BioMed Central Ltd
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