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A unified phylogeny-based nomenclature for histone variants

Paul B Talbert1, Kami Ahmad2, Geneviève Almouzni3, Juan Ausió4, Frederic Berger5, Prem L Bhalla6, William M Bonner7, W Zacheus Cande8, Brian P Chadwick9, Simon W L Chan10, George A M Cross11, Liwang Cui12, Stefan I Dimitrov13, Detlef Doenecke14, José M Eirin-López15, Martin A Gorovsky16, Sandra B Hake17, Barbara A Hamkalo18, Sarah Holec5, Steven E Jacobsen19, Kinga Kamieniarz20, Saadi Khochbin21, Andreas G Ladurner22, David Landsman23, John A Latham1, Benjamin Loppin24, Harmit S Malik1, William F Marzluff25, John R Pehrson26, Jan Postberg27, Robert Schneider2028, Mohan B Singh6, M Mitchell Smith29, Eric Thompson30, Maria-Elena Torres-Padilla31, David John Tremethick32, Bryan M Turner33, Jakob Harm Waterborg34, Heike Wollmann5, Ramesh Yelagandula5, Bing Zhu35 and Steven Henikoff1*

Author Affiliations

1 Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA

2 Department of BCMP, Harvard Medical School, Boston, MA, 02115, USA

3 CNRS, UMR 218, Institut Curie, Centre de Recherche, Paris, F-75248 cx 05, France

4 Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada

5 Temasek Lifesciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore

6 Plant Molecular Biology and Biotechnology Group, Melbourne School of Land and Environment, The University of Melbourne, Parkville, VIC, 3010, Australia

7 Laboratory of Molecular Pharmacology, CCR, NCI, NIH, Bethesda, MD, 20892, USA

8 Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720-3200, USA

9 Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA

10 Department of Plant Biology, UC Davis / HHMI, Davis, CA, 95616, USA

11 Laboratory of Molecular Parasitology, The Rockefeller University, New York, NY, 10065, USA

12 Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA

13 Laboratoire de Biologie Moléculaire et Cellulaire de la Différenciation, Institut Albert Bonniot, INSERM/UJF U821, Grenoble, France

14 Department of Biochemistry, University of Goettingen, Goettingen, D-37073, Germany

15 Department of Cellular and Molecular Biology, University of A Coruna, A Coruna, E15071, Spain

16 Department of Biology, University of Rochester, Rochester, NY 14627, USA

17 Center for Integrated Protein Science Munich at the Adolf-Butenandt Institute, Department for Molecular Biology, Ludwig-Maximilians-University Munich, Munich, 80336, Germany

18 Department of Molecular Biology and Biochemistry, University of CA, Irvine, CA, 92697, USA

19 Howard Hughes Medical Institute, Department of Molecular Cellular and Developmental Biology, University of California, Los Angeles, CA, 9009, USA

20 Max Planck Institute for Immunbiology and Epigenetics, Freiburg, 79108, Germany

21 INSERM, U823; Université Joseph Fourier - Grenoble 1, La Tronche, F-38706, France

22 Department of Physiological Chemistry, Butenandt Institute and Biomedical Center, Ludwig Maximilians University of Munich, Munich, 81377, Germany

23 National Center for Biotechnology Information, National institutes of Health, Bethesda, MD, 20894, USA

24 CGphiMC - CNRS UMR5534, Claude Bernard University Lyon1 - University of Lyon, Villeurbanne, 69622 Cedex, France

25 Program in Molecular Biology and Biotechnology, University of North Carolina, Chapel Hill, NC, 27599, USA

26 Department of Animal Biology, University of Pennsylvania, Philadelphia, PA, 19104-6046, USA

27 HELIOS Medical Centre Wuppertal, Paediatrics Centre, Witten/Herdecke University, Wuppertal, D-42283, Germany

28 Institut de Genetique et Biologie Moleculaire et Cellulaire, Illkirch, 67404, France

29 Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, 22908, USA

30 Sars International Center for Marine Molecular Biology and Department of Biology, University of Bergen, Bergen, N-5008, Norway

31 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

32 The John Curtin School of Medical Research, Genome Biology Department, The Australian National University, Canberra, ACT 2601, Australia

33 College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK

34 Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, 64110, USA

35 Chromatin Lab, National Institute of Biological Sciences, Beijing, Beijing, 102206, China

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Epigenetics & Chromatin 2012, 5:7  doi:10.1186/1756-8935-5-7

Published: 31 May 2012

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.