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A unified phylogeny-based nomenclature for histone variants

Paul Talbert 1 Kami Ahmad 2 Geneviève Almouzni 3 Juan Ausió 4 Frederic Berger 5 Prem Bhalla 6 William Bonner 7 Zacheus Cande 8 Brian Chadwick 9 Simon Chan 10 George Cross 11 Liwang Cui 12 Stefan Dimitrov 13 Detlef Doenecke 14 José Eirin-López 15 Martin Gorovsky 16 Sandra Hake 17 Barbara Hamkalo 18 Sarah Holec 5 Steven Jacobsen 19 Kinga Kamieniarz 20 Saadi Khochbin 21 Andreas Ladurner 22 David Landsman 23 John Latham 1 Benjamin Loppin 24 Harmit Malik 1 William Marzluff 25 John Pehrson 26 Jan Postberg 27 Robert Schneider 20, 28 Mohan Singh 6 Mitchell Smith 29 Eric Thompson 30 Maria-Elena Torres-Padilla 28 David Tremethick 31 Bryan Turner 32 Jakob Waterborg 33 Heike Wollmann 5 Ramesh Yelagandula 5 Bing Zhu 34 Steven Henikoff 1, *
* Corresponding author
1 Basic Sciences Division
2 DBCMP - Department of Biological Chemistry and Molecular Pharmacology
3 DNPG - Dynamique nucléaire et plasticité du génome
4 Department of Biochemistry and Microbiology
5 Temasek Lifesciences Laboratory
6 Plant Molecular Biology and Biotechnology Group
7 Laboratory of Molecular Pharmacology
8 Department of Molecular & Cell Biology [Berkeley]
9 Department of Biological Science
10 Department of Plant Biology
11 Laboratory of Molecular Parasitology
12 Department of Entomology
13 INSERM U823, équipe 4 (Chromatine et Epigénétique)
INSERM U823 - Institut d'oncologie/développement Albert Bonniot de Grenoble
14 Department of Biochemistry
15 Department of Cellular and Molecular Biology
16 Department of Biology
17 CIPSM - Center for Integrated Protein Science
18 Department of Molecular Biology and Biochemistry
19 Department of Molecular Cellular and Developmental Biology
20 MPI-IE - Max Planck Institute of Immunobiology and Epigenetics
21 INSERM U823, équipe 6 (Epigénétique et Signalisation Cellulaire)
INSERM U823 - Institut d'oncologie/développement Albert Bonniot de Grenoble
22 Department of Physiological Chemistry
23 NCBI - National Center for Biotechnology Information
24 CGPhiMC - Centre de génétique et de physiologie moléculaire et cellulaire
25 Program in Molecular Biology and Biotechnology
26 Department of Animal Biology
27 HELIOS Medical Centre Wuppertal
28 IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire
29 Department of Microbiology, Immunology, and Cancer Biology
30 BIO / UiB - Department of Biological Sciences [Bergen]
31 Genome Biology Department
32 College of Medical and Dental Sciences
33 Cell Biology and Biophysics
34 Chromatin Lab
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.
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Submitted on : Thursday, June 21, 2012 - 9:07:01 PM
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Paul Talbert, Kami Ahmad, Geneviève Almouzni, Juan Ausió, Frederic Berger, et al.. A unified phylogeny-based nomenclature for histone variants. Epigenetics & Chromatin, BioMed Central, 2012, 5 (1), pp.7. ⟨10.1186/1756-8935-5-7⟩. ⟨inserm-00710902⟩

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