A unified phylogeny-based nomenclature for histone variants

Paul B. Talbert, Kami Ahmad, Geneviève Almouzni, Juan Ausiá, Frederic Berger, Prem L. Bhalla, William M. Bonner, W. Zacheus Cande, Brian P. Chadwick, Simon W L Chan, George A M Cross, Liwang Cui, Stefan I. Dimitrov, Detlef Doenecke, José M. Eirin-Lápez, Martin A. Gorovsky, Sandra B. Hake, Barbara A. Hamkalo, Sarah Holec, Steven E. JacobsenKinga Kamieniarz, Saadi Khochbin, Andreas G. Ladurner, David Landsman, John A. Latham, Benjamin Loppin, Harmit S. Malik, William F. Marzluff, John R. Pehrson, Jan Postberg, Robert Schneider, Mohan B. Singh, M. Mitchell Smith, Eric Thompson, Maria Elena Torres-Padilla, David John Tremethick, Bryan M. Turner, Jakob Harm Waterborg, Heike Wollmann, Ramesh Yelagandula, Bing Zhu, Steven Henikoff

Research output: Contribution to journalReview article

166 Citations (Scopus)

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.

Original languageEnglish
Article number7
JournalEpigenetics and Chromatin
Volume5
Issue number1
DOIs
Publication statusPublished - 2012
Externally publishedYes

Fingerprint

Phylogeny
Terminology
Histones
Names
Chromatin
Protein Isoforms
Databases
benzoylprop-ethyl

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Talbert, P. B., Ahmad, K., Almouzni, G., Ausiá, J., Berger, F., Bhalla, P. L., ... Henikoff, S. (2012). A unified phylogeny-based nomenclature for histone variants. Epigenetics and Chromatin, 5(1), [7]. https://doi.org/10.1186/1756-8935-5-7

A unified phylogeny-based nomenclature for histone variants. / Talbert, Paul B.; Ahmad, Kami; Almouzni, Geneviève; Ausiá, Juan; Berger, Frederic; Bhalla, Prem L.; Bonner, William M.; Cande, W. Zacheus; Chadwick, Brian P.; Chan, Simon W L; Cross, George A M; Cui, Liwang; Dimitrov, Stefan I.; Doenecke, Detlef; Eirin-Lápez, José M.; Gorovsky, Martin A.; Hake, Sandra B.; Hamkalo, Barbara A.; Holec, Sarah; Jacobsen, Steven E.; Kamieniarz, Kinga; Khochbin, Saadi; Ladurner, Andreas G.; Landsman, David; Latham, John A.; Loppin, Benjamin; Malik, Harmit S.; Marzluff, William F.; Pehrson, John R.; Postberg, Jan; Schneider, Robert; Singh, Mohan B.; Smith, M. Mitchell; Thompson, Eric; Torres-Padilla, Maria Elena; Tremethick, David John; Turner, Bryan M.; Waterborg, Jakob Harm; Wollmann, Heike; Yelagandula, Ramesh; Zhu, Bing; Henikoff, Steven.

In: Epigenetics and Chromatin, Vol. 5, No. 1, 7, 2012.

Research output: Contribution to journalReview article

Talbert, PB, Ahmad, K, Almouzni, G, Ausiá, J, Berger, F, Bhalla, PL, Bonner, WM, Cande, WZ, Chadwick, BP, Chan, SWL, Cross, GAM, Cui, L, Dimitrov, SI, Doenecke, D, Eirin-Lápez, JM, Gorovsky, MA, Hake, SB, Hamkalo, BA, Holec, S, Jacobsen, SE, Kamieniarz, K, Khochbin, S, Ladurner, AG, Landsman, D, Latham, JA, Loppin, B, Malik, HS, Marzluff, WF, Pehrson, JR, Postberg, J, Schneider, R, Singh, MB, Smith, MM, Thompson, E, Torres-Padilla, ME, Tremethick, DJ, Turner, BM, Waterborg, JH, Wollmann, H, Yelagandula, R, Zhu, B & Henikoff, S 2012, 'A unified phylogeny-based nomenclature for histone variants', Epigenetics and Chromatin, vol. 5, no. 1, 7. https://doi.org/10.1186/1756-8935-5-7
Talbert PB, Ahmad K, Almouzni G, Ausiá J, Berger F, Bhalla PL et al. A unified phylogeny-based nomenclature for histone variants. Epigenetics and Chromatin. 2012;5(1). 7. https://doi.org/10.1186/1756-8935-5-7
Talbert, Paul B. ; Ahmad, Kami ; Almouzni, Geneviève ; Ausiá, Juan ; Berger, Frederic ; Bhalla, Prem L. ; Bonner, William M. ; Cande, W. Zacheus ; Chadwick, Brian P. ; Chan, Simon W L ; Cross, George A M ; Cui, Liwang ; Dimitrov, Stefan I. ; Doenecke, Detlef ; Eirin-Lápez, José M. ; Gorovsky, Martin A. ; Hake, Sandra B. ; Hamkalo, Barbara A. ; Holec, Sarah ; Jacobsen, Steven E. ; Kamieniarz, Kinga ; Khochbin, Saadi ; Ladurner, Andreas G. ; Landsman, David ; Latham, John A. ; Loppin, Benjamin ; Malik, Harmit S. ; Marzluff, William F. ; Pehrson, John R. ; Postberg, Jan ; Schneider, Robert ; Singh, Mohan B. ; Smith, M. Mitchell ; Thompson, Eric ; Torres-Padilla, Maria Elena ; Tremethick, David John ; Turner, Bryan M. ; Waterborg, Jakob Harm ; Wollmann, Heike ; Yelagandula, Ramesh ; Zhu, Bing ; Henikoff, Steven. / A unified phylogeny-based nomenclature for histone variants. In: Epigenetics and Chromatin. 2012 ; Vol. 5, No. 1.
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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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AU - Ausiá, Juan

AU - Berger, Frederic

AU - Bhalla, Prem L.

AU - Bonner, William M.

AU - Cande, W. Zacheus

AU - Chadwick, Brian P.

AU - Chan, Simon W L

AU - Cross, George A M

AU - Cui, Liwang

AU - Dimitrov, Stefan I.

AU - Doenecke, Detlef

AU - Eirin-Lápez, José M.

AU - Gorovsky, Martin A.

AU - Hake, Sandra B.

AU - Hamkalo, Barbara A.

AU - Holec, Sarah

AU - Jacobsen, Steven E.

AU - Kamieniarz, Kinga

AU - Khochbin, Saadi

AU - Ladurner, Andreas G.

AU - Landsman, David

AU - Latham, John A.

AU - Loppin, Benjamin

AU - Malik, Harmit S.

AU - Marzluff, William F.

AU - Pehrson, John R.

AU - Postberg, Jan

AU - Schneider, Robert

AU - Singh, Mohan B.

AU - Smith, M. Mitchell

AU - Thompson, Eric

AU - Torres-Padilla, Maria Elena

AU - Tremethick, David John

AU - Turner, Bryan M.

AU - Waterborg, Jakob Harm

AU - Wollmann, Heike

AU - Yelagandula, Ramesh

AU - Zhu, Bing

AU - Henikoff, Steven

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