A unified phylogeny-based nomenclature for histone variants

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.

Structure of human nucleosome containing the testis-specific histone variant TSH2B

“…In addition to the canonical histones, H2A, H2B and H3 variants with production that is not restricted to the S-phase have been identified (Talbert et al, 2012). The mammalian histone H2B variant TSH2B was initially found in histone extracts from rat testes (Branson et al, 1975;Shires et al, 1975).…”

A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis

“…They are also the most variable of the histones, with numerous nonallelic variants coexisting in the same cell. In vertebrates, several evolutionarily conserved subfamilies of H1 can be distinguished (Talbert et al, 2012) and appear to play both redundant and specific roles during development and cellular differentiation (McBryant et al, 2010). There is accumulating evidence that, in animals, regulation of the proportions of H1 variants with different dynamic behavior in chromatin is involved in controlling the accessibility of DNA to trans-acting factors (Jullien et al, 2010;Shahhoseini et al, 2010;Zhang et al, 2012a;Pérez-Montero et al, 2013;Christophorou et al, 2014).…”

“…Plant H1s can be divided into ubiquitously and stably expressed major (main) variants and stress-inducible minor variants (Jerzmanowski et al, 2000;Talbert et al, 2012). The minor variants subfamily is evolutionarily conserved and ancient, since it appeared before the split into monocotyledonous and dicotyledonous plants (Jerzmanowski et al, 2000).…”

Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications

“…H2A.B, previously known as H2A.Bbd (see [76]), is the smallest and most divergent H2A variant [77,78]. This variant was initially found to be excluded from the Barr body (the inactive X chromosome in female cells) and, thus, was named as Barr body-deficient (Bbd).…”