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Table 1 Summary of nomenclature guidelines

From: A unified phylogeny-based nomenclature for histone variants

Naming feature Recommendation Examples
Core histone name Use in an inclusive sense for the protein family. Specify subgroups with a descriptor, prefix, letter suffix, or number suffix. ‘H2A can be ubiquitylated.’ ‘H3 can be methylated on K4.’
Capitalization Upper and lower case are equivalent in meaning, but upper case is preferred for designating core histones, their suffixes, and modifiable amino acids. Use lowercase for modifications and for prefixes. H3.3K4me3, H2BK123ub1, cenH3
Descriptors Descriptors can be used before the core histone name to specify a feature, group variants developmentally or functionally, indicate the species of origin, or other uses. There should be a space between the descriptor and the core histone name. There is no requirement that a descriptor specifies a clade. RC H2A, early H4, testis-specific H3.4 or TS H3.4, Hs H2A.X or human H2A.X, GC H2As, oocyte H1s
Prefixes These should be few in number and specify a structurally distinct clade of a core histone that is universal or characteristic of a high-level taxonomic clade. Lower case is preferred for prefixes. macroH2A, cenH3, subH2B
Letter suffixes These should be preceded by a period (.) and specify a structurally distinct monophyletic clade of a histone family (exception: H2A.X). A suffix may be applied judiciously at any taxon level. H2A.Z, H3.X, H2A.B
Number suffixes These should be preceded by a period (.) and specify a particular variant of a core histone, without constraint as to distinctiveness and without implication as to phylogeny. Number suffixes should be assumed to be species-specific, but it is convenient to name variants in related species consistently where unique orthologies are clear. A number suffix should be the default designation of new variants. H3.5, H2A.1, macroH2A.2, H1.0
Punctuation Use a period (.) after core histone names to indicate a subtype (letter or number suffix). Use additional periods as necessary to separate finer divisions of subtypes. A period is equivalent to a branch point in a phylogenetic tree. H2A.Z.1, H2A.L.1
Splice variants Use a period (.) before a splice variant number. Treat the same as paralog number suffixes, except that a lowercase ‘s’ may precede the number to indicate that the isoform is a splice variant. macroH2A.1.2, H2A.Z.s3
Synonyms For names changed by this nomenclature, refer to both old and new synonyms in the abstract of papers to facilitate literature searches. Optional descriptors can aid identification. ‘Avian H1.0, also known as H5’