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’ |