Understanding the nomenclature for histone variants can sometimes be like deciphering an ancient language without a translation app. And as more variants are discovered without a naming convention to guide the process, the confusion just keeps growing. That’s why Steve Henikoff and the rest of the attendees of the EMBO Workshop on Histone Variants last October in Strasbourg, France decided it was time to sit down and define the rules for properly naming histone variants.
Since the first histone naming conventions were established in 1975 at the Ciba Foundation Symposium, new discoveries have outgrown that structure and a wide variety of naming styles, multiple synonyms and misleading homographs have muddied variant relationships and complicated database and literature searches. For example, the group found that a PubMed search for H2A.Z or H2A.Z* returned 269 papers on this variant, but missed 126 others using the names D2, H2Az, Htz1, H2A.F or H2A.F/Z, hv1, H2Av or H2AvD.
The EMBO group proposed 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 new nomenclature takes into account the historical usage of naming types, but also adds in phylogenetic relationships, which have strong ties to structure and function. They attendees agreed on the rules regarding several nomenclature factors including:
- Core histone name
- Letter suffixes
- Number suffixes
- Splice variants
The resulting system is a “phylogeny-based nomenclature that utilizes consistent punctuation with letter and number suffixes and (rare) prefixes to arrive at a cogent machine-searchable scheme that is based on expectation of common structure and function through orthology, but which is flexible enough to accommodate new discoveries that will emerge from genome sequencing projects in the coming years.” Hopefully, this new nomenclature set up won’t need to be revamped for at least another 40 years.
See what this histone naming thing is all about at Epigenetics & Chromatin, May 2012.