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.

The morphology of active structural and putative ribosomal RNA genes was observed by electron microscopy after lysis of fragile Escherichia coli cells. Conclusions drawn are: most of the chromosome is not genetically active at any one instant; translation is completely coupled with transcription; the 16S and 23S ribosomal RNA cistrons occur in tandem, in regions which are widely spaced on the chromosome.

Linker histones bind to the nucleosomes and linker DNA of chromatin fibers, causing changes in linker DNA structure and stabilization of higher order folded and oligomeric chromatin structures. Linker histones affect chromatin structure acting primarily through their ~100 residue C-terminal domain (CTD). We have previously shown that the ability of the linker histone H1° to alter chromatin structure was localized to two discontinuous 24-/25-residue CTD regions (Lu, X., and Hansen, J. C. (2004) J Biol Chem 279, 8701-8707). To determine the biochemical basis for these results, we have characterized chromatin model systems assembled with endogenous mouse somatic H1 isoforms, or recombinant H1° CTD mutants in which the primary sequence has been scrambled, the amino acid composition mutated, or the location of various CTD regions swapped. Our results indicate that specific amino acid composition plays a fundamental role in molecular recognition and function by the H1 CTD. Additionally, these experiments support a new molecular model for CTD function, and provide a biochemical basis for the redundancy observed in H1 isoform knockout experiments in vivo.Linker histones (e.g., H1, H5) are chromatin architectural proteins found in all eukaryotes (1, 2). They are abundant, with a stoichiometry of ~0.8 total linker histones per nucleosome in most tissues (3 and references therein). Linker histones are modularly structured proteins that have an ~35 residue unstructured N-terminal domain (NTD) 1 , a central globular winged helix domain, and an ~100 residue unstructured C-terminal domain (CTD) (4). Linker histones bind to chromatin fibers through interaction of the globular domain with nucleosomal sites(s) (1,2,5), and the CTD with linker DNA (6,7). Higher eukaryotes have at least six somatic linker histone isoforms, which differ primarily in their CTD primary sequences (1,8). The H1 isoform CTDs do, however, share a very similar and characteristic amino acid composition (9). At the molecular level, little is known about the actions of the isoforms. Linker histones are multifunctional, with roles in chromatin condensation (1,2,10,11), nucleosome spacing (12, 13), specific gene expression (13) and references therein), DNA methylation (13) and other nuclear processes. In addition to chromatin, linker histones bind to many nuclear proteins, e.g., † This work was supported by NIH grant GM45916 to JCH. *To whom correspondence should be addressed: Department of Biochemistry and Molecular Biology, Campus Delivery 1870, Colorado State University, Fort Collins, CO, 80523-1870. Tel.: 970-491-5440; Fax: 970-491-0494; E-mail: jeffrey.c The relationships between linker histones, nucleosomal arrays, and chromatin fiber structure are well documented (1,2,10). In vitro, nucleosomal arrays are in salt-dependent equilibrium between unfolded, folded, and oligomeric conformational states (10,11). Binding of linker histones to nucleosomal arrays affects chromatin structure in at least three distinct ways: the linker DNA between nucleosome...