H1 histones: current perspectives and challenges

Published online 14 August 2013 Nucleic Acids Research, 2013, Vol. 41, No. 21 9593–9609 doi:10.1093/nar/gkt700 SURVEY AND SUMMARY H1 histones: current perspectives and challenges Sean W. Harshman1,2, Nicolas L. Young3, Mark R. Parthun2,4,* and Michael A. Freitas1,2,* 1 Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, USA, 2College of Medicine and Arthur G. James Comprehensive Cancer Center, Columbus, Ohio, USA, 3 National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA and 4Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio, USA Received March 22, 2013; Revised July 12, 2013; Accepted July 15, 2013 ABSTRACT CHROMATOSOME STRUCTURE Histones are evolutionarily conserved proteins responsible for condensation, organization and regulation of the DNA within the nucleus of all eukaryotes. The basic structural element of DNA compaction, the nucleosome core particle, is made up of superhelical DNA wrapped about a protein octamer composed of two copies of each core histone H2A, H2B, H3 and H4 (1–4). Structurally, each core histone has a long central helix with a helix-strandhelix motif on each end forming what is termed the histone fold (5). Hydrophobic interactions between two core histone monomers form heterodimers in a headto-tail configuration called the handshake motif (2–7). The heterodimers of histones H3 and H4 further associate *To whom correspondence should be addressed. Tel: +1 614 292 6215; Fax: +1 614 292 4118; Email: Correspondence may also be addressed to Michael A. Freitas. Tel: +1 614 688 8432; Fax: +1 614 688 8675; Email: ß The Author(s) 2013. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. H1 and related linker histones are important both for maintenance of higher-order chromatin structure and for the regulation of gene expression. The biology of the linker histones is complex, as they are evolutionarily variable, exist in multiple isoforms and undergo a large variety of posttranslational modifications in their long, unstructured, NH2- and COOH-terminal tails. We review recent progress in understanding the structure, genetics and posttranslational modifications of linker histones, with an emphasis on the dynamic interactions of these proteins with DNA and transcriptional regulators. We also discuss various experimental challenges to the study of H1 and related proteins, including limitations of immunological reagents and practical difficulties in the analysis of posttranslational modifications by mass spectrometry. to form tetramers (5,6). The histone octamer is assembled from two H2A–H2B dimers binding opposite the H3–H4 tetramer (7). Micrococcal nuclease digestion of chromatin exposed to increasing salt concentrations shows symmetrical association of 146 base pairs of left-handed superhelical DNA wrapped 1.65 turns around the histone octamer forming the nucleosome core particle (5,8–12). Crystallography orients the histone octamer with the H3–H4 tetramer centered between and in direct contact with the DNA entry and exit points and the H2A–H2B tetramer centered opposite. Higher-order chromatin structures are produced through the binding of a linker histone, histone H1, to the nucleosome core particle to form the chromatosome (13–16). Nucleosomal stabilization facilitated by the chromatosome is provided through the binding of histone H1 to the nucleosomal dyad and the linker DNA entering and exiting the core particle (16–26). Recent OH radical footprinting experiments show that the positioning of histone H1 at the nucleosomal dyad axis protects an additional 20 base pairs of DNA, 10 base pairs from both the entering and exiting linker DNA, from micrococcal nuclease digestion (8,10,17,25,26). Additional experimental evidence illustrates the influence of histone H1 on chromatin arrangement and compaction (14,19,27–33). However, the specific folding of the 30-nm filament remains controversial and potentially variable in nature (32). In any case, recent studies suggest histone H1 binding provides stabilization and protection through the formation of a dynamic and polymorphic linker histone/ linker DNA stem structure (25,26,30,32). Stem-to-stem interactions of neighboring nucleosomes are hypothesized to stabilize folding into higher-order chromatin fibers (26). No matter how the 30-nm chromatin fiber ultimately folds, the influence of histone H1 is dependent on its unique structural characteristics. 9594 Nucleic Acids Research, 2013, Vol. 41, No. 21 HISTONE H1 STRUCTURE HISTONE H1 GENE FAMILY The histone H1 gene family in lower organisms is less evolutionarily conserved than that of the core histones. For example, in Saccharomyces cerevisiae, the sequence homology between Hho1, the S. cerevisiae histone H1 homolog, and Homo sapien H1 is 31% identical and 44% similar, whereas histone H4 between the species is 92% identical and 96% similar. Conversely, in higherorder organisms such as the Gallus gallus (chicken), the erythrocyte linker histone, H5, shows high sequence homology (66%) to the human histone H1.0, with the greatest sequence divergence found in the CTD (56). In addition to sequence variation, histone H1 proteins also display a range of structures. For instance, S. cerevisiae Hho1p contains two globular domains, whereas Tetrahymena completely lacks a globular domain (57,58). Eukaryotes also differ in the number of histone H1 variants present. H. sapiens and Mus musculus both have 11 distinct variants, whereas Caenorhabditis elegans has eight and Xenopus laevis has five (59). The H. sapien family of histone H1 proteins contains five somatic variants (H1.1, H1.2, H1.3, H1.4 and H1.5), which are expressed in nearly all cells (60–62). Six additional H1 variants have been identified in specific tissues, such as H1t and H1T2 in the testis, or cell types, such as H1.0 Histone H1 has a tripartite structure containing an evolutionarily conserved central globular domain with flanking variable domains. X-ray crystallography of the globular domain of the avian erythrocyte linker histone H5 (considered a member of the H1 family) shows a winged-helix motif consisting of three alpha helices with a C-terminal beta hairpin (34). An antiparallel beta sheet is formed between the C-terminal beta hairpin and a short beta strand connecting the first and second alpha helices (34). Conformational studies on the globular domain of the erythrocyte linker histone show that H5 binds asymmetrically to two DNA duplexes through two clusters of highly conserved, positively charged residues on opposite sides of the globular H5 molecule (18,34). Initial positional studies of linker histone H5 on chicken (...truncated)