Centromere protein A (CENP-A) is a histone H3 variant that specifies centromere location, but the histone composition and stoichiometry of CENP-A nucleosomes have been controversial. ChIP-seq and biochemical analyses of in vitro–reconstituted CENP-A nucleosomes now demonstrate that the predominant form at functional centromeres is an octamer with loose DNA ends. The centromere is the chromosomal locus that ensures fidelity in genome transmission at cell division. Centromere protein A (CENP-A) is a histone H3 variant that specifies centromere location independently of DNA sequence. Conflicting evidence has emerged regarding the histone composition and stoichiometry of CENP-A nucleosomes. Here we show that the predominant form of the CENP-A particle at human centromeres is an octameric nucleosome. CENP-A nucleosomes are very highly phased on α-satellite 171-base-pair monomers at normal centromeres and also display strong positioning at neocentromeres. At either type of functional centromere, CENP-A nucleosomes exhibit similar DNA-wrapping behavior, as do octameric CENP-A nucleosomes reconstituted with recombinant components, having looser DNA termini than those on conventional nucleosomes containing canonical histone H3. Thus, the fundamental unit of the chromatin that epigenetically specifies centromere location in mammals is an octameric nucleosome with loose termini.

The hallmark of all eukaryotic centromeres is the presence of a histone H3 variant, CENP-A, but the nature of the epigenetic centromere mark is the subject of great debate. The crystal structure of the human CENP-A–H4 complex has now been determined. It reveals the structural basis for the rigidity that CENP-A imparts to nucleosomes, as well as several surprising global and local structural alterations that have major implications for epigenetic centromere marking. CENP-A seems to alter the chromatin into which it assembles — not by switching the handedness of DNA wrapping or disrupting the octameric histone stoichiometry, but by altering nucleosome structure. The centromeres of chromosomes are specified epigenetically, and the histone H3 variant CENP-A is assembled into the chromatin of all active centromeres. Here, the crystal structure of CENP-A in a tetrameric complex with histone H4 reveals the physical features of centromeric chromatin. CENP-A seems to mark the centromere by altering nucleosome structure from within its folded histone core. Centromeres are specified epigenetically, and the histone H3 variant CENP-A is assembled into the chromatin of all active centromeres1. Divergence from H3 raises the possibility that CENP-A generates unique chromatin features to mark physically centromere location. Here we report the crystal structure of a subnucleosomal heterotetramer, human (CENP-A–H4)2, that reveals three distinguishing properties encoded by the residues that comprise the CENP-A targeting domain (CATD; ref. 2): (1) a CENP-A–CENP-A interface that is substantially rotated relative to the H3–H3 interface; (2) a protruding loop L1 of the opposite charge as that on H3; and (3) strong hydrophobic contacts that rigidify the CENP-A–H4 interface. Residues involved in the CENP-A–CENP-A rotation are required for efficient incorporation into centromeric chromatin, indicating specificity for an unconventional nucleosome shape. DNA topological analysis indicates that CENP-A-containing nucleosomes are octameric with conventional left-handed DNA wrapping, in contrast to other recent proposals3,4,5,6. Our results indicate that CENP-A marks centromere location by restructuring the nucleosome from within its folded histone core.

Building stable centromeres: Each of our chromosomes has a single centromere, seen as a constriction during cell division, which is required for accurate chromosome segregation to daughter cells. Falk et al. show that the special histone protein known as CENP-A, which forms part of the nucleosomes at centromeres, makes the chromatin at these constrictions very stable and long-lived. This stability is conferred by a protein-binding partner, CENP-C, recruited to the centromere by the CENP-A histone. Binding of CENP-C to CENP-A–containing nucleosomes alters the behavior of the macromolecular centromere complex to help it maintain its identity Science , this issue p. 699

Here, a small core protein of human adenoviruses is shown to associate with histones, sequestering proteins on host chromatin and preventing inflammatory proteins from being released and triggering inflammation. Matthew Weitzman and colleagues reveal a previously unknown method by which a virus can subvert the host inflammatory response. They show that a small core protein of human adenoviruses associates with histones and can alter the sequestration of proteins on host chromatin. Specifically, adenovirus protein VII forms complexes with nucleosomes and leads to the retention of the inflammatory protein HMGB1 on chromatin, preventing it from being released and triggering inflammation. Viral proteins mimic host protein structure and function to redirect cellular processes and subvert innate defenses1. Small basic proteins compact and regulate both viral and cellular DNA genomes. Nucleosomes are the repeating units of cellular chromatin and play an important part in innate immune responses2. Viral-encoded core basic proteins compact viral genomes, but their impact on host chromatin structure and function remains unexplored. Adenoviruses encode a highly basic protein called protein VII that resembles cellular histones3. Although protein VII binds viral DNA and is incorporated with viral genomes into virus particles4,5, it is unknown whether protein VII affects cellular chromatin. Here we show that protein VII alters cellular chromatin, leading us to hypothesize that this has an impact on antiviral responses during adenovirus infection in human cells. We find that protein VII forms complexes with nucleosomes and limits DNA accessibility. We identified post-translational modifications on protein VII that are responsible for chromatin localization. Furthermore, proteomic analysis demonstrated that protein VII is sufficient to alter the protein composition of host chromatin. We found that protein VII is necessary and sufficient for retention in the chromatin of members of the high-mobility-group protein B family (HMGB1, HMGB2 and HMGB3). HMGB1 is actively released in response to inflammatory stimuli and functions as a danger signal to activate immune responses6,7. We showed that protein VII can directly bind HMGB1 in vitro and further demonstrated that protein VII expression in mouse lungs is sufficient to decrease inflammation-induced HMGB1 content and neutrophil recruitment in the bronchoalveolar lavage fluid. Together, our in vitro and in vivo results show that protein VII sequesters HMGB1 and can prevent its release. This study uncovers a viral strategy in which nucleosome binding is exploited to control extracellular immune signalling.