Faithful to the Marseille tradition: Unique and intriguing-that's how Marseillevirus packs its DNA.

Not only does Marseillevirus bear the name of the city where it was identified, it also encompasses its values and what makes Marseille a wonderful city. Marseillevirus is unique and intriguing. As such, Bryson et al. in this issue of Molecular Cell reveal how virion-associated Marseillevirus DNA is packed with nucleosomes.

Structural Basis of Heterochromatin Formation by Human HP1.

Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1ß, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin.

Atomic distribution and local structure in-situ VII from in situ neutron diffraction.

Ice polymorphs show extraordinary structural diversity depending on pressure and temperature. The behavior of hydrogen-bond disorder not only is a key ingredient for their structural diversity but also controls their physical properties. However, it has been a challenge to determine the details of the disordered structure in ice polymorphs under pressure, because of the limited observable reciprocal space and inaccuracies related to high-pressure techniques. Here, we present an elucidation of the disordered structure of ice VII, the dominant high-pressure form of water, at 2.2 GPa and 298 K, from both single-crystal and powder neutron-diffraction techniques. We reveal the three-dimensional atomic distributions from the maximum entropy method and unexpectedly find a ring-like distribution of hydrogen in contrast to the commonly accepted discrete sites. In addition, total scattering analysis at 274 K clarified the difference in the intermolecular structure from ice VIII, the ordered counterpart of ice VII, despite an identical molecular geometry. Our complementary structure analyses robustly demonstrate the unique disordered structure of ice VII. Furthermore, these findings are related to proton dynamics, which drastically vary with pressure, and will contribute to an understanding of the structural origin of anomalous physical properties of ice VII under pressures.

Anomalous hydrogen dynamics of the ice VII-VIII transition revealed by high-pressure neutron diffraction.

Above 2 GPa the phase diagram of water simplifies considerably and exhibits only two solid phases up to 60 GPa, ice VII and ice VIII. The two phases are related to each other by hydrogen ordering, with the oxygen sublattice being essentially the same. Here we present neutron diffraction data to 15 GPa which reveal that the rate of hydrogen ordering at the ice VII-VIII transition decreases strongly with pressure to reach timescales of minutes at 10 GPa. Surprisingly, the ordering process becomes more rapid again upon further compression. We show that such an unusual change in transition rate can be explained by a slowing down of the rotational dynamics of water molecules with a simultaneous increase of translational motion of hydrogen under pressure, as previously suspected. The observed cross-over in the hydrogen dynamics in ice is likely the origin of various hitherto unexplained anomalies of ice VII in the 10-15 GPa range reported by Raman spectroscopy, X-ray diffraction, and proton conductivity.

Exploring histone loading on HIV DNA reveals a dynamic nucleosome positioning between unintegrated and integrated viral genome.

The aim of the present study was to understand the biology of unintegrated HIV-1 DNA and reveal the mechanisms involved in its transcriptional silencing. We found that histones are loaded on HIV-1 DNA after its nuclear import and before its integration in the host genome. Nucleosome positioning analysis along the unintegrated and integrated viral genomes revealed major differences in nucleosome density and position. Indeed, in addition to the well-known nucleosomes Nuc0, Nuc1, and Nuc2 loaded on integrated HIV-1 DNA, we also found NucDHS, a nucleosome that covers the DNase hypersensitive site, in unintegrated viral DNA. In addition, unintegrated viral DNA-associated Nuc0 and Nuc2 were positioned slightly more to the 5' end relative to their position in integrated DNA. The presence of NucDHS in the proximal region of the long terminal repeat (LTR) promoter was associated with the absence of RNAPII and of the active histone marks H3K4me3 and H3ac at the LTR. Conversely, analysis of integrated HIV-1 DNA showed a loss of NucDHS, loading of RNAPII, and enrichment in active histone marks within the LTR. We propose that unintegrated HIV-1 DNA adopts a repressive chromatin structure that competes with the transcription machinery, leading to its silencing.

H3K14 ubiquitylation promotes H3K9 methylation for heterochromatin assembly.

The methylation of histone H3 at lysine 9 (H3K9me), performed by the methyltransferase Clr4/SUV39H, is a key event in heterochromatin assembly. In fission yeast, Clr4, together with the ubiquitin E3 ligase Cul4, forms the Clr4 methyltransferase complex (CLRC), whose physiological targets and biological role are currently unclear. Here, we show that CLRC-dependent H3 ubiquitylation regulates Clr4's methyltransferase activity. Affinity-purified CLRC ubiquitylates histone H3, and mass spectrometric and mutation analyses reveal that H3 lysine 14 (H3K14) is the preferred target of the complex. Chromatin immunoprecipitation analysis shows that H3K14 ubiquitylation (H3K14ub) is closely associated with H3K9me-enriched chromatin. Notably, the CLRC-mediated H3 ubiquitylation promotes H3K9me by Clr4, suggesting that H3 ubiquitylation is intimately linked to the establishment and/or maintenance of H3K9me. These findings demonstrate a cross-talk mechanism between histone ubiquitylation and methylation that is involved in heterochromatin assembly.

Observation of Dihydrogen Bonds in High-Pressure Phases of Ammonia Borane by X-ray and Neutron Diffraction Measurements.

High-pressure X-ray and neutron diffraction analyses of an ambient-pressure phase (AP) and two high-pressure phases (HP1 and HP2) of ammonia borane (i.e., NH3BH3 and ND3BD3) were conducted to investigate the relationship between their crystal structures and dihydrogen bonds. It was confirmed that the hydrogen atoms in AP formed dihydrogen bonds between adjacent molecules, and the H-H distance between the hydrogen atoms forming this interaction was shorter than 2.4 Å, which was nearly 2 times larger than the van der Waals radius of hydrogen. In the case of half of the hydrogen bonds, a phase transition from AP to the first high-pressure phase (HP1) at ∼1.2 GPa resulted in an increase in the H-H distances, which suggested that the dihydrogen bonds were broken. However, when HP1 was further pressurized to ∼4 GPa, all of the H-H distances became shorter than 2.4 Å again, which implied the occurrence of pressure-induced re-formation of the dihydrogen bonds. It was speculated that the re-formation was consistent with a second-order phase transition suggested in previous studies by Raman spectroscopy and X-ray diffraction measurement. Furthermore, at ∼11 GPa, HP1 transformed to the second high-pressure phase (HP2), and its structure was determined to be P21 (Z = 2). In this phase transition, the inclination of the molecule axis became larger, and the number of types of dihydrogen bonds increased from 6 to 11. At 18.9 GPa, which was close to the upper pressure limit of HP2, the shortest dihydrogen bond decreased to ∼1.65 Å. Additionally, the X-ray diffraction results suggested another phase transition to the third high-pressure phase (HP3) at ∼20 GPa. The outcomes of this study confirmed experimentally for the first time that the structural change under pressure causes the breakage and re-formation of the dihydrogen bonds of NH3BH3.

Structure refinement of black phosphorus under high pressure.

The structure refinement of black phosphorus was performed at pressures of up to 3.2 GPa at room temperature by powder neutron diffraction techniques. The bond lengths and bond angles between the phosphorus atoms at pressures were precisely determined and confirmed to be consistent with those of the previous single crystal x-ray analysis [A. Brown and S. Rundqvist, Acta Cryst. 19, 684 (1965)]. Although the lattice parameters exhibited an anisotropic compressibility, the covalent P1-P2 and P1-P3 bond lengths were almost independent of pressure and only the P3-P1-P2 bond angle was reduced significantly. On the basis of our results, the significant discrepancy in the bond length reported by Cartz et al. [J. Chem. Phys. 71, 1718 (1979)] has been resolved. Our structural data will contribute to the elucidation of the Dirac semimetal state of black phosphorus under high pressure.

SYCP3 regulates strand invasion activities of RAD51 and DMC1.

The synaptonemal complex is a higher-ordered proteinaceous architecture formed between homologous chromosomes. SYCP3 is a major component of the lateral/axial elements in the synaptonemal complex and is essential for meiotic recombination. Previous genetic studies showed that SYCP3 functions in meiotic homologous recombination biased to interhomologous chromosomes, by regulating the strand invasion activities of the RAD51 and DMC1 recombinases. However, the mechanism by which SYCP3 regulates RAD51- and DMC1-mediated strand invasion remains elusive. In this study, we found that SYCP3 significantly suppresses the RAD51-mediated, but not the DMC1-mediated, strand invasion reaction by competing with HOP2-MND1, which is an activator for both RAD51 and DMC1. A SYCP3 mutant with defective RAD51 binding does not inhibit the RAD51-mediated homologous recombination in human cells. Therefore, SYCP3 may promote the DMC1-driven homologous recombination by attenuating the RAD51 activity during meiosis.

Xeroderma pigmentosum group C protein interacts with histones: regulation by acetylated states of histone H3.

In the mammalian global genome nucleotide excision repair pathway, two damage recognition factors, XPC and UV-DDB, play pivotal roles in the initiation of the repair reaction. However, the molecular mechanisms underlying regulation of the lesion recognition process in the context of chromatin structures remain to be understood. Here, we show evidence that damage recognition factors tend to associate with chromatin regions devoid of certain types of acetylated histones. Treatment of cells with histone deacetylase inhibitors retarded recruitment of XPC to sites of UV-induced DNA damage and the subsequent repair process. Biochemical studies showed novel multifaceted interactions of XPC with histone H3, which were profoundly impaired by deletion of the N-terminal tail of histone H3. In addition, histone H1 also interacted with XPC. Importantly, acetylation of histone H3 markedly attenuated the interaction with XPC in vitro, and local UV irradiation of cells decreased the level of H3K27ac in the damaged areas. Our results suggest that histone deacetylation plays a significant role in the process of DNA damage recognition for nucleotide excision repair and that the localization and functions of XPC can be regulated by acetylated states of histones.

Energy level diagram of HC(NH2)2PbI3 single crystal evaluated by electrical and optical analyses.

Recently, organic-inorganic halide perovskites have received attention for applications in solar cells. Measurements of high-quality single crystals reveal lower defect densities and longer carrier lifetimes than those of conventional thin films, which result in improved electrical and optical properties. However, single crystal surfaces are sensitive to exposure to ambient conditions, and degrade under long-term storage in air. The surface also shows differences from the bulk in terms of its optical and electronic characteristics. For a heterojunction device, the interface at the single crystal is important. Understanding the difference between the surface and bulk properties offers insights into device design. Here, we prepared non-sliced and sliced formamidinium lead iodide (FAPbI3; FA+ = HC(NH2)2+) single crystals with a bandgap of 1.4 eV, which matches well with the requirements for solar cell photoabsorption layers. We evaluate the energy level diagrams of the surface and bulk regions, respectively. Our data indicate that the valence band maximum of the surface region is at a higher energy level than that of the bulk region. We also discuss hypotheses for the well-known and unexplained phenomena (multiple bandgaps and bandgap narrowing) seen in the absorption and photoluminescence spectra of single crystals. We conclude that these effects are likely caused by a combination of the degraded surface, Rashba-splitting in bulk, and self-absorption by the single crystal itself.

Behavior of intermolecular interactions in α-glycine under high pressure.

Pressure-response on the crystal structure of deuterated α-glycine was investigated at room temperature, using powder and single-crystal X-ray diffraction, and powder neutron diffraction measurements under high pressure. No phase change was observed up to 8.7 GPa, although anisotropy of the lattice compressibility was found. No significant changes in the compressibility and the intramolecular distance between non-deuterated α-glycine and deuterated α-glycine were observed. Neutron diffraction measurements indicated the distance of the intermolecular D⋯O bond along with the c-axis increased with compression up to 6.4 GPa. The distance of another D⋯O bond along with the a-axis decreased with increasing pressure and became the shortest intermolecular hydrogen bond above 3 GPa. In contrast, the lengths of the bifurcated N-D⋯O and C-D⋯O hydrogen bonds, which are formed between the layers of the α-glycine molecules along the b-axis, decreased significantly with increasing pressure. The decrease of the intermolecular distances resulted in the largest compressibility of the b-axis, compared to the other two axes. The Hirshfeld analysis suggested that the reduction of the void region size, rather than shrinkage of the strong N-D⋯O hydrogen bonds, occurred with compression.

Structure and function of human histone H3.Y nucleosome.

Histone H3.Y is a primate-specific, distant H3 variant. It is evolutionarily derived from H3.3, and may function in transcription regulation. However, the mechanism by which H3.Y regulates transcription has not been elucidated. In the present study, we determined the crystal structure of the H3.Y nucleosome, and found that many H3.Y-specific residues are located on the entry/exit sites of the nucleosome. Biochemical analyses revealed that the DNA ends of the H3.Y nucleosome were more flexible than those of the H3.3 nucleosome, although the H3.Y nucleosome was stable in vitro and in vivo Interestingly, the linker histone H1, which compacts nucleosomal DNA, appears to bind to the H3.Y nucleosome less efficiently, as compared to the H3.3 nucleosome. These characteristics of the H3.Y nucleosome are also conserved in the H3.Y/H3.3 heterotypic nucleosome, which may be the predominant form in cells. In human cells, H3.Y preferentially accumulated around transcription start sites (TSSs). Taken together, H3.Y-containing nucleosomes around transcription start sites may form relaxed chromatin that allows transcription factor access, to regulate the transcription status of specific genes.

Bivalent interaction of the PZP domain of BRPF1 with the nucleosome impacts chromatin dynamics and acetylation.

BRPF1 (bromodomain PHD finger 1) is a core subunit of the MOZ histone acetyltransferase (HAT) complex, critical for normal developmental programs and implicated in acute leukemias. BRPF1 contains a unique assembly of zinc fingers, termed a PZP domain, the physiological role of which remains unclear. Here, we elucidate the structure-function relationship of this novel epigenetic reader and detail the biological and mechanistic consequences of its interaction with nucleosomes. PZP has a globular architecture and forms a 2:1 stoichiometry complex with the nucleosome, bivalently interacting with histone H3 and DNA. This binding impacts the nucleosome dynamics, shifting the DNA unwrapping/rewrapping equilibrium toward the unwrapped state and increasing DNA accessibility. We demonstrate that the DNA-binding function of the BRPF1 PZP domain is required for the MOZ-BRPF1-ING5-hEaf6 HAT complex to be recruited to chromatin and to acetylate nucleosomal histones. Our findings reveal a novel link between chromatin dynamics and MOZ-mediated acetylation.

Relaxed Chromatin Formation and Weak Suppression of Homologous Pairing by the Testis-Specific Linker Histone H1T.

Linker histones bind to nucleosomes and compact polynucleosomes into a higher-order chromatin configuration. Somatic and germ cell-specific linker histone subtypes have been identified and may have distinct functions. In this study, we reconstituted polynucleosomes containing human histones H1.2 and H1T, as representative somatic and germ cell-specific linker histones, respectively, and found that H1T forms less compacted chromatin, as compared to H1.2. An in vitro homologous pairing assay revealed that H1T weakly inhibited RAD51/RAD54-mediated homologous pairing in chromatin, although the somatic H1 subtypes, H1.0, H1.1, H1.2, H1.3, H1.4, and H1.5, substantially suppressed it. An in vivo recombination assay revealed that H1T overproduction minimally affected the recombination frequency, but significant suppression was observed when H1.2 was overproduced in human cells. These results suggested that the testis-specific linker histone, H1T, possesses a specific function to produce the chromatin architecture required for proper chromosome regulation, such as homologous recombination.

hCAS/CSE1L regulates RAD51 distribution and focus formation for homologous recombinational repair.

Homologous recombinational repair (HR) is one of the major repair systems for DNA double-strand breaks. RAD51 is a key molecule in HR, and the RAD51 concentration in the cell nucleus increases after DNA damage induction. However, the mechanism that regulates the intracellular distribution of RAD51 is still unclear. Here, we show that hCAS/CSE1L associates with RAD51 in human cells. We found that hCAS/CSE1L negatively regulates the nuclear protein level of RAD51 under normal conditions. hCAS/CSE1L is also required to repress the DNA damage-induced focus formation of RAD51. Moreover, we show that hCAS/CSE1L plays roles in the regulation of the HR activity and in chromosome stability. These findings suggest that hCAS/CSE1L is responsible for controlling the HR activity by directly interacting with RAD51.

N-terminal phosphorylation of HP1α increases its nucleosome-binding specificity.

Heterochromatin protein 1 (HP1) is an evolutionarily conserved chromosomal protein that binds to lysine 9-methylated histone H3 (H3K9me), a hallmark of heterochromatin. Although HP1 phosphorylation has been described in several organisms, the biological implications of this modification remain largely elusive. Here we show that HP1's phosphorylation has a critical effect on its nucleosome binding properties. By in vitro phosphorylation assays and conventional chromatography, we demonstrated that casein kinase II (CK2) is the kinase primarily responsible for phosphorylating the N-terminus of human HP1α. Pull-down assays using in vitro-reconstituted nucleosomes showed that unmodified HP1α bound H3K9-methylated and H3K9-unmethylated nucleosomes with comparable affinity, whereas CK2-phosphorylated HP1α showed a high specificity for H3K9me3-modified nucleosomes. Electrophoretic mobility shift assays showed that CK2-mediated phosphorylation diminished HP1α's intrinsic DNA binding, which contributed to its H3K9me-independent nucleosome binding. CK2-mediated phosphorylation had a similar effect on the nucleosome-binding specificity of fly HP1a and S. pombe Swi6. These results suggested that HP1 phosphorylation has an evolutionarily conserved role in HP1's recognition of H3K9me-marked nucleosomes.

Hydrogen bond symmetrisation in D2O ice observed by neutron diffraction.

Hydrogen bond symmetrisation is the phenomenon where a hydrogen atom is located at the centre of a hydrogen bond. Theoretical studies predict that hydrogen bonds in ice VII eventually undergo symmetrisation upon increasing pressure, involving nuclear quantum effect with significant isotope effect and drastic changes in the elastic properties through several intermediate states with varying hydrogen distribution. Despite numerous experimental studies conducted, the location of hydrogen and hence the transition pressures reported up to date remain inconsistent. Here we report the atomic distribution of deuterium in D2O ice using neutron diffraction above 100 GPa and observe the transition from a bimodal to a unimodal distribution of deuterium at around 80 GPa. At the transition pressure, a significant narrowing of the peak widths of 110 is also observed, attributed to the structural relaxation by the change of elastic properties.

Slightly Hydrogen-Ordered State of Ice IV Evidenced by In Situ Neutron Diffraction.

Ice IV is a metastable high-pressure phase of ice in which the water molecules exhibit orientational disorder. Although orientational ordering is commonly observed for other ice phases, it has not been reported for ice IV. We conducted in situ powder neutron diffraction experiments for DCl-doped D2O ice IV to investigate its hydrogen ordering. We found abrupt changes in the temperature derivative of unit-cell volume, dV/dT, at ∼120 K, and revealed a slightly ordered structure at low temperatures based on the Rietveld method. The occupancy of the D1 site deviates from 0.5 in particular; it increased when samples were cooled at higher pressures and reached 0.174(14) at 2.38 GPa, 58 K. Our results evidence the presence of a low-symmetry hydrogen-ordered state corresponding to ice IV. It seems, however, difficult to experimentally access the completely ordered phase corresponding to ice IV by slow cooling at high pressure.