The zinc-finger protein Z4 cooperates with condensin II to regulate somatic chromosome pairing and 3D chromatin organization.

Chromosome pairing constitutes an important level of genome organization, yet the mechanisms that regulate pairing in somatic cells and the impact on 3D chromatin organization are still poorly understood. Here, we address these questions in Drosophila, an organism with robust somatic pairing. In Drosophila, pairing preferentially occurs at loci consisting of numerous architectural protein binding sites (APBSs), suggesting a role of architectural proteins (APs) in pairing regulation. Amongst these, the anti-pairing function of the condensin II subunit CAP-H2 is well established. However, the factors that regulate CAP-H2 localization and action at APBSs remain largely unknown. Here, we identify two factors that control CAP-H2 occupancy at APBSs and, therefore, regulate pairing. We show that Z4, interacts with CAP-H2 and is required for its localization at APBSs. We also show that hyperosmotic cellular stress induces fast and reversible unpairing in a Z4/CAP-H2 dependent manner. Moreover, by combining the opposite effects of Z4 depletion and osmostress, we show that pairing correlates with the strength of intrachromosomal 3D interactions, such as active (A) compartment interactions, intragenic gene-loops, and polycomb (Pc)-mediated chromatin loops. Altogether, our results reveal new players in CAP-H2-mediated pairing regulation and the intimate interplay between inter-chromosomal and intra-chromosomal 3D interactions.

Large-scale analyses of the X chromosome in 2,354 infertile men discover recurrently affected genes associated with spermatogenic failure.

Although the evolutionary history of the X chromosome indicates its specialization in male fitness, its role in spermatogenesis has largely been unexplored. Currently only three X chromosome genes are considered of moderate-definitive diagnostic value. We aimed to provide a comprehensive analysis of all X chromosome-linked protein-coding genes in 2,354 azoospermic/cryptozoospermic men from four independent cohorts. Genomic data were analyzed and compared with data in normozoospermic control individuals and gnomAD. While updating the clinical significance of known genes, we propose 21 recurrently mutated genes strongly associated with and 34 moderately associated with azoospermia/cryptozoospermia not previously linked to male infertility (novel). The most frequently affected prioritized gene, RBBP7, was found mutated in ten men across all cohorts, and our functional studies in Drosophila support its role in germ stem cell maintenance. Collectively, our study represents a significant step towards the definition of the missing genetic etiology in idiopathic severe spermatogenic failure and significantly reduces the knowledge gap of X-linked genetic causes of azoospermia/cryptozoospermia contributing to the development of future diagnostic gene panels.

The embryonic linker histone dBigH1 alters the functional state of active chromatin.

Linker histones H1 are principal chromatin components, whose contribution to the epigenetic regulation of chromatin structure and function is not fully understood. In metazoa, specific linker histones are expressed in the germline, with female-specific H1s being normally retained in the early-embryo. Embryonic H1s are present while the zygotic genome is transcriptionally silent and they are replaced by somatic variants upon activation, suggesting a contribution to transcriptional silencing. Here we directly address this question by ectopically expressing dBigH1 in Drosophila S2 cells, which lack dBigH1. We show that dBigH1 binds across chromatin, replaces somatic dH1 and reduces nucleosome repeat length (NRL). Concomitantly, dBigH1 expression down-regulates gene expression by impairing RNApol II binding and histone acetylation. These effects depend on the acidic N-terminal ED-domain of dBigH1 since a truncated form lacking this domain binds across chromatin and replaces dH1 like full-length dBigH1, but it does not affect NRL either transcription. In vitro reconstitution experiments using Drosophila preblastodermic embryo extracts corroborate these results. Altogether these results suggest that the negatively charged N-terminal tail of dBigH1 alters the functional state of active chromatin compromising transcription.

Crystallographically Textured Nanomaterials Produced from the Liquid Phase Sintering of Bi xSb2- xTe3 Nanocrystal Building Blocks.

Bottom-up approaches for producing bulk nanomaterials have traditionally lacked control over the crystallographic alignment of nanograins. This limitation has prevented nanocrystal-based nanomaterials from achieving optimized performances in numerous applications. Here we demonstrate the production of nanostructured Bi xSb2- xTe3 alloys with controlled stoichiometry and crystallographic texture through proper selection of the starting building blocks and the adjustment of the nanocrystal-to-nanomaterial consolidation process. In particular, we hot pressed disk-shaped Bi xSb2- xTe3 nanocrystals and tellurium nanowires using multiple pressure and release steps at a temperature above the tellurium melting point. We explain the formation of the textured nanomaterials though a solution-reprecipitation mechanism under a uniaxial pressure. Additionally, we further demonstrate these alloys to reach unprecedented thermoelectric figures of merit, up to ZT = 1.96 at 420 K, with an average value of ZTave = 1.77 for the record material in the temperature range 320-500 K, thus potentially allowing up to 60% higher energy conversion efficiencies than commercial materials.

Supported Mn3O4 Nanosystems for Hydrogen Production through Ethanol Photoreforming.

Photoreforming promoted by metal oxide nanophotocatalysts is an attractive route for clean and sustainable hydrogen generation. In the present work, we propose for the first time the use of supported Mn3O4 nanosystems, both pure and functionalized with Au nanoparticles (NPs), for hydrogen generation by photoreforming. The target oxide systems, prepared by chemical vapor deposition (CVD) and decorated with gold NPs by radio frequency (RF) sputtering, were subjected to a thorough chemico-physical characterization and utilized for a proof-of-concept H2 generation in aqueous ethanolic solutions under simulated solar illumination. Pure Mn3O4 nanosystems yielded a constant hydrogen production rate of 10 mmol h-1 m-2 even for irradiation times up to 20 h. The introduction of Au NPs yielded a significant enhancement in photocatalytic activity, which decreased as a function of irradiation time. The main phenomena causing the Au-containing photocatalyst deactivation have been investigated by morphological and compositional analysis, providing important insights for the design of Mn3O4-based photocatalysts with improved performances.

Histone H1: Lessons from Drosophila.

Eukaryotic genomes are structured in the form of chromatin with the help of a set of five small basic proteins, the histones. Four of them are highly conserved through evolution, form the basic unit of the chromatin, the nucleosome, and have been intensively studied and are well characterized. The fifth histone, histone H1, adds to this basic structure through its interaction at the entry/exit site of DNA in the nucleosome and makes an essential contribution to the higher order folding of the chromatin fiber. Histone H1 is the less conserved histone and the less known of them. Though for long time considered as a general repressor of gene expression, recent studies in Drosophila have rejected this view and have contributed to uncover important functions on genome stability and development. Here we present some of the most recent data obtained in the Drosophila model system and discuss how the lessons learnt in these studies compare and could be applied to all other eukaryotes.

Germline-specific H1 variants: the "sexy" linker histones.

The eukaryotic genome is packed into chromatin, a nucleoprotein complex mainly formed by the interaction of DNA with the abundant basic histone proteins. The fundamental structural and functional subunit of chromatin is the nucleosome core particle, which is composed by 146 bp of DNA wrapped around an octameric protein complex formed by two copies of each core histone H2A, H2B, H3, and H4. In addition, although not an intrinsic component of the nucleosome core particle, linker histone H1 directly interacts with it in a monomeric form. Histone H1 binds nucleosomes near the exit/entry sites of linker DNA, determines nucleosome repeat length and stabilizes higher-order organization of nucleosomes into the ∼30 nm chromatin fiber. In comparison to core histones, histone H1 is less well conserved through evolution. Furthermore, histone H1 composition in metazoans is generally complex with most species containing multiple variants that play redundant as well as specific functions. In this regard, a characteristic feature is the presence of specific H1 variants that replace somatic H1s in the germline and during early embryogenesis. In this review, we summarize our current knowledge about their structural and functional properties.

Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing.

An important mechanism for gene regulation involves chromatin changes via histone modification. One such modification is histone H3 lysine 4 trimethylation (H3K4me3), which requires histone methyltranferase complexes (HMT) containing the trithorax-group (trxG) protein ASH2. Mutations in ash2 cause a variety of pattern formation defects in the Drosophila wing. We have identified genome-wide binding of ASH2 in wing imaginal discs using chromatin immunoprecipitation combined with sequencing (ChIP-Seq). Our results show that genes with functions in development and transcriptional regulation are activated by ASH2 via H3K4 trimethylation in nearby nucleosomes. We have characterized the occupancy of phosphorylated forms of RNA Polymerase II and histone marks associated with activation and repression of transcription. ASH2 occupancy correlates with phosphorylated forms of RNA Polymerase II and histone activating marks in expressed genes. Additionally, RNA Polymerase II phosphorylation on serine 5 and H3K4me3 are reduced in ash2 mutants in comparison to wild-type flies. Finally, we have identified specific motifs associated with ASH2 binding in genes that are differentially expressed in ash2 mutants. Our data suggest that recruitment of the ASH2-containing HMT complexes is context specific and points to a function of ASH2 and H3K4me3 in transcriptional pausing control.

In situ single particle characterization of the themoresponsive and co-nonsolvent behavior of PNIPAM microgels and silica@PNIPAM core-shell colloids.

Poly(N-isopropylacrylamide) (PNIPAM) microgels and PNIPAM colloidal shells attract continuous strong interest due to their thermoresponsive behavior, as their size and properties can be tuned by temperature. The direct single particle observation and characterization of pure, unlabeled PNIPAM microgels in their native aqueous environment relies on imaging techniques that operate either at interfaces or in cryogenic conditions, thus limiting the observation of their dynamic nature. Liquid Cell (Scanning) Transmission Electron Microscopy (LC-(S) TEM) imaging allows the characterization of materials and dynamic processes such as nanoparticle growth, etching, and diffusion, at nanometric resolution in liquids. Here we show that via a facile post-synthetic in situ polymer labelling step with high-contrast marker core-shell Au@SiO2 nanoparticles (NPs) it is possible to determine the full volume of PNIPAM microgels in water. The labelling allowed for the successful characterization of the thermoresponsive behavior of PNIPAM microgels and core shell silica@PNIPAM hybrid microgels, as well as the co-nonsolvency of PNIPAM in aqueous alcoholic solutions. The interplay between electron beam irradiation and PNIPAM systems in water resulted in irreversible shrinkage due to beam induced water radiolysis products, which in turn also affected the thermoresponsive behavior of PNIPAM. The addition of 2-propanol as radical scavenger improved PNIPAM stability in water under electron beam irradiation.

Splay-bend nematic phases of bent colloidal silica rods induced by polydispersity.

Liquid crystal (LC) phases are in between solids and liquids with properties of both. Nematic LCs composed of rod-like molecules or particles exhibit long-range orientational order, yielding characteristic birefringence, but they lack positional order, allowing them to flow like a liquid. This combination of properties as well as their sensitivity to external fields make nematic LCs fundamental for optical applications e.g. liquid crystal displays (LCDs). When rod-like particles become bent, spontaneous bend deformations arise in the LC, leading to geometric frustration which can be resolved by complementary twist or splay deformations forming intriguing twist-bend (NTB) and splay-bend (NSB) nematic phases. Here, we show experimentally that the elusive NSB phases can be stabilized in systems of polydisperse micron-sized bent silica rods. Our results open avenues for the realization of NTB and NSB phases of colloidal and molecular LCs.

Frequency-controlled electrophoretic mobility of a particle within a porous, hollow shell.

The unique properties of yolk-shell or rattle-type particles make them promising candidates for applications ranging from switchable photonic crystals, to catalysts, to sensors. To realize many of these applications it is important to gain control over the dynamics of the core particle independently of the shell. HYPOTHESIS: The core particle may be manipulated by an AC electric field with rich frequency-dependent behavior. EXPERIMENTS: Here, we explore the frequency-dependent dynamic electrophoretic mobility of a charged core particle within a charged, porous shell in AC electric fields both experimentally using liquid-phase electron microscopy and numerically via the finite-element method. These calculations solve the Poisson-Nernst-Planck-Stokes equations, where the core particle moves according to the hydrodynamic and electric forces acting on it. FINDINGS: In experiments the core exhibited three frequency-dependent regimes of field-driven motion: (i) parallel to the field, (ii) diffusive in a plane orthogonal to the field, and (iii) unbiased random motion. The transitions between the three observed regimes can be explained by the level of matching between the time required to establish ionic gradients in the shell and the period of the AC field. We further investigated the effect of shell porosity, ionic strength, and inner-shell radius. The former strongly impacted the core's behavior by attenuating the field inside the shell. Our results provide physical understanding on how the behavior of yolk-shell particles may be tuned, thereby enhancing their potential for use as building blocks for switchable photonic crystals.

Structural diversity in three-dimensional self-assembly of nanoplatelets by spherical confinement.

Nanoplatelets offer many possibilities to construct advanced materials due to new properties associated with their (semi)two-dimensional shapes. However, precise control of both positional and orientational order of the nanoplatelets in three dimensions, which is required to achieve emerging and collective properties, is challenging to realize. Here, we combine experiments, advanced electron tomography and computer simulations to explore the structure of supraparticles self-assembled from nanoplatelets in slowly drying emulsion droplets. We demonstrate that the rich phase behaviour of nanoplatelets, and its sensitivity to subtle changes in shape and interaction potential can be used to guide the self-assembly into a wide range of different structures, offering precise control over both orientation and position order of the nanoplatelets. Our research is expected to shed light on the design of hierarchically structured metamaterials with distinct shape- and orientation- dependent properties.

The tumour suppressor brain tumour (Brat) regulates linker histone dBigH1 expression in the Drosophila female germline and the early embryo.

Linker histones H1 are essential chromatin components that exist as multiple developmentally regulated variants. In metazoans, specific H1s are expressed during germline development in a tightly regulated manner. However, the mechanisms governing their stage-dependent expression are poorly understood. Here, we address this question in Drosophila, which encodes for a single germline-specific dBigH1 linker histone. We show that during female germline lineage differentiation, dBigH1 is expressed in germ stem cells and cystoblasts, becomes silenced during transit-amplifying (TA) cystocytes divisions to resume expression after proliferation stops and differentiation starts, when it progressively accumulates in the oocyte. We find that dBigH1 silencing during TA divisions is post-transcriptional and depends on the tumour suppressor Brain tumour (Brat), an essential RNA-binding protein that regulates mRNA translation and stability. Like other oocyte-specific variants, dBigH1 is maternally expressed during early embryogenesis until it is replaced by somatic dH1 at the maternal-to-zygotic transition (MZT). Brat also mediates dBigH1 silencing at MZT. Finally, we discuss the situation in testes, where Brat is not expressed, but dBigH1 is translationally silenced too.

In Situ Study of the Wet Chemical Etching of SiO2 and Nanoparticle@SiO2 Core-Shell Nanospheres.

The recent development of liquid cell (scanning) transmission electron microscopy (LC-(S)TEM) has opened the unique possibility of studying the chemical behavior of nanomaterials down to the nanoscale in a liquid environment. Here, we show that the chemically induced etching of three different types of silica-based silica nanoparticles can be reliably studied at the single particle level using LC-(S)TEM with a negligible effect of the electron beam, and we demonstrate this method by successfully monitoring the formation of silica-based heterogeneous yolk-shell nanostructures. By scrutinizing the influence of electron beam irradiation, we show that the cumulative electron dose on the imaging area plays a crucial role in the observed damage and needs to be considered during experimental design. Monte-Carlo simulations of the electron trajectories during LC-(S)TEM experiments allowed us to relate the cumulative electron dose to the deposited energy on the particles, which was found to significantly alter the silica network under imaging conditions of nanoparticles. We used these optimized LC-(S)TEM imaging conditions to systematically characterize the wet etching of silica and metal(oxide)-silica core-shell nanoparticles with cores of gold and iron oxide, which are representative of many other core-silica-shell systems. The LC-(S)TEM method reliably reproduced the etching patterns of Stöber, water-in-oil reverse microemulsion (WORM), and amino acid-catalyzed silica particles that were reported before in the literature. Furthermore, we directly visualized the formation of yolk-shell structures from the wet etching of Au@Stöber silica and Fe3O4@WORM silica core-shell nanospheres.

Tunability of Interactions between the Core and Shell in Rattle-Type Particles Studied with Liquid-Cell Electron Microscopy.

Yolk-shell or rattle-type particles consist of a core particle that is free to move inside a thin shell. A stable core with a fully accessible surface is of interest in fields such as catalysis and sensing. However, the stability of a charged nanoparticle core within the cavity of a charged thin shell remains largely unexplored. Liquid-cell (scanning) transmission electron microscopy is an ideal technique to probe the core-shell interactions at nanometer spatial resolution. Here, we show by means of calculations and experiments that these interactions are highly tunable. We found that in dilute solutions adding a monovalent salt led to stronger confinement of the core to the middle of the geometry. In deionized water, the Debye length κ-1 becomes comparable to the shell radius Rshell, leading to a less steep electric potential gradient and a reduced core-shell interaction, which can be detrimental to the stability of nanorattles. For a salt concentration range of 0.5-250 mM, the repulsion was relatively long-ranged due to the concave geometry of the shell. At salt concentrations of 100 and 250 mM, the core was found to move almost exclusively near the shell wall, which can be due to hydrodynamics, a secondary minimum in the interaction potential, or a combination of both. The possibility of imaging nanoparticles inside shells at high spatial resolution with liquid-cell electron microscopy makes rattle particles a powerful experimental model system to learn about nanoparticle interactions. Additionally, our results highlight the possibilities for manipulating the interactions between core and shell that could be used in future applications.

The zinc-finger proteins WOC and ROW play distinct functions within the HP1c transcription complex.

In Drosophila, the Heterochromatin Protein 1c (HP1c) forms a transcriptional complex with the zinc-finger proteins WOC and ROW, and the extraproteasomal ubiquitin receptor Dsk2. This complex localizes at promoters of active genes and it is required for transcription. The functions played by the different components of the HP1c complex are not fully understood. In this study we show that WOC and ROW are required for chromatin binding of both Dsk2 and HP1c. However, while impairing chromatin binding strongly destabilizes HP1c, it does not affect Dsk2 stability. We also show that WOC, but not ROW, is required for nuclear localization of Dsk2. Moreover, WOC and Dsk2 co-immunoprecitate upon ROW depletion. These results suggest that WOC and Dsk2 interact to form a subcomplex that mediates nuclear translocation of Dsk2. We also show that ROW mediates chromatin binding of the WOC/Dsk2 subcomplex, as well as of HP1c. Altogether these observations favor a model by which the interaction with WOC recruits Dsk2 to the HP1c complex that, in its turn, binds chromatin in a ROW-dependent manner.

Chromatin remodeling in Drosophila preblastodermic embryo extract.

Chromatin is known to undergo extensive remodeling during nuclear reprogramming. However, the factors and mechanisms involved in this remodeling are still poorly understood and current experimental approaches to study it are not best suited for molecular and genetic analyses. Here we report on the use of Drosophila preblastodermic embryo extracts (DREX) in chromatin remodeling experiments. Our results show that incubation of somatic nuclei in DREX induces changes in chromatin organization similar to those associated with nuclear reprogramming, such as rapid binding of the germline specific linker histone dBigH1 variant to somatic chromatin, heterochromatin reorganization, changes in the epigenetic state of chromatin, and nuclear lamin disassembly. These results raise the possibility of using the powerful tools of Drosophila genetics for the analysis of chromatin changes associated with this essential process.

Epigenetic mechanisms in health and disease: BCEC 2017.

The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled "Epigenetic Mechanisms in Health and Disease" was held in Barcelona, October 26-26, 2017. The 2017 BCEC was the fifth and last edition of a series of annual conferences organized as a joint effort of five leading Barcelona research institutes together with B-Debate. This edition was organized by Albert Jordan from the Molecular Biology Institute of Barcelona (IBMB-CSIC) and Marcus Bushbeck from the Josep Carreras Leukaemia Research Institute (IJC). Jordi Bernués, Marian Martínez-Balbás, and Ferran Azorín were also part of the scientific committee. In 22 talks and 51 posters, researchers presented their latest results in the fields of histone variants, epigenetic regulation, and chromatin 3D organization to an audience of around 250 participants from 16 countries. This year, a broad number of talks focused on the epigenetic causes and possible related treatments of complex diseases such as cancer. Participants at the 2017 BCEC elegantly closed the series, discussing progress made in the field of epigenetics and highlighting its role in human health and disease.

Colloidal Synthesis of CsX Nanocrystals (X = Cl, Br, I).

A facile colloidal synthesis of highly ionic cesium halide nanocrystals is reported. Colloidal nanocrystals of CsI, CsCl and CsBr with unprecedentedly small dimensions are obtained using oleylammonium halides and cesium oleate as precursors. The ease and adaptability of our method enables its universalization for the formation of other highly ionic nanocrystals.

The Germline Linker Histone dBigH1 and the Translational Regulator Bam Form a Repressor Loop Essential for Male Germ Stem Cell Differentiation.

Drosophila spermatogenesis constitutes a paradigmatic system to study maintenance, proliferation, and differentiation of adult stem cell lineages. Each Drosophila testis contains 6-12 germ stem cells (GSCs) that divide asymmetrically to produce gonialblast cells that undergo four transit-amplifying (TA) spermatogonial divisions before entering spermatocyte differentiation. Mechanisms governing these crucial transitions are not fully understood. Here, we report the essential role of the germline linker histone dBigH1 during early spermatogenesis. Our results suggest that dBigH1 is a general silencing factor that represses Bam, a key regulator of spermatogonia proliferation that is silenced in spermatocytes. Reciprocally, Bam represses dBigH1 during TA divisions. This double-repressor mechanism switches dBigH1/Bam expression from off/on in spermatogonia to on/off in spermatocytes, regulating progression into spermatocyte differentiation. dBigH1 is also required for GSC maintenance and differentiation. These results show the critical importance of germline H1s for male GSC lineage differentiation, unveiling a regulatory interaction that couples transcriptional and translational repression.