Project description:Membraneless pericentromeric heterochromatin (PCH) domains play vital roles in chromosome dynamics and genome stability. However, our current understanding of 3D genome organization does not include PCH domains because of technical challenges associated with repetitive sequences enriched in PCH genomic regions. We investigated the 3D architecture of Drosophila melanogaster PCH domains and their spatial associations with the euchromatic genome by developing a novel analysis method that incorporates genome-wide Hi-C reads originating from PCH DNA. Combined with cytogenetic analysis, we reveal a hierarchical organization of the PCH domains into distinct "territories." Strikingly, H3K9me2-enriched regions embedded in the euchromatic genome show prevalent 3D interactions with the PCH domain. These spatial contacts require H3K9me2 enrichment, are likely mediated by liquid-liquid phase separation, and may influence organismal fitness. Our findings have important implications for how PCH architecture influences the function and evolution of both repetitive heterochromatin and the gene-rich euchromatin.
Project description:We study the 3D conformation of euchromatic regions enriched with suppressive H3K9me2 epigenetic marks Overall design: We performed ChIP-seq targeting H3K9me2 at 16-18hr Drosophila melanogaster embryos. Five genotypes were assayed and each genotype has two replicates of IP. IP samples, along with their corresponding INPUT, were sequenced with Illumina Hiseq4000
Project description:Anisotropy is a key factor regarding mechanical or transport properties and thus the functionality of porous materials. However, the ability to deliberately design the pore structure of hierarchically organized porous networks toward anisotropic features is limited. Here, we report two straightforward routes toward hierarchically structured porous carbon monoliths with an anisotropic alignment of the microstructure on the level of macro- and mesopores. One approach is based on nanocasting (NC) of carbon precursors into hierarchical and anisotropic silica hard templates. The second route, a direct synthesis approach based on soft templating (ST), makes use of the flexibility of hierarchically structured resorcinol-formaldehyde gels, which are compressed and simultaneously carbonized in the deformed state. We present structural data of both types of carbon monoliths obtained by electron microscopy, nitrogen adsorption analysis, and SAXS measurements. In addition, we demonstrate how the degree of anisotropy can easily be controlled via the ST route.
Project description:Advances in materials synthesis bring about many opportunities for technological applications, but are often accompanied by unprecedented complexity. This is clearly illustrated by the case of hierarchically organized zeolite catalysts, a class of crystalline microporous solids that has been revolutionized by the engineering of multilevel pore architectures, which combine unique chemical functionality with efficient molecular transport. Three key attributes, the crystal, the pore and the active site structure, can be expected to dominate the design process. This review examines the adequacy of the palette of techniques applied to characterize these distinguishing features and their catalytic impact.
Project description:Constitutive heterochromatin is enriched in repetitive sequences and histone H3-methylated-at-lysine 9. Both components contribute to heterochromatin's ability to silence euchromatic genes. However, heterochromatin also harbors hundreds of expressed genes in organisms such as Drosophila. Recent studies have provided a detailed picture of sequence organization of D. melanogaster heterochromatin, but how histone modifications are associated with heterochromatic sequences at high resolution has not been described. Here, distributions of modified histones in the vicinity of heterochromatic genes of normal embryos and embryos homozygous for a chromosome rearrangement were characterized using chromatin immunoprecipitation and genome tiling arrays. We found that H3-di-methylated-at-lysine 9 (H3K9me2) was depleted at the 5' ends but enriched throughout transcribed regions of heterochromatic genes. The profile was distinct from that of euchromatic genes and suggests that heterochromatic genes are integrated into, rather than insulated from, the H3K9me2-enriched domain. Moreover, the profile was only subtly affected by a Su(var)3-9 null mutation, implicating a histone methyltransferase other than SU(VAR)3-9 as responsible for most H3K9me2 associated with heterochromatic genes in embryos. On a chromosomal scale, we observed a sharp transition to the H3K9me2 domain, which coincided with increased retrotransposon density in the euchromatin-heterochromatin (eu-het) transition zones on the long chromosome arms. Thus, a certain density of retrotransposons, rather than specific boundary elements, may demarcate Drosophila pericentric heterochromatin. We also demonstrate that a chromosome rearrangement that created a new eu-het junction altered H3K9me2 distribution and induced new euchromatic sites of enrichment as far as several megabases away from the breakpoint. Taken together, the findings argue against simple classification of H3K9me as the definitive signature of silenced genes, and clarify roles of histone modifications and repetitive DNAs in heterochromatin. The results are also relevant for understanding the effects of chromosome aberrations and the megabase scale over which epigenetic position effects can operate in multicellular organisms.
Project description:The brain recruits neuronal populations in a temporally coordinated manner in task and at rest. However, the extent to which large-scale networks exhibit their own organized temporal dynamics is unclear. We use an approach designed to find repeating network patterns in whole-brain resting fMRI data, where networks are defined as graphs of interacting brain areas. We find that the transitions between networks are nonrandom, with certain networks more likely to occur after others. Further, this nonrandom sequencing is itself hierarchically organized, revealing two distinct sets of networks, or metastates, that the brain has a tendency to cycle within. One metastate is associated with sensory and motor regions, and the other involves areas related to higher order cognition. Moreover, we find that the proportion of time that a subject spends in each brain network and metastate is a consistent subject-specific measure, is heritable, and shows a significant relationship with cognitive traits.
Project description:We aim to investigate the spatial contacts between heterochromatin domain and the euchromatic genome. We found that euchromatic transposable elements, which are usually associated with H3K9me2 enrichment, are in 3D contacts with the main heterochromatin domain Overall design: genomic DNA sequencing of Drosophila melanogaster Oregon-R w1118
Project description:BACKGROUND: Chromosome banding is widely used in cytogenetics. However, the biological nature of hierarchically organized splitting of chromosomal bands of human chromosomes is an enigma and has not been, as yet, studied. RESULTS: Here we present for the first time the hierarchically organized splitting of chromosomal bands in their sub-bands for all human chromosomes. To do this, array-proved multicolor banding (aMCB) probe-sets for all human chromosomes were applied to normal metaphase spreads of three different G-band levels. We confirmed for all chromosomes to be a general principle that only Giemsa-dark bands split into dark and light sub-bands, as we demonstrated previously by chromosome stretching. Thus, the biological band splitting is in > 50% of the sub-bands different than implemented by the ISCN nomenclature suggesting also a splitting of G-light bands. Locus-specific probes exemplary confirmed the results of MCB. CONCLUSION: Overall, the present study enables a better understanding of chromosome architecture. The observed difference of biological and ISCN band-splitting may be an explanation why mapping data from human genome project do not always fit the cytogenetic mapping.
Project description:Structural hierarchy, porosity, and isotropy/anisotropy are highly relevant factors for mechanical properties and thereby the functionality of porous materials. However, even though anisotropic and hierarchically organized, porous materials are well known in nature, such as bone or wood, producing the synthetic counterparts in the laboratory is difficult. We report for the first time a straightforward combination of sol-gel processing and shear-induced alignment to create hierarchical silica monoliths exhibiting anisotropy on the levels of both, meso- and macropores. The resulting material consists of an anisotropic macroporous network of struts comprising 2D hexagonally organized cylindrical mesopores. While the anisotropy of the mesopores is an inherent feature of the pores formed by liquid crystal templating, the anisotropy of the macropores is induced by shearing of the network. Scanning electron microscopy and small-angle X-ray scattering show that the majority of network forming struts is oriented towards the shearing direction; a quantitative analysis of scattering data confirms that roughly 40% of the strut volume exhibits a preferred orientation. The anisotropy of the material's macroporosity is also reflected in its mechanical properties; i.e., the Young's modulus differs by nearly a factor of 2 between the directions of shear application and perpendicular to it. Unexpectedly, the adsorption-induced strain of the material exhibits little to no anisotropy.