Cohesin Loss Eliminates All Loop Domains.

The human genome folds to create thousands of intervals, called "contact domains," that exhibit enhanced contact frequency within themselves. "Loop domains" form because of tethering between two loci-almost always bound by CTCF and cohesin-lying on the same chromosome. "Compartment domains" form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.

Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity.

Higher-order chromatin structure and DNA methylation are implicated in multiple developmental processes, but their relationship to cell state is unknown. Here, we find that large (>7.3 kb) DNA methylation nadirs (termed "grand canyons") can form long loops connecting anchor loci that may be dozens of megabases (Mb) apart, as well as inter-chromosomal links. The interacting loci cover a total of ∼3.5 Mb of the human genome. The strongest interactions are associated with repressive marks made by the Polycomb complex and are diminished upon EZH2 inhibitor treatment. The data are suggestive of the formation of these loops by interactions between repressive elements in the loci, forming a genomic subcompartment, rather than by cohesion/CTCF-mediated extrusion. Interestingly, unlike previously characterized subcompartments, these interactions are present only in particular cell types, such as stem and progenitor cells. Our work reveals that H3K27me3-marked large DNA methylation grand canyons represent a set of very-long-range loops associated with cellular identity.

Somatic structural variant formation is guided by and influences genome architecture.

The occurrence and formation of genomic structural variants (SVs) is known to be influenced by the 3D chromatin architecture, but the extent and magnitude have been challenging to study. Here, we apply Hi-C to study chromatin organization before and after induction of chromothripsis in human cells. We use Hi-C to manually assemble the derivative chromosomes following the occurrence of massive complex rearrangements, which allows us to study the sources of SV formation and their consequences on gene regulation. We observe an action-reaction interplay whereby the 3D chromatin architecture directly impacts the location and formation of SVs. In turn, the SVs reshape the chromatin organization to alter the local topologies, replication timing, and gene regulation in cis We show that SVs have a strong tendency to occur between similar chromatin compartments and replication timing regions. Moreover, we find that SVs frequently occur at 3D loop anchors, that SVs can cause a switch in chromatin compartments and replication timing, and that this is a major source of SV-mediated effects on nearby gene expression changes. Finally, we provide evidence for a general mechanistic bias of the 3D chromatin on SV occurrence using data from more than 2700 patient-derived cancer genomes.

Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice.

Warming climate and increasing desertification urge the identification of genes involved in heat and dehydration tolerance to better inform and target biodiversity conservation efforts. Comparisons among extant desert-adapted species can highlight parallel or convergent patterns of genome evolution through the identification of shared signatures of selection. We generate a chromosome-level genome assembly for the canyon mouse (Peromyscus crinitus) and test for a signature of parallel evolution by comparing signatures of selective sweeps across population-level genomic resequencing data from another congeneric desert specialist (Peromyscus eremicus) and a widely distributed habitat generalist (Peromyscus maniculatus), that may be locally adapted to arid conditions. We identify few shared candidate loci involved in desert adaptation and do not find support for a shared pattern of parallel evolution. Instead, we hypothesize divergent molecular mechanisms of desert adaptation among deer mice, potentially tied to species-specific historical demography, which may limit or enhance adaptation. We identify a number of candidate loci experiencing selective sweeps in the P. crinitus genome that are implicated in osmoregulation (Trypsin, Prostasin) and metabolic tuning (Kallikrein, eIF2-alpha kinase GCN2, APPL1/2), which may be important for accommodating hot and dry environmental conditions.

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes.

We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer. Combining Hi-C data and novel mathematical theorems, we show that contact domains are also not consistent with a fractal globule. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during polymer condensation leads to formation of an anisotropic "tension globule." In the other, CCCTC-binding factor (CTCF) and cohesin act together to extrude unknotted loops during interphase. Both models are consistent with the observed contact domains and with the observation that contact domains tend to form inside loops. However, the extrusion model explains a far wider array of observations, such as why loops tend not to overlap and why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The convergent rule correctly predicts the affected loops in every case. Moreover, the extrusion model accurately predicts in silico the 3D maps resulting from each experiment using only the location of CTCF-binding sites in the WT. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

Accelerated Weathering Testing (AWT) and Bacterial Biodegradation Effects on Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/Rapeseed Microfiber Biocomposites Properties.

In the context of sustainable materials, this study explores the effects of accelerated weathering testing and bacterial biodegradation on poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/rapeseed microfiber biocomposites. Accelerated weathering, simulating outdoor environmental conditions, and bacterial biodegradation, representing natural degradation processes in soil, were employed to investigate the changes in the mechanical, thermal and morphological properties of these materials during its post-production life cycle. Attention was paid to the assessment of the change of structural, mechanical and calorimetric properties of alkali and N-methylmorpholine N-oxide (NMMO)-treated rapeseed microfiber (RS)-reinforced plasticized PHBV composites before and after accelerated weathering. Results revealed that accelerated weathering led to an increase in stiffness, but a reduction in tensile strength and elongation at break, of the investigated PHBV biocomposites. Additionally, during accelerated weathering, the crystallinity of PHBV biocomposites increased, especially in the presence of RS, due to both the hydrolytic degradation of the polymer matrix and the nucleating effect of the filler. It has been observed that an increase in PHBV crystallinity, determined by DSC measurements, correlates with the intensity ratio I1225/1180 obtained from FTIR-ATR data. The treatment of RS microfibers increased the biodegradation capability of the developed PHBV composites, especially in the case of chemically untreated RS. All the developed PHBV composites demonstrated faster biodegradation in comparison to neat PHBV matrix.

Effect of Agricultural Biomass Residues on the Properties of Recycled Polypropylene/Polyethylene Composites.

The aim of the study was to assess the usefulness of agricultural biomass residues as reinforcement in recycled polymer matrices. In this study, recycled polypropylene and high-density polyethylene composites (rPPPE) filled with three types of biomass residues, sweet clover straws (SCS), buckwheat straws (BS) and rapeseed straws (RS), are presented. The effects of the fiber type and the fibers content on the rheological behavior, mechanical properties (including tensile, flexural and impact strength), thermal stability and moisture absorbance were determined, in addition to morphological analysis. It was revealed that the addition of SCS, BS or RS increased the materials' stiffness and strength. The reinforcement effect increased as the loading of the fibers was increased, especially for BS composites in the flexural test. After the moisture absorbance test, it was found that the reinforcement effect slightly increased for the composites with 10% fibers but decreases with 40% fibers. The results highlight that the selected fibers are a feasible reinforcement for recycled polyolefin blend matrices.

Visco-Elastic and Thermal Properties of Microbiologically Synthesized Polyhydroxyalkanoate Plasticized with Triethyl Citrate.

The current research is devoted to the investigation of the plasticization of polyhydroxybutyrate (PHB) and polyhydroxybutyrate-co-hydroxyvalerate (PHBV) with triethyl citrate (TEC). Three different PHB or PHBV-based systems with 10, 20, and 30 wt.% of TEC were prepared by two-roll milling. The effect of TEC on the rheological, thermal, mechanical, and calorimetric properties of the developed compression-molded PHB and PHBV-based systems was determined. It was revealed that the addition of TEC significantly influenced the melting behavior of both polyhydroxyalkanoates (PHA), reducing their melting temperatures and decreasing viscosities. It was also revealed that all the investigated systems demonstrated less than 2% weight loss until 200 °C and rapid degradation did not occur until 240-260 °C in an oxidative environment. Apart from this, a remarkable increase (ca 2.5 times) in ultimate tensile deformation εB was observed by increasing the amount of TEC in either PHB or PHBV. A concomitant, considerable drop in ultimate strength σB and modulus of elasticity E was observed. Comparatively, the plasticization efficiency of TEC was greater in the case of PHBV.

The ENCODE Uniform Analysis Pipelines.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.

The ENCODE Uniform Analysis Pipelines.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.

Characterisation of Nanoclay and Spelt Husk Microfiller-Modified Polypropylene Composites.

Current research is devoted to the investigation of spelt husk (SH) and nanoclay-modified compatibilised polypropylene (PP) binary and ternary composites for injection-moulding applications. PP composites were obtained using twin-screw extrusion. The content of mechanically milled SH microfiller with aspect ratio within 2 and 6 was fixed at 40 wt.%, whereas the amount of nanoclay functional filler in the polypropylene matrix was changed in the range from 0.5 to 5 wt.%. Nanoclay filler was introduced in the polypropylene matrix either in the form of nanoclay powder (C) or as a masterbatch (M). Regular distribution of the clay nanofiller within the polymer matrix has been observed, disregarding its form and concentration. The effects of the individual or combined addition of SH microreinforcement and nanoclay fillers on the rheological, mechanical, calorimetric, and thermal properties of the developed PP composites were investigated. It is revealed that the addition of the nanoclay fillers insignificantly influences the viscosity of both PP nanocomposites and hybrid composites with SH. Additionally, for PP nanocomposites, remarkable increases in tensile and flexural modules and strength are observed by maintaining considerable ultimate deformations, mainly in the case of M-containing systems. Concomitantly, because of the addition of the nanoclay filler, the improvement in thermal stability of PP nanocomposites and PP hybrid composites with SH is observed. As a result of SH addition, considerable increases in tensile and flexural modules are also observed. Results of the research demonstrate the potential of the use of natural materials (agricultural residues and clay minerals) for the development of PP composites with increased stiffness and thermal properties.