Contact Domain Research Articles

Контактная задача для трансверсально изотропного слоя с трением

It is investigated the spatial contact problem of asymmetric interaction of two punches on a transversally isotropic layer with friction forces taken into account in an unknown contact domain. The planes of isotropy are parallel to the layer faces. The friction forces are taken into account along one coordinate axis. The lower layer face is subjected to sliding support. The layer material is characterized by five independent elastic parameters. The problem is reduced to an integral equation with respect to the contact pressure with the help of a double Fourier transformation together with the Coulomb law. The anisotropy degree is characterized be three dimensionless parameters arising in the kernel of the integral equation, two of which satisfy characteristic equation. In particular cases, the integral equation coincides with those well-known for the corresponding contact problems with friction for the isotropic layer and half-space. The B.A. Galanov method is used for numerical solutions. A system of the integral equation and integral inequality is considered. A rectangle is taken which a priori contains the unknown contact domain. By introducing special nonlinear operators, the system is reduced to only one nonlinear equation of the Hammerstein type which can be solved by the successive approximations method. The contact domain is determined by nodes at which the function required is positive. The punches are taken in the form of asymmetric elliptic paraboloids. The method allows us to investigate percolation, i.e. the process of junction of the discrete contact domains due to increasing the forces applied and settlements of the punches. Calculations are made for different friction coefficients, materials and relative thicknesses of the transversally isotropic layer.

Cohesin-mediated 3D contacts tune enhancer-promoter regulation.

Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with the promoters of their target genes. However, genome-wide depletions of architectural proteins such as cohesin result in only limited changes in gene expression, despite a loss of contact domains and loops. Consequently, the role of cohesin and 3D contacts in enhancer function remains debated. Here, we developed CRISPRi of regulatory elements upon degron operation (CRUDO), a novel approach to measure how changes in contact frequency impact enhancer effects on target genes by perturbing enhancers with CRISPRi and measuring gene expression in the presence or absence of cohesin. We systematically perturbed all 1,039 candidate enhancers near five cohesin-dependent genes and identified 34 enhancer-gene regulatory interactions. Of 26 regulatory interactions with sufficient statistical power to evaluate cohesin dependence, 18 show cohesin-dependent effects. A decrease in enhancer-promoter contact frequency upon removal of cohesin is frequently accompanied by a decrease in the regulatory effect of the enhancer on gene expression, consistent with a contact-based model for enhancer function. However, changes in contact frequency and regulatory effects on gene expression vary as a function of distance, with distal enhancers (e.g., >50Kb) experiencing much larger changes than proximal ones (e.g., <50Kb). Because most enhancers are located close to their target genes, these observations can explain how only a small subset of genes - those with strong distal enhancers - are sensitive to cohesin. Together, our results illuminate how 3D contacts, influenced by both cohesin and genomic distance, tune enhancer effects on gene expression.

Behaviors of nucleosomes with mutant histone H4s in euchromatic domains of living human cells.

Since Robert Feulgen first stained DNA in the cell, visualizing genome chromatin has been a central issue in cell biology to uncover how chromatin is organized and behaves in the cell. To approach this issue, we have developed single-molecule imaging of nucleosomes, a basic unit of chromatin, to unveil local nucleosome behavior in living cells. In this study, we investigated behaviors of nucleosomes with various histone H4 mutants in living HeLa cells to address the role of H4 tail acetylation, including H4K16Ac and others, which are generally associated with more transcriptionally active chromatin regions. We ectopically expressed wild-type (wt) or mutated H4s (H4K16 point; H4K5,8,12,16 quadruple; and H4 tail deletion) fused with HaloTag in HeLa cells. Cells that expressed wtH4-Halo, H4K16-Halo mutants, and multiple H4-Halo mutants had euchromatin-concentrated distribution. Consistently, the genomic regions of the wtH4-Halo nucleosomes corresponded to Hi-C contact domains (or topologically associating domains, TADs)with active chromatin marks (A-compartment). Utilizing single-nucleosome imaging, we found that none of the H4 deacetylation or acetylation mimicked H4 mutants altered the overall local nucleosome motion. This finding suggests that H4 mutant nucleosomes embedded in the condensed euchromatic domains with excess endogenous H4 nucleosomes cannot cause an observable change in the local motion. Interestingly, H4 with four lysine-to-arginine mutations displayed a substantial freely diffusing fraction in the nucleoplasm, whereas H4 with a truncated N-terminal tail was incorporated in heterochromatic regions as well as euchromatin. Our study indicates the power of single-nucleosome imaging to understand individual histone/nucleosome behavior reflecting chromatin environments in living cells.

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

BackgroundInsulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) insulator-binding protein to genome topology remains unclear.ResultsIn this study, we provide evidence for the existence of long-range interactions between chromatin bound Su(Hw) and Combgap, which was first characterised as Polycomb response elements binding protein. Loss of Su(Hw) binding to chromatin results in the disappearance of Su(Hw)-Combgap long-range interactions and in a decrease in spatial self-interactions among a subset of Su(Hw)-bound genome sites. Our findings suggest that Su(Hw)-Combgap long-range interactions are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators’ binding.ConclusionsThis study demonstrates that Su(Hw) insulator binding protein can form long-range interactions with Combgap, Polycomb response elements binding protein, and that these interactions are associated with active chromatin factors rather than with Polycomb dependent repression.

SAFB restricts contact domain boundaries associated with L1 chimeric transcription

Long interspersed element-1 (LINE-1 or L1) comprises 17% of the human genome, continuously generates genetic variations, and causes disease in certain cases. However, the regulation and function of L1 remain poorly understood. Here, we uncover that L1 can enrich RNA polymerase IIs (RNA Pol IIs), express L1 chimeric transcripts, and create contact domain boundaries in human cells. This impact of L1 is restricted by a nuclear matrix protein scaffold attachment factor B (SAFB) that recognizes transcriptionally active L1s by binding L1 transcripts to inhibit RNA Pol II enrichment. Acute inhibition of RNA Pol II transcription abolishes the domain boundaries associated with L1 chimeric transcripts, indicating a transcription-dependent mechanism. Deleting L1 impairs domain boundary formation, and L1 insertions during evolution have introduced species-specific domain boundaries. Our data show that L1 can create RNA Pol II-enriched regions that alter genome organization and that SAFB regulates L1 and RNA Pol II activity to preserve gene regulation.

Effect of loops on the mean-square displacement of Rouse-model chromatin.

Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.

CONTACT OF AN ANISOTROPIC LAYER WITH A RIGID PERIODICALLY CONVEX SURFACE

By using Fourier integral transforms applied to integral equations, exact solutions are constructed for spatial problems of full contact of a transversely isotropic layer with a rigid doubly periodic sinusoidal surface. One layer face is subjected to sliding or rigid support, and isotropy planes are parallel to the layer faces. It is established that the full contact over the whole layer face is always possible except the degenerate case of isotropic incompressible layer with one face rigidly fixed. It is indicated that the full contact is also realizable for the case of isotropy planes perpendicular to the layer faces when one face is subjected to sliding support. The problems of partial contact are also considered for the transversely isotropic layer with a rigid surface relief of which is described by a doubly periodic function in the form of a system of paraboloids of revolution. On the base of the theory of generalized functions, the problems are reduced to integral equations kernels of which do not contain integrals. The complication of the problems of partial contact is that the contact domain is a priori unknown that leads us to additional inequalities and nonlinearities. With the help of the B.A. Galanov method, the system of the integral equation and inequality can be reduced to only one nonlinear integral equation for which the modified Newton numerical method can be applied. The exact solutions for the full contact are usable to check calculations. Contact domains and contact pressures are determined. Mechanical characteristics are calculated for the percolation process of initially discrete contact spots in the strengthening contact. Minimal settlements of the paraboloids of revolution are calculated to begin or complete percolation for an anisotropic material.

Stabilize Various Novel Network Structures via the Alternate Arrangement of A/C Domains in Close Contact by Tailoring ABC Miktoarm Star Architectures

Stabilize Various Novel Network Structures via the Alternate Arrangement of A/C Domains in Close Contact by Tailoring ABC Miktoarm Star Architectures

3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.

Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages: the trophectoderm, the epiblast and the primitive endoderm. Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements through which transcriptional regulators enact these fates remain understudied. Here, we characterize, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observe extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although distinct groups of genes are irresponsive to topological changes. In each lineage, a high degree of connectivity, or 'hubness', positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a predictive model for transcriptional regulation (3D-HiChAT) that outperforms models using only 1D promoter or proximal variables to predict levels and cell-type specificity of gene expression. Using 3D-HiChAT, we identify, in silico, candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments, we validate several enhancers that control gene expression in their respective lineages. Our study identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to comprehensively understand lineage-specific transcriptional behaviors.

Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture.

The resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here, we report two 3C-derived methods, Tri-4C and Tri-HiC, which utilize multirestriction enzyme digestions for ultrafine mapping of targeted and genome-wide chromatin interaction, respectively, at up to one hundred basepair resolution. Tri-4C identified CRE loop interaction networks and quantitatively revealed their alterations underlying dynamic gene control. Tri-HiC uncovered global fine-gauge regulatory interaction networks, identifying >20-fold more enhancer:promoter (E:P) loops than in situ Hi-C. In addition to vastly improved identification of subkilobase-sized E:P loops, Tri-HiC also uncovered interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically associating domain boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high-resolution interactome maps required for characterizing fine-gauge regulatory chromatin interactions in analysis of development, homeostasis, and disease.

Optimization of a punch shape with a doubly connected contact domain

The objective is to optimize the distribution of the normal pressure under a rigid punch (indenter) having a doubly connected contact domain close to a circular ring and interacting with a homogeneous isotropic elastic half-space. In the problem considered here, the required design variable is the punch shape. The functional to be minimized is the root-mean-square deviation of the present pressure distribution from some given distribution. An analytical technique is developed for solving the problem for the punches with doubly connected shape, by reducing to a sequence of similar problems for the circular ring punches using expansions of the simple layer potential. The method of expansion in terms of a small parameter is used. The simple layer potential expansion is proposed when mapping a doubly connected integration domain onto a circular ring by transforming the integration variables and transforming the coordinates of the pole of the kernel. As a result, a set of similar problems was obtained for a circular ring to determine the functions characterizing the normal pressure distribution over a non-circular ring contact domain under the punch, as well as the normal displacements, from where the optimal punch shape is determined.

Solving three-dimensional contact problems for foundation design in green building

Design of foundations on an elastic base is carried out using the solution of three-dimensional problems of contact interaction. Improving the accuracy of engineering calculations is necessary to ensure economic efficiency and increase energy savings in green building. The problems of indentation of punches with a flat base bounded by doubly connected close to polygonal contact areas are researched in the present work. Small parameter method is used to obtain explicit analytical expressions for the contact pressure distribution and the punch displacement dependence in a simplified form, which is convenient for engineering practice. The found load-displacement dependence satisfies the known inequalities that are valid for an arbitrary contact domain. Also a numerical-analytical method is in consideration. It uses the simple layer potential expansion and successive approximations for the problems accounting roughness of the elastic half-space. Roughness coefficient is considered as a parameter of regularization of the integral equation for the smooth contact problem. The results of both methods coincide with sufficient accuracy.

Accessible gene borders establish a core structural unit for chromatin architecture in Arabidopsis.

Three-dimensional (3D) chromatin structure is linked to transcriptional regulation in multicellular eukaryotes including plants. Taking advantage of high-resolution Hi-C (high-throughput chromatin conformation capture), we detected a small structural unit with 3D chromatin architecture in the Arabidopsis genome, which lacks topologically associating domains, and also in the genomes of tomato, maize, and Marchantia polymorpha. The 3D folding domain unit was usually established around an individual gene and was dependent on chromatin accessibility at the transcription start site (TSS) and transcription end site (TES). We also observed larger contact domains containing two or more neighboring genes, which were dependent on accessible border regions. Binding of transcription factors to accessible TSS/TES regions formed these gene domains. We successfully simulated these Hi-C contact maps via computational modeling using chromatin accessibility as input. Our results demonstrate that gene domains establish basic 3D chromatin architecture units that likely contribute to higher-order 3D genome folding in plants.

Identification of Two Subsets of Subcompartment A1 Associated with High Transcriptional Activity and Frequent Loop Extrusion.

Three-dimensional genome organization has been increasingly recognized as an important determinant of the precise regulation of gene expression in mammalian cells, yet the relationship between gene transcriptional activity and spatial subcompartment positioning is still not fully comprehended. Here, we first utilized genome-wide Hi-C data to infer eight types of subcompartment (labeled A1, A2, A3, A4, B1, B2, B3, and B4) in mouse embryonic stem cells and four primary differentiated cell types, including thymocytes, macrophages, neural progenitor cells, and cortical neurons. Transitions of subcompartments may confer gene expression changes in different cell types. Intriguingly, we identified two subsets of subcompartments defined by higher gene density and characterized by strongly looped contact domains, named common A1 and variable A1, respectively. We revealed that common A1, which includes highly expressed genes and abundant housekeeping genes, shows a ~2-fold higher gene density than the variable A1, where cell type-specific genes are significantly enriched. Thus, our study supports a model in which both types of genomic loci with constitutive and regulatory high transcriptional activity can drive the subcompartment A1 formation. Special chromatin subcompartment arrangement and intradomain interactions may, in turn, contribute to maintaining proper levels of gene expression, especially for regulatory non-housekeeping genes.

Obtaining The Finite Difference Approximation of The Lame System By Using Barycentric Coordinates

The elasto-plastic contact problem with an unknown contact domain (UCD) has attracted mathematicians, mechanics and engineers for decades. So, the problem of determining the stresses in the UCD is very important nowadays in terms of engineering and applied mathematics. To improve the finite element model, the remeshing algorithm is used for the considered indentation problem. The algorithm allows the determination of the UCD at each step of the indentation with high accuracy. This paper presents the analysis and numerical solution of the boundary value problem for the Lame system, and the modeling of the contact problem for rigid materials. By using barycentric coordinates, the finite difference approximation of the mathematical model of the deformation problem with undetermined bounded is obtained and the relations between the finite elements and finite differences are investigated.

On Boussinesq's Problem for a Power-Law Graded Elastic Half-Space on Elliptical and General Contact Domains.

The indentation of a power-law graded elastic half-space by a rigid counter body is considered in the framework of linear elasticity. Poisson's ratio is assumed to be constant over the half-space. For indenters with an ellipsoidal power-law shape, an exact contact solution is derived, based on the generalizations of Galin's theorem and Barber's extremal principle for the inhomogeneous half-space. As a special case, the elliptical Hertzian contact is revisited. Generally, elastic grading with a positive grading exponent reduces the contact eccentricity. Fabrikant's approximation for the pressure distribution under a flat punch of arbitrary planform is generalized for power-law graded elastic media and compared with rigorous numerical calculations based on the boundary element method (BEM). Very good agreement between the analytical asymptotic solution and the numerical simulation is obtained for the contact stiffness and the contact pressure distribution. A recently published approximate analytic solution for the indentation of a homogeneous half-space by a counter body, whose shape slightly deviates from axial symmetry but is otherwise arbitrary, is generalized for the power-law graded half-space. The approximate procedure for the elliptical Hertzian contact exhibits the same asymptotic behavior as the exact solution. The approximate analytic solution for the indentation by a pyramid with square planform is in very good agreement with a BEM-based numerical solution of the same problem.

PIBF1 regulates multiple gene expression via impeding long-range chromatin interaction to drive the malignant transformation of HPV16 integration epithelial cells

IntroductionHuman papillomavirus (HPV) integration can induce gene expression dysregulation by destroying higher-order chromatin structure in cervical cancer. ObjectivesWe established a 13q22 site-specific HPV16 gene knock-in cell model to interrogate the changes in chromatin structure at the initial stages of host cell malignant transformation. MethodsWe designed a CRISPR-Cas9 system with sgRNA targeting 13q22 site and constructed the HPV16 gene donor. Cells were cotransfected, screened, and fluorescence sorted. The whole genome sequencing (WGS) was used to confirm the precise HPV16 gene integration site. Western blot and qRT-PCR were used to measure gene expression. In vitro and in vivo analysis were performed to estimate the tumorigenic potential of the HPV16 knock-in cell model. Combined Hi-C, chromatin immunoprecipitation and RNA sequencing analyses revealed correlations between chromatin structure and gene expression. We performed a coimmunoprecipitation assay with anti-PIBF1 antibody to identify endogenous interacting proteins. In vivo analysis was used to determine the role of PIBF1 in the tumor growth of cervical cancer cells. ResultsWe successfully established a 13q22 site-specific HPV16 gene knock-in cell model. We found that HPV integration promoted cell proliferation, invasion and stratified growth in vitro, and monoclonal proliferation in vivo. HPV integration divided the affected topologically associated domain (TAD) into two smaller domains, and the progesterone-induced blocking factor 1 (PIBF1) gene near the integration site was upregulated, although PIBF1 was not enriched at the domain boundary by CUT-Tag signal analysis. Moreover, PIBF1 was found to interact with the cohesin complex off chromatin to reduce contact domain formation by disrupting the cohesin ring-shaped structure, causing dysregulation of tumorigenesis-related genes. Xenograft experiments determined the role of PIBF1 in the proliferation in cervical cancer cells. ConclusionWe highlight that PIBF1, a potential chromatin structure regulatory protein, is activated by HPV integration, which provides new insights into HPV integration-driven cervical carcinogenesis.

Condensed but liquid-like domain organization of active chromatin regions in living human cells.

In eukaryotes, higher-order chromatin organization is spatiotemporally regulated as domains, for various cellular functions. However, their physical nature in living cells remains unclear (e.g., condensed domains or extended fiber loops; liquid-like or solid-like). Using novel approaches combining genomics, single-nucleosome imaging, and computational modeling, we investigated the physical organization and behavior of early DNA replicated regions in human cells, which correspond to Hi-C contact domains with active chromatin marks. Motion correlation analysis of two neighbor nucleosomes shows that nucleosomes form physically condensed domains with ~150-nm diameters, even in active chromatin regions. The mean-square displacement analysis between two neighbor nucleosomes demonstrates that nucleosomes behave like a liquid in the condensed domain on the ~150 nm/~0.5 s spatiotemporal scale, which facilitates chromatin accessibility. Beyond the micrometers/minutes scale, chromatin seems solid-like, which may contribute to maintaining genome integrity. Our study reveals the viscoelastic principle of the chromatin polymer; chromatin is locally dynamic and reactive but globally stable.

Self-reported restrictions in different life domains and associated factors among people with multiple sclerosis in Sweden.

The heterogeneous symptoms of multiple sclerosis (MS) can considerably impact the lives of people with MS (PwMS). The aim of this study was to describe the extent of restrictions in different life domains that PwMS experience in relation to their symptoms and level of disability. A cross-sectional survey was conducted among working-age PwMS in Sweden. The 4052 participants who answered the questions on restrictions in work and private life domains (family, leisure activities, and contact with friends/acquaintances) were included. Predictors of restrictions in the four domains were determined through multinomial logistic regression. Approximately one-third of the PwMS reported no restrictions in the domains of work (35.7%), family (38.7%), leisure activities (31.1%) or contact with friends/acquaintances (40.3%), the remaining participants reported moderate to severe restrictions. Tiredness/fatigue was the most commonly reported most-limiting symptom (49.5%). PwMS with Expanded Disability Status Scale (EDSS) scores of zero reported restrictions in life domains ranging from 39.6% (friends/acquaintances) to 45.7% (leisure activities). Age, sex, education, type of living area, MS type, type of most-limiting symptom, and EDSS score predicted restrictions in work and private life domains. Most PwMS reported similar levels of restrictions in both their work and private lives. Restrictions in these life domains were also reported by PwMS with low disability levels (EDSS = 0) and were often associated with invisible symptoms such as fatigue. Even in a contemporary MS cohort, close to 90% of PwMS report limitations due to MS.

A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth

Epstein-Barr virus (EBV) immortalization of resting B lymphocytes (RBLs) to lymphoblastoid cell lines (LCLs) models human DNA tumor virus oncogenesis. RBL and LCL chromatin interaction maps are compared to identify the spatial and temporal genome architectural changes during EBV B cell transformation. EBV induces global genome reorganization where contact domains frequently merge or subdivide during transformation. Repressed B compartments in RBLs frequently switch to active A compartments in LCLs. LCLs gain 40% new contact domain boundaries. Newly gained LCL boundaries have strong CTCF binding at their borders while in RBLs, the same sites have much less CTCF binding. Some LCL CTCF sites also have EBV nuclear antigen (EBNA) leader protein EBNALP binding. LCLs have more local interactions than RBLs at LCL dependency factors and super-enhancer targets. RNA Pol II HiChIP and FISH of RBL and LCL further validate the Hi-C results. EBNA3A inactivation globally alters LCL genome interactions. EBNA3A inactivation reduces CTCF and RAD21 DNA binding. EBNA3C inactivation rewires the looping at the CDKN2A/B and AICDA loci. Disruption of a CTCF site at AICDA locus increases AICDA expression. These data suggest that EBV controls lymphocyte growth by globally reorganizing host genome architecture to facilitate the expression of key oncogenes.