RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins.

Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA-DNA proximity ligation techniques has been developed. However, neither of these techniques examines proteins involved in RNA-chromatin interactions. Here, we introduce RedChIP, a technique combining RNA-DNA proximity ligation and chromatin immunoprecipitation for identifying RNA-chromatin interactions mediated by a particular protein. Using antibodies against architectural protein CTCF and the EZH2 subunit of the Polycomb repressive complex 2, we identify a spectrum of cis- and trans-acting ncRNAs enriched at Polycomb- and CTCF-binding sites in human cells, which may be involved in Polycomb-mediated gene repression and CTCF-dependent chromatin looping. By providing a protein-centric view of RNA-DNA interactions, RedChIP represents an important tool for studies of nuclear ncRNAs.

Effect of ion distribution on stress relaxation in polyelectrolyte complex gels.

Solutions of polyelectrolytes consisting of polycations and polyanions in equal proportions were studied in the present work. Due to the physical cross-links formed by the charged groups, physical gels were formed in such systems. The mechanical properties and structure of the obtained gels depending on the charge arrangement along the backbone and the dimensionless Bjerrum length λ were investigated. The response of the systems to a uniaxial affine deformation was studied first. It was found that the systems can be divided into three groups depending on the charge arrangement: showing an almost elastic response; showing a viscoelastic response with a very long relaxation time; and showing a weak viscoelastic response with a short relaxation time. Interestingly, no stable aggregates were formed in the systems with the charges located on spacers, probably because of the increased mobility of the charges in such systems. The obtained stress relaxation curves had different functional forms, indicating that the relaxation has at least two characteristic times, which are different for different systems. In order to understand the molecular nature of the observed mechanical response, the temporal evolution of the network structure of a system showing a viscoelastic response with a very long relaxation time was studied; the aggregates were found to be dynamic, which leads to the relaxation of the "subchains" conformation.

Cohesin Complex: Structure and Principles of Interaction with DNA.

Accurate duplication and separation of long linear genomic DNA molecules is associated with a number of purely mechanical problems. SMC complexes are key components of the cellular machinery that ensures decatenation of sister chromosomes and compaction of genomic DNA during division. Cohesin, one of the essential eukaryotic SMC complexes, has a typical ring structure with intersubunit pore through which DNA molecules can be threaded. Capacity of cohesin for such topological entrapment of DNA is crucial for the phenomenon of post-replicative association of sister chromatids better known as cohesion. Recently, it became apparent that cohesin and other SMC complexes are, in fact, motor proteins with a very peculiar movement pattern leading to formation of DNA loops. This specific process has been called loop extrusion. Extrusion underlies multiple functions of cohesin beyond cohesion, but molecular mechanism of the process remains a mystery. In this review, we summarized the data on molecular architecture of cohesin, effect of ATP hydrolysis cycle on this architecture, and known modes of cohesin-DNA interactions. Many of the seemingly disparate facts presented here will probably be incorporated in a unified mechanistic model of loop extrusion in the not-so-distant future.

Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology.

The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.

Effect of the counterion size on microphase separation in charged-neutral diblock copolymers.

In this work, the question of the influence of the counterion size on the self-assembly in melts of diblock copolymers with one charged block was studied using coarse-grained molecular dynamics simulations. It was assumed that the blocks were fully compatible, i.e., the Flory-Huggins parameter χ between them was equal to 0. Due to the presence of correlation attraction (electrostatic cohesion) between the charged species, the systems with all types of counterions underwent transitions to ordered states, forming various morphologies, including lamellae, perforated lamellae, and hexagonally packed cylinders. Phase diagrams were constructed by varying the chain composition fc and locating the order-disorder transition positions in terms of the electrostatic strength parameter λ (dimensionless Bjerrum length). Despite having a rather large ion size mismatch, the systems with smaller counterions demonstrated an even better tendency to form microphase separated states than the systems with larger ones. It was found that the differences between the phase diagrams of the systems with different counterions can be roughly rationalized by using coordinates (volume fraction of the charged block φc-modified interaction parameter λ*). The latter parameter assumes that the electrostatic energy is simply inversely proportional to the characteristic distance between the ions of different signs. Such an approach appeared to be rather effective and allowed the diagrams obtained for different counterion sizes to almost coincide. The results of this work suggest that the counterion size can be used as a tool to control the system morphology as well as the effective incompatibility between the blocks.

Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells.

Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes within the cell nucleus. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)-mediated LLPS disruption/modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome clutches and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions and TAD insulation but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels.

Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface.

Polymer microgels synthesized in silico were studied at a liquid-liquid interface via mesoscopic computer simulations and compared to microgels with ideal (diamond-like) structure. The effect of crosslinkers reactivity ratio on the single particle morphology at the interface and monolayer behavior was examined. It was demonstrated that single particles deform into an explicit core-corona morphology when adsorbed at the interface. An increase in the crosslinker reactivity ratio decreased both the deformation ratio and the ratio between the core and corona sizes. Meanwhile, the compression of microgel monolayers revealed the existence of five distinct interparticle contact regimes, which have been observed experimentally in the literature. The crosslinker reactivity ratio appeared to define the compression range in these regimes and the sharpness of the transition between them. In particular, the higher the crosslinker reactivity ratio, the smaller the corona, and in turn, the narrower the range of the intermediate regime comprising both core-core and corona-corona contacts. The obtained results demonstrate that the more realistic model of microgels synthesized via precipitation polymerization allows for a more accurate prediction of the properties of the microgels at a liquid-liquid interface in comparison to the conventional diamond-like lattice model.

Correction: Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface.

Correction for 'Effect of network topology and crosslinker reactivity on microgel structure and ordering at liquid-liquid interface' by Rustam A. Gumerov et al., Soft Matter, 2022, 18, 3738-3747, https://doi.org/10.1039/D2SM00269H.

An exotic microstructured globular state formed by a single multiblock copolymer chain.

In this work, we studied the equilibrium structures formed by a single (AB)k multiblock copolymer chain. Within our model, the interactions between the A-type beads were repulsive and the B-type beads could form pairwise reversible bonds with each other (BB-bonds). Our goal was to investigate how the formation of pairwise reversible bonds between the A-type beads and the B-type beads (AB-bonds) affected the structure of the chain. We observed the formation of well-studied intramolecular micelles when the AB-bonds were absent; however, the chain folding changed dramatically when the formation of the AB-bonds was introduced. In this case, the multiblock copolymer formed a globule, which had a unique heterogeneous checkerboard-like distribution of the contact density. We discovered that contacts of beads of different types (i.e., AB-contacts) occurred much more frequently than contacts of beads of the same type (i.e., AA- and BB-contacts) in these structures. This effect can be explained by a simple model of chemical equilibrium in a two-component fluid of reversibly interacting particles, which can be solved exactly. This novel type of folding can serve as a basic model for any (AB)k multiblock copolymer chain with a non-vanishing attraction between A and B blocks.

Non-coding RNAs in chromatin folding and nuclear organization.

One of the most intriguing questions facing modern biology concerns how the genome directs the construction of cells, tissues, and whole organisms. It is tempting to suggest that the part of the genome that does not encode proteins contains architectural plans. We are still far from understanding how these plans work at the level of building tissues and the body as a whole. However, the results of recent studies demonstrate that at the cellular level, special non-coding RNAs serve as scaffolds for the construction of various intracellular structures. The term "architectural RNAs" was proposed to designate this subset of non-coding RNAs. In this review, we discuss the role of architectural RNAs in the construction of the cell nucleus and maintenance of the three-dimensional organization of the genome.

Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics.

Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

Recurrent Translocations in Topoisomerase Inhibitor-Related Leukemia Are Determined by the Features of DNA Breaks Rather Than by the Proximity of the Translocating Genes.

Topoisomerase inhibitors are widely used in cancer chemotherapy. However, one of the potential long-term adverse effects of such therapy is acute leukemia. A key feature of such therapy-induced acute myeloid leukemia (t-AML) is recurrent chromosomal translocations involving AML1 (RUNX1) or MLL (KMT2A) genes. The formation of chromosomal translocation depends on the spatial proximity of translocation partners and the mobility of the DNA ends. It is unclear which of these two factors might be decisive for recurrent t-AML translocations. Here, we used fluorescence in situ hybridization (FISH) and chromosome conformation capture followed by sequencing (4C-seq) to investigate double-strand DNA break formation and the mobility of broken ends upon etoposide treatment, as well as contacts between translocation partner genes. We detected the separation of the parts of the broken AML1 gene, as well as the increased mobility of these separated parts. 4C-seq analysis showed no evident contacts of AML1 and MLL with loci, implicated in recurrent t-AML translocations, either before or after etoposide treatment. We suggest that separation of the break ends and their increased non-targeted mobility-but not spatial predisposition of the rearrangement partners-plays a major role in the formation of these translocations.

C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries.

Studies performed using Hi-C and other high-throughput whole-genome C-methods have demonstrated that 3D organization of eukaryotic genomes is functionally relevant. Unfortunately, ultra-deep sequencing of Hi-C libraries necessary to detect loop structures in large vertebrate genomes remains rather expensive. However, many studies are in fact aimed at determining the fine-scale 3D structure of comparatively small genomic regions up to several Mb in length. Such studies typically focus on the spatial structure of domains of coregulated genes, molecular mechanisms of loop formation, and interrogation of functional significance of GWAS-revealed polymorphisms. Therefore, a handful of molecular techniques based on Hi-C have been developed to address such issues. These techniques commonly rely on in-solution hybridization of Hi-C/3C-seq libraries with pools of biotinylated baits covering the region of interest, followed by deep sequencing of the enriched library. Here, we describe a new protocol of this kind, C-TALE (Chromatin TArget Ligation Enrichment). Preparation of hybridization probes from bacterial artificial chromosomes and an additional round of enrichment make C-TALE a cost-effective alternative to existing many-versus-all C-methods.

The effect of explicit polarity on the conformational behavior of a single polyelectrolyte chain.

In this work using dissipative particle dynamics simulations with explicit treatment of polar species we demonstrate that the molecular nature of dielectric media has a significant impact on swelling and collapse of a polyelectrolyte chain in a dilute solution. We show that the small-scale effects related to the presence of polar species lead to the intensification of the electrostatic interactions when the charges are close to each other and/or their density is high enough. As a result, the electrostatic strength , usually regarded as the main parameter governing the polyelectrolyte chain collapse, does not have a universal meaning: the value of λ at which the coil-to-globule transition occurs is found to be dependent on the specific fixed value of the solvent bulk permittivity ε while varying the monomer unit charge Q and vice versa. This effect is observed even when the backbone and the counterions have the same polarity as the solvent beads, i.e. no dielectric mismatch is present. The reason for such behavior is rationalized in terms of the "effective" dielectric permittivity εeff which depends on the volume fraction φ of charged units inside the polymer chain volume; using εeff instead of ε collapses all data onto one master curve describing the chain shrinking with λ. Furthermore, it is shown that a polar chain adopts less swollen conformations in the polyelectrolyte regime and collapses more easily compared to a non-polar chain.

Two contributions to the dielectric response of polar liquids.

In this Note, we study the total conservative force {instead of pure electrostatic force as it was carried out in the work by Gavrilov [J. Chem. Phys. 152, 164101 (2020)]} acting on two charges in a polar liquid using dissipative particle dynamics and coarse-grained molecular dynamics simulations. We show that such force (instead of the electrostatic force) obeys Coulomb's law at large distances between the charges. Apparently, the dielectric response of a polar liquid (at least, within such coarse-grained models) can be decomposed into two contributions: the reorientation of the dipoles (i.e., electrostatic contribution) and the density redistribution (i.e., volume interaction contribution).

Influence of Charges on the Behavior of Polyelectrolyte Microgels Confined to Oil-Water Interfaces.

The role of electrostatics on the interfacial properties of polyelectrolyte microgels has been discussed controversially in the literature. It is not yet clear if, or how, Coulomb interactions affect their behavior under interfacial confinement. In this work, we combine compression isotherms, atomic force microscopy imaging, and computer simulations to further investigate the behavior of pH-responsive microgels at oil-water interfaces. At low compression, charged microgels can be compressed more than uncharged microgels. The in-plane effective area of charged microgels is found to be smaller in comparison to uncharged ones. Thus, the compressibility is governed by in-plane interactions of the microgels with the interface. At high compression, however, charged microgels are less compressible than uncharged microgels. Microgel fractions located in the aqueous phase interact earlier for charged than for uncharged microgels because of their different swelling perpendicular to the interface. Therefore, the compressibility at high compression is controlled by out-of-plane interactions. In addition, the size of the investigated microgels plays a pivotal role. The charge-dependent difference in compressibility at low compression is only observed for small but not for large microgels, while the behavior at high compression does not depend on the size. Our results highlight the complex nature of soft polymer microgels as compared to rigid colloidal particles. We clearly demonstrate that electrostatic interactions affect the interfacial properties of polyelectrolyte microgels.

Dissipative particle dynamics for systems with polar species: Interactions in dielectric media.

In this work, we develop a method for simulating polar species in the dissipative particle dynamics (DPD) method. The main idea behind the method is to treat each bead as a dumb-bell, i.e., two sub-beads kept at a fixed distance, instead of a point-like particle. The relation between the bead dipole moment and the bulk dielectric permittivity was obtained. The interaction force of single charges in polar liquid showed that the effective dielectric permittivity is somewhat smaller than that obtained for the bulk case at large separation between the charges. In order to understand the reasons behind the observed drop in the dielectric permittivity, we calculate the electric field of an isolated charge in a polar liquid; no permittivity drop is observed for this case. We can assume that the behavior observed for the force is due to the fact that the probing point is always associated with the charged bead, which is a force center, which essentially leads to a non-homogeneous density distribution around it on average; this is not the case when the field is measured. The interaction of a single charge with an interface between two liquids with different permittivities was studied after that; the model is found to correctly reproduce the "mirror image" effects. Finally, we show why it is necessary to treat the polar species in DPD explicitly by investigating the behavior of a charged colloidal particle at a liquid-liquid interface.

Quantitative differences in TAD border strength underly the TAD hierarchy in Drosophila chromosomes.

Chromosomes in many organisms, including Drosophila and mammals, are folded into topologically associating domains (TADs). Increasing evidence suggests that TAD folding is hierarchical, wherein subdomains combine to form larger superdomains, instead of a sequence of nonoverlapping domains. Here, we studied the hierarchical structure of TADs in Drosophila. We show that the boundaries of TADs of different hierarchical levels are characterized by the presence of different portions of active chromatin, but do not vary in the binding of architectural proteins, such as CCCTC binding factor or cohesin. The apparent hierarchy of TADs in Drosophila chromosomes is not likely to have functional importance but rather reflects various options of long-range chromatin folding directed by the distribution of active and inactive chromatin segments and may represent population average.

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains.

Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)(+) RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.

Evolution of the Genome 3D Organization: Comparison of Fused and Segregated Globin Gene Clusters.

The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here, we have studied the 3D organization and regulation of zebrafish globin gene domain and compared its organization and regulation with those of other vertebrate species. In birds and mammals, the α- and ß-globin genes are segregated into separate clusters located on different chromosomes and organized into chromatin domains of different types, whereas in cold-blooded vertebrates, including Danio rerio, α- and ß-globin genes are organized into common clusters. The major globin gene locus of Danio rerio is of particular interest as it is located in a genomic area that is syntenic in vertebrates and is controlled by a conserved enhancer. We have found that the major globin gene locus of Danio rerio is structurally and functionally segregated into two spatially distinct subloci harboring either adult or embryo-larval globin genes. These subloci demonstrate different organization at the level of chromatin domains and different modes of spatial organization, which appears to be due to selective interaction of the upstream enhancer with the sublocus harboring globin genes of the adult type. These data are discussed in terms of evolution of linear and 3D organization of gene clusters in vertebrates.