Long-range Regulation Research Articles

Ti3C2Tx MXene-mediating near- and long-range electronic effect on atomically dispersed Co for efficient lithium-sulfur batteries

Sluggish sulfur conversion kinetics pose an ongoing challenge in lithium-sulfur batteries (LSBs). Here, we present a solution through far-reaching long-range electronic regulation (LRER) on single-atom active sites. N-doped carbons (Co-NC) are implanted with densely-distributed Co single atoms, and supported on Ti3C2Tx MXene substrates to assemble 3D Co-NC/MXene catalyst. MXene effectively mediates interlayer charge transfer (∼0.70 |e|) contrasted with popular carbon materials (∼0.06 |e|) to produce LRER through surrounding carbon atoms. The synergy of LRER with near-range electronic regulation (NRER) tunes electronic structures, and enhances heterostructural stability, thus provoking desirous catalytic kinetics of Co single atoms in sulfur reduction. Thereby, the Co-NC/MXene/S cathodes exhibit impressive rate performance and excellent cycling stability (only 0.015% capacity decay per cycle over 600 cycles at 4 C) in LSBs, surpassing state-of-the-art sulfur cathodes. This work reveals the importance of LRER for improved catalysis, and provides new guidance to tailor heterostructures to achieve high-efficient catalysts in various process.

Ancestry of the major long-range regulatory site of the α-globin genes in the Portuguese population with the common 3.7 kb α-thalassemia deletion

BackgroundThe α-Major Regulatory Element (α-MRE), also known as HS-40, is located upstream of the α-globin gene cluster and has a crucial role in the long-range regulation of the α-globin gene expression. This enhancer is polymorphic and several haplotypes were identified in different populations, with haplotype D almost exclusively found in African populations. The purpose of this research was to identify the HS-40 haplotype associated with the 3.7 kb α-thalassemia deletion (-α3.7del) in the Portuguese population, and determine its ancestry and influence on patients’ hematological phenotype.Methods and resultsWe selected 111 Portuguese individuals previously analyzed by Gap-PCR to detect the presence of the -α3.7del: 50 without the -α3.7del, 34 heterozygous and 27 homozygous for the -α3.7del. The HS-40 region was amplified by PCR followed by Sanger sequencing. Four HS-40 haplotypes were found (A to D). The distribution of HS-40 haplotypes and genotypes are significantly different between individuals with and without the -α3.7del, being haplotype D and genotype AD the most prevalent in patients with this deletion in homozygosity. Furthermore, multiple correspondence analysis revealed that individuals without the -α3.7del are grouped with other European populations, while samples with the -α3.7del are separated from these and found more closely related to the African population.ConclusionThis study revealed for the first time an association of the HS-40 haplotype D with the -α3.7del in the Portuguese population, and its likely African ancestry. These results may have clinical importance as in vitro analysis of haplotype D showed a decrease in its enhancer activity on α-globin gene.

A Bidirectional Non-Coding RNA Promoter Mediates Long-Range Gene Expression Regulation.

Recent evidence suggests that human gene promoters display gene expression regulatory mechanisms beyond the typical single gene local transcription modulation. In mammalian genomes, genes with an associated bidirectional promoter are abundant; bidirectional promoter architecture serves as a regulatory hub for a gene pair expression. However, it has been suggested that its contribution to transcriptional regulation might exceed local transcription initiation modulation. Despite their abundance, the functional consequences of bidirectional promoter architecture remain largely unexplored. This work studies the long-range gene expression regulatory role of a long non-coding RNA gene promoter using chromosome conformation capture methods. We found that this particular bidirectional promoter contributes to distal gene expression regulation in a target-specific manner by establishing promoter-promoter interactions. In particular, we validated that the promoter-promoter interactions of this regulatory element with the promoter of distal gene BBX contribute to modulating the transcription rate of this gene; removing the bidirectional promoter from its genomic context leads to a rearrangement of BBX promoter-enhancer interactions and to increased gene expression. Moreover, long-range regulatory functionality is not directly dependent on its associated non-coding gene pair expression levels.

Inter-site structural heterogeneity induction of single atom Fe catalysts for robust oxygen reduction

Metal-nitrogen-carbon catalysts with hierarchically dispersed porosity are deemed as efficient geometry for oxygen reduction reaction (ORR). However, catalytic performance determined by individual and interacting sites originating from structural heterogeneity is particularly elusive and yet remains to be understood. Here, an efficient hierarchically porous Fe single atom catalyst (Fe SAs-HP) is prepared with Fe atoms densely resided at micropores and mesopores. Fe SAs-HP exhibits robust ORR performance with half-wave potential of 0.94 V and turnover frequency of 5.99 e−1s−1site−1 at 0.80 V. Theoretical simulations unravel a structural heterogeneity induced optimization, where mesoporous Fe-N4 acts as real active centers as a result of long-range electron regulation by adjacent microporous sites, facilitating O2 activation and desorption of key intermediate *OH. Multilevel operando characterization results identify active Fe sites undergo a dynamic evolution from basic Fe-N4 to active Fe-N3 under working conditions. Our findings reveal the structural origin of enhanced intrinsic activity for hierarchically porous Fe-N4 sites.

Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq.

Enhancers are DNA sequences that can strengthen transcription initiation. However, the global identification of plant enhancers is complicated due to uncertainty in the distance and orientation of enhancers, especially in species with large genomes. In this study, we performed self-transcribing active regulatory region sequencing (STARR-seq) for the first time to identify enhancers across the barley genome. A total of 7323 enhancers were successfully identified, and among 45 randomly selected enhancers, over 75% were effective as validated by a dual-luciferase reporter assay system in the lower epidermis of tobacco leaves. Interestingly, up to 53.5% of the barley enhancers were repetitive sequences, especially transposable elements (TEs), thus reinforcing the vital role of repetitive enhancers in gene expression. Both the common active mark H3K4me3 and repressive mark H3K27me3 were abundant among the barley STARR-seq enhancers. In addition, the functional range of barley STARR-seq enhancers seemed much broader than that of rice or maize and extended to ±100 kb of the gene body, and this finding was consistent with the high expression levels of genes in the genome. This study specifically depicts the unique features of barley enhancers and provides available barley enhancers for further utilization.

Structural insights into the HDAC4-MEF2A-DNA complex and its implication in long-range transcriptional regulation.

Class IIa Histone deacetylases (HDACs), including HDAC4, 5, 7and 9, play key roles in multiple important developmental and differentiation processes. Recent studies have shown that class IIa HDACs exert their transcriptional repressive function by interacting with tissue-specific transcription factors, such as members of the myocyte enhancer factor 2 (MEF2) family of transcription factors. However, the molecular mechanism is not well understood. In this study, we determined the crystal structure of an HDAC4-MEF2A-DNA complex. This complex adopts a dumbbell-shaped overall architecture, with a 2:4:2 stoichiometry of HDAC4, MEF2A and DNA molecules. In the complex, two HDAC4 molecules form a dimer through the interaction of their glutamine-rich domain (GRD) to form the stem of the 'dumbbell'; while two MEF2A dimers and their cognate DNA molecules are bridged by the HDAC4 dimer. Our structural observations were then validated using biochemical and mutagenesis assays. Further cell-based luciferase reporter gene assays revealed that the dimerization of HDAC4 is crucial in its ability to repress the transcriptional activities of MEF2 proteins. Taken together, our findings not only provide the structural basis for the assembly of the HDAC4-MEF2A-DNA complex but also shed light on the molecular mechanism of HDAC4-mediated long-range gene regulation.

Topological structures and syntenic conservation in sea anemone genomes

There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.

Single Nuclei Multiomics Analysis of Transcriptional and Chromatin Accessibility of Tumor Cells Uncovers Molecular Signatures and Regulatory Elements of Malignant Clonal Evolution in Multiple Myeloma

Category Multiple Myeloma and Plasma Cell Dyscrasias: Basic and Translational Introduction Multiple myeloma (MM) is a hematological cancer resulting from abnormal proliferation of plasma cells (PC) in bone marrow. The progression of the disease from Monoclonal Gammopathy of Undetermined Significance (MGUS), Smoldering Multiple Myeloma (SMM), to MM involves multiple drivers and dynamic interactions of premalignant/malignant cells. In the advancement of single-cell technologies, the same-cell readouts of nucleus RNA sequencing (snRNA-seq) and Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) provide a less biased measurement of gene expressions and chromatin accessible regions. Profiling and analyzing both omics data at different stages of MM may reveal essential molecular signatures and regulatory elements for microenvironmental modification and evolution. These insights could benefit MM patients as novel targets for early therapeutic intervention at different stages of progression. Methods Bone marrow aspirates were collected from 33 individuals: Healthy donors (n=3), patients with MGUS (n=2), SMM (n=5), MM (n=21), and Plasma Cell Leukemia (PCL; n=2). Viable mononuclear cells underwent CD138+ sorting and nuclei isolation prior to library preparation. Libraries were prepared with the Chromium Multiome kit (10X Genomics) and sequenced on NovaSeq S4 flow cells at UAMS. The clonal V(D)J arrangements of each sample and expression level from HD samples were used to distinguish malignant (MM) from normal plasma cells (PC). The MM data from snATAC-seq and snRNA-seq were integrated using Signac with the weighted nearest neighbor methods from Seurat. All inter- and intra-tumor clusters were evaluated for markers of high-risk disease, differential gene expression, differentially accessible regions, and transcription factor activities. Results We performed snRNA-seq and snATAC-seq sequencing to generate multi-stage, molecular classified-specific chromatin accessibility and transcriptional profiles of plasma cell neoplasms comprising 439,134 cells across 33 samples. The malignant plasma cells for each sample were extracted by the unique clonotypic signature of the immunoglobulin gene rearrangement. Of these, we detected the highest clonality in MGUS samples, suggesting clonal competition at the premalignant stage. Based on our primary microarray data, we detected the overexpression of molecular signatures for most cells in each sample, confirming the intratumor cell heterogeneity. Furthermore, we used the ratio of 70-gene signature of aggressive disease and proliferation signatures to investigate the clonal composition of MM cells corresponding to the risk of relapse. Surprisingly, the proportion of high-risk cells increased respectively from low to high-risk samples. The expansion of high-risk clonality might exhibit competition among malignant cell subpopulations regarding microenvironmental adaptation. The multiomics integration generated less distinct clusters between MGUS and SMM, indicating the gradual complex alterations of subclonal gene expression and chromatin accessibility in malignant transformation. Interestingly, most accessible regions were found in intronic/distal intergenic regions implying the long-range gene regulation from cis-regulatory elements. Based on the positive/negative correlation of binding motifs within differentially accessible regions, we identified unique enriched transcription factors for each disease stage, suggesting the mechanism patterns in the evolutionary process of malignant cells. Conclusion In the largest multiomics study to date of CD138+ cells, we demonstrate the malignant clonal evolution using gene expression and chromatin accessibility profiling from patients with early-stage disease to highly aggressive form. Throughout the time of disease progression, we found an increase in the proportion of malignant cells with high-risk signatures. Also, we uncover unique signatures of chromatin accessibility for each molecular classification that can further refine our understanding of functional heterogeneity in multiple myeloma. Collectively, our joint single nuclei profiling reveals additional insights into the malignant clonal evolution and investigates novel regulatory elements involved in disease progression.

Long-range gene regulation in hormone-dependent cancer.

The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts. Chromatin loops formed within TADs through enhancer and promoter interactions are elastic, allowing transcriptional heterogeneity and stochasticity. Over the past decade, it has become evident that the 3D genome structure, also referred to as the chromatin architecture, is central to many transcriptional cellular decisions. In this Review, we delve into the intricate relationship between steroid receptors and LRIs, discussing how steroid receptors interact with and modulate these chromatin interactions. Genetic alterations in the many processes involved in organizing the nuclear architecture are often associated with the development of hormone-dependent cancers. A better understanding of the interplay between architectural proteins and hormone regulatory networks can ultimately be exploited to develop improved approaches for cancer treatment.

Long-Range Regulation of Se Doping for Oxygen Reduction of Atomically Dispersed Sb Catalysts for Ultralow-Temperature Solid-State Zn–Air Batteries

Regulating the p-orbital valence electrons of atomically dispersed main-group metals to improve the inherent electrocatalytic activity has attracted extensive concerns. Herein, we designed and synthesized an atomically dispersed Sb–SeNC catalyst containing SbN2C2 and SeC2 structures, which have been identified by X-ray absorption spectroscopy and density functional theory (DFT) calculations. Sb–SeNC exhibits a high activity for the oxygen reduction reaction (ORR), and a Sb–SeNC-based flexible solid-state zinc–air battery (ZAB) can work efficiently at −40 °C, with a peak power density of 54.1 mW cm–2 and a rate discharge operation of about 44 h. DFT calculations further confirm the long-range regulation mechanism of the SeC2 moiety for the ORR of SbN2C2 and obtain the volcano relationship of Uonset vs the Se–N distance. When the Se–N distance is 7.4 Å, the adsorption ability of active site Sb can be regulated to an optimal state related to the RDS: *O → *OH, while the smaller Se–N distance in short-range would lead to the excessive attenuation of adsorption ability of active site and decrease of ORR activity, which therefore yields the long-range regulation effect of Se doping on the ORR activity of SbN2C2. This long-range regulation strategy may provide a promising approach to boost the catalytic activity of main-group metal catalysts to achieve its application in ultralow-temperature solid-state ZABs.

Supramolecular Cucurbit[7]uril@Ferrocene Complexation on Surface: From Nanostructure Differentiation to Guest Quantitation

ConspectusCucurbit[7]uril (CB[7]), an important member of the macrocyclic cucurbit[n]uril host family, has attracted much attention due to its ability to form ultrastable inclusion complexes with aromatic or “ring”-structured compounds. In particular, for the CB[7]@ferrocene (Fc) host–guest complex, its exceptionally high binding affinity, ideal redox activity, and extreme stability against biological media have promoted its potential to substitute traditional natural binding pairs (antigen/antibody and biotin/avidin complexes as examples) in many biochemical applications, such as purification, labeling, and biomolecular assembly. In recent years, the immobilization of CB[7]@Fc host–guest complex on electrode surface via various strategies has expanded its use for fabricating electroactive biofunctional devices, such as electrochemical biosensors and switches, where the redox response of Fc/Fc+ can be used as both characterization and sensing signal. These applications require in-depth understanding of the interfacial CB[7]@Fc host–guest binding behavior, which is different from that in a homogeneous solution phase; such studies, in turn, will facilitate the design and development of more efficient interfacial host–guest binding systems.With the advantages of easy preparation, high stability, and reversible redox response, ferrocenyl alkanethiolate self-assembled monolayers (SAMs) on gold have been widely employed as an electroanalytical platform for studying electron transfer behavior and molecular interactions (i.e., ion pairing) and probing microenvironmental changes. In order to achieve an “ideal” redox response for these applications (e.g., a single pair of redox peaks), mixed Fc-alkanethiolate SAMs with low Fc coverage are usually prepared, where the influences from different structural domains and nonuniform distribution of Fc terminal groups in the SAM are minimized.In the past decade, our team has been exploring the renewed applications of Fc-alkanethiolate SAMs, while performing characterizations of their structural properties by electrochemistry and other surface techniques. In particular, we employed redox-active Fc-alkanethiolate SAMs to quantitatively study the interfacial CB[7]@Fc host–guest binding and explored a range of applications for nanostructure differentiation, long-range electron transfer regulation, and quantitation of non-redox-active guests. Besides, we have extended our electrochemical study of interfacial CB[7]@Fc host–guest binding with CB[7]-terminated alkanethiolate SAMs, where the electrochemical quantitation of the CB[7]@Fc host–guest complex formed on an electrode surface becomes straightforward.In this Account, we first provide a brief literature review of the CB[7]@Fc host–guest chemistry, including fundamental studies in solution as well as the challenges for its application on surfaces. Subsequently, we describe our studies of interfacial CB[7]@Fc host–guest complexation on binary SAMs on gold, including fundamental voltammetric evaluation of binding thermodynamics and kinetics, as well as its applications. Lastly, we introduce our recent electrochemical study on interfacial CB[7]@Fc complexation by tethering CB[7] on alkanethiolate SAMs (via click chemistry). These research accomplishments shed light on the profound ability of forming interfacial CB[7]@Fc host–guest binding systems for both fundamental studies and practical applications; the knowledge obtained herein paves the way to further understanding of surface-immobilized supramolecular host–guest systems.

Near- and Long-Range Electronic Modulation of Single Metal Sites to Boost CO2 Electrocatalytic Reduction.

Tuning the electronic structure of the active center is effective to improve the intrinsic activity of single-atom catalysts but the realization of precise regulation remains challenging. Herein, a strategy of "synergistically near- and long-range regulation" is reported to effectively modulate the electronic structure of single-atom sites. ZnN4 sites decorated with axial sulfur ligand in the first coordination and surrounded phosphorus atoms in the carbon matrix are successfully constructed in the hollow carbon supports (ZnN4 S1 /P-HC). ZnN4 S1 /P-HC exhibits excellent performance for CO2 reduction reaction (CO2 RR) with a Faraday efficiency of CO close to 100%. The coupling of the CO2 RR with thermodynamically favorable hydrazine oxidation reaction to replace oxygen evolution reaction in a two-electrode electrolyzer can greatly lower the cell voltage by 0.92V at a current density of 5mA cm-2 , theoretically saving 46% of energy consumption. Theoretical calculation reveals that the near-range regulation with axial thiophene-S ligand and long-range regulation with neighboring P atoms can synergistically lead to the increase of electron localization around the Zn sites, which strengthens the adsorption of *COOH intermediate and therefore boosts the CO2 RR.

Nuclear SUN1 stabilizes endothelial cell junctions via microtubules to regulate blood vessel formation.

Endothelial cells line all blood vessels, where they coordinate blood vessel formation and the blood-tissue barrier via regulation of cell-cell junctions. The nucleus also regulates endothelial cell behaviors, but it is unclear how the nucleus contributes to endothelial cell activities at the cell periphery. Here, we show that the nuclear-localized linker of the nucleoskeleton and cytoskeleton (LINC) complex protein SUN1 regulates vascular sprouting and endothelial cell-cell junction morphology and function. Loss of murine endothelial Sun1 impaired blood vessel formation and destabilized junctions, angiogenic sprouts formed but retracted in SUN1-depleted sprouts, and zebrafish vessels lacking Sun1b had aberrant junctions and defective cell-cell connections. At the cellular level, SUN1 stabilized endothelial cell-cell junctions, promoted junction function, and regulated contractility. Mechanistically, SUN1 depletion altered cell behaviors via the cytoskeleton without changing transcriptional profiles. Reduced peripheral microtubule density, fewer junction contacts, and increased catastrophes accompanied SUN1 loss, and microtubule depolymerization phenocopied effects on junctions. Depletion of GEF-H1, a microtubule-regulated Rho activator, or the LINC complex protein nesprin-1 rescued defective junctions of SUN1-depleted endothelial cells. Thus, endothelial SUN1 regulates peripheral cell-cell junctions from the nucleus via LINC complex-based microtubule interactions that affect peripheral microtubule dynamics and Rho-regulated contractility, and this long-range regulation is important for proper blood vessel sprouting and junction integrity.

Long-range regulation of cytochrome c binding to bc1 complex.

The cytochrome bc1 complex (Complex III, ubiquinol-cytochrome c oxidoreductase) is a highly conserved multi-subunit protein found in the mitochondria and is a key complex in the electron transport chain. During oxidative phosphorylation, cytochrome (cyt) c, a mobile electron carrier, binds to one cyt c1 subunit of a bc1 complex dimer and shuttles electrons from Complex III to Complex IV. X-ray crystallographic studies revealed that only one molecule of cyt c binds to one bc1 complex dimer, despite two cytochrome c1 subunits available for binding, pointing toward the existence of a regulation mechanism preventing the docking of a second cyt c substrate. However, the structural basis for such a mechanism of long-range (>30 Å) regulation of substrate binding is not clear from static structural studies. We employed all-atom molecular dynamics simulations to uncover a possible mechanism of regulation. Our results reveal that a finger-like extended domain of the vacant cyt c1 subunit undergoes a conformational change with its tip moving towards cyt c, transferring mechanical motion and causing distortion of the vacant cyt c binding site. In addition, we explored the role of naturally occurring methylated Lys-72 residue of cyt c in substrate binding and its likely role in the regulation of the bc1 complex activity. Finally, our results of experimental verification of computational predictions are presented.

A Liquid Crystal Ionomer-Type Electrolyte toward Ordering-Induced Regulation for Highly Reversible Zinc Ion Battery.

Novel electrolyte is being pursued toward exploring Zn chemistry in zinc ion batteries. Here, a fluorine-free liquid crystal (LC) ionomer-type zinc electrolyte is presented, achieving simultaneous regulated water activity and long-range ordering of conduction channels and SEI. Distinct from water network or local ordering in current advances, long-range ordering of layered water channels is realized. Via manipulating water activity, conductivities range from ≈0.34 to 15 mS cm-1 , and electrochemical window can be tuned from ≈2.3-4.3V. The Zn|Zn symmetric cell with LC gel exhibits highly reversible Zn stripping/plating at 5mA cm-2 and 5 mAh cm-2 for 800h, with retained ordering of water channels. The capability of gel for inducing in situ formation of long-range ordered layer SEI associated with alkylbenzene sulfonate anion is uncovered. V2 O5 /Zn cell with the gel shows much improved cycling stability comparing to conventional zinc electrolytes, where the preserved structure of V2 O5 is associated with the efficiently stabilized Zn anode by the gel. Via long-range ordering-induced regulation on ion transport, electrochemical stability, and interfacial reaction, the development of LC electrolyte provides a pathway toward advancing aqueous rechargeable batteries.

Guiding the design of well-powered Hi-C experiments to detect differential loops.

Three-dimensional chromatin structure plays an important role in gene regulation by connecting regulatory regions and gene promoters. The ability to detect the formation and loss of these loops in various cell types and conditions provides valuable information on the mechanisms driving these cell states and is critical for understanding long-range gene regulation. Hi-C is a powerful technique for characterizing 3D chromatin structure; however, Hi-C can quickly become costly and labor-intensive, and proper planning is required to ensure efficient use of time and resources while maintaining experimental rigor and well-powered results. To facilitate better planning and interpretation of human Hi-C experiments, we conducted a detailed evaluation of statistical power using publicly available Hi-C datasets, paying particular attention to the impact of loop size on Hi-C contacts and fold change compression. In addition, we have developed Hi-C Poweraid, a publicly hosted web application to investigate these findings. For experiments involving well-replicated cell lines, we recommend a total sequencing depth of at least 6 billion contacts per condition, split between at least two replicates to achieve the power to detect differences in the majority of loops. For experiments with higher variation, more replicates and deeper sequencing depths are required. Values for specific cases can be determined by using Hi-C Poweraid. This tool simplifies Hi-C power calculations, allowing for more efficient use of time and resources and more accurate interpretation of experimental results. Hi-C Poweraid is available as an R Shiny application deployed at http://phanstiel-lab.med.unc.edu/poweraid/, with code available at https://github.com/sarmapar/poweraid.

Cohesin and CTCF control the dynamics of chromosome folding

In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, how long they last and how they depend on the dynamics of chromosome folding and loop extrusion activity of cohesin. By imaging chromosomal locations at high spatial and temporal resolution in living cells, we show that interactions within topologically associating domains are transient and occur frequently during the course of a cell cycle. Interactions become more frequent and longer in the presence of convergent CTCF sites, resulting in suppression of variability in chromosome folding across time. Supported by physical models of chromosome dynamics, our data suggest that CTCF-anchored loops last around 10 min. Our results show that long-range transcriptional regulation might rely on transient physical proximity, and that cohesin and CTCF stabilize highly dynamic chromosome structures, facilitating selected subsets of chromosomal interactions.

Multilevel view on chromatin architecture alterations in cancer.

Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.

Alphafold Predictions Provide Insights into the Structural Features of the Functional Oligomers of All Members of the KCTD Family.

Oligomerization endows proteins with some key properties such as extra-stabilization, long-range allosteric regulation(s), and partnerships not accessible to their monomeric counterparts. How oligomerization is achieved and preserved during evolution is a subject of remarkable scientific relevance. By exploiting the abilities of the machine-learning algorithms implemented in AlphaFold (AF) in predicting protein structures, herein, we report a comprehensive analysis of the structural states of functional oligomers of all members of the KCTD protein family. Interestingly, our approach led to the identification of reliable three-dimensional models for the pentameric states of KCNRG, KCTD6, KCTD4, KCTD7, KCTD9, and KCTD14 and possibly for KCTD11 and KCTD21 that are involved in key biological processes and that were previously uncharacterized from a structural point of view. Although for most of these proteins, the CTD domains lack any sequence similarity, they share some important structural features, such as a propeller-like structure with a central cavity delimited by five exposed and regular β-strands. Moreover, the structure of the related proteins KCTD7 and KCTD14, although pentameric, appears to be characterized by a different organization of the CTD region, with the five chains forming a circle-like structure with a large cavity. Our predictions also suggest that other members of the family, such as KCTD10, KCTD13, and TNFAIP1, present a strong propensity to assume dimeric states. Although the structures of the functional oligomers reported herein represent models that require additional validations, they provide a consistent and global view of KCTD protein oligomerization.

Evaluating Genetic Modifiers of Duchenne Muscular Dystrophy Disease Progression Using Modeling and MRI.

Duchenne muscular dystrophy (DMD) is a progressive muscle degenerative disorder with a well-characterized disease phenotype but considerable interindividual heterogeneity that is not well understood. The aim of this study was to evaluate the effects of dystrophin variations and genetic modifiers of DMD on rate and age of muscle replacement by fat. One hundred seventy-five corticosteroid treated participants from the ImagingDMD natural history study underwent repeated magnetic resonance spectroscopy (MRS) of the vastus lateralis (VL) and soleus (SOL) to determine muscle fat fraction (FF). MRS was performed annually in most instances; however, some individuals had additional visits at 3 or 6 monthss intervals. FF changes over time were modeled using nonlinear mixed effects to estimate disease trajectories based on the age that the VL or SOL reached half-maximum change in FF (mu) and the time required for FF change (sigma). Computed mu and sigma values were evaluated for dystrophin variations that have demonstrated the ability to lead to a mild phenotype as well as compared between different genetic polymorphism groups. Participants with dystrophin gene deletions amenable to exon 8 skipping (n = 4) had minimal increases in SOL FF and had an increase in VL mu value by 4.4 years compared with a reference cohort (p = 0.039). Participants with nonsense variations within exons that may produce milder phenotypes (n = 11) also had minimal increases in SOL and VL FFs. No differences in estimated FF trajectories were seen for individuals amenable to exon 44 skipping (n = 10). Modeling of the SPP1, LTBP4, and thrombospondin-1 (THBS1) genetic modifiers did not result in significant differences in muscle FF trajectories between genotype groups (p > 0.05); however, trends were noted for the polymorphisms associated with long-range regulation of LTBP4 and THBS1 that deserve further follow-up. The results of this study link the historically mild phenotypes seen in individuals amenable to exon 8 skipping and with certain nonsense variations with alterations in trajectories of lower extremity muscle replacement by fat.