Despite the well-established role of condensin II in mitotic chromosome assembly, its function in interphase chromosome organization remains poorly understood. Here, we applied multiscale FISH techniques to human cell lines engineered for single or double depletion of condensin II and cohesin and examined their functional collaboration at two distinct stages of the cell cycle. Our results demonstrate that a functional interplay between condensin II and cohesin during the mitosis-to-G1 transition is critical for establishing chromosome territories (CTs) in the newly assembling nucleus. During the G2 phase, condensin II and cohesin cooperate to maintain global CT morphology, although they act at different genomic scales. Strikingly, double depletion of both complexes causes CTs to collapse and accumulate abnormally at the nucleolar periphery. Based on these findings, we will discuss how the condensin and cohesin complexes act in an orderly and cooperative manner to orchestrate chromatin dynamics across genomic scales, thereby supporting higher-order chromosome organization throughout the cell cycle.

Bacterial chromosomes are organized by condensins, such as Structural Maintenance of Chromosomes (SMC) proteins. In Streptomyces, a genus of sporulating bacteria, SMC proteins align chromosomal arms and promote efficient compaction of chromosomal DNA during spore formation. We hypothesized that disrupting nucleoid architecture by deleting the smc gene would affect the positioning of the origin of replication (oriC) or the process of chromosome replication during spore germination. To test this hypothesis, we conducted marker frequency analyses and microscopy studies to observe the positioning of labelled oriC and replisomes in both wild type and Δsmc backgrounds. Additionally, we investigated the positioning of three chromosomal loci in early vegetative cells. Our results indicate that the deletion of smc impairs chromosome replication and hinders germ tube development. Furthermore, detailed analysis of chromosome organization revealed that, in the absence of SMC, the oriC region becomes mispositioned within the nucleoid. These findings underscore the important role of SMC in maintaining nucleoid architecture during the early growth stages of Streptomyces.

Background: Bariatric surgery, particularly Roux-en-Y gastric bypass (RYGB), is an effective treatment for extreme obesity, but some patients experience inadequate weight loss or weight regain. This study aimed to identify blood biomarkers that predict effective weight loss following RYGB. Methods: A microarray profile (GSE83223) was utilized to identify differentially expressed genes (DEGs) that could preoperatively predict body mass index (BMI) reduction after RYGB. Thirteen patients were divided into two groups based on their postsurgery BMI reduction: high (group A, n = 4) and low (group B, n = 9). DEGs were identified based on significant log fold change (LFC) ( p < 0.05, │LFC│>1). Analyses included data preprocessing, protein-protein interactions, gene ontology, pathway analysis, and identification of hub genes. Results: Notable DEGs before surgery included SEBOX, NOCT, and TYK2, primarily involved in chromosome organization and macromolecule metabolism. Seventeen genes were consistently down-regulated pre and postsurgery, with SNRPB and BCL11A showing the highest │LFC│. Transcription factors MYC and ATF2 were identified as upstream regulators of these DEGs. Conclusion: The expression levels of these genes may serve as prognostic indicators for predicting the efficacy of bariatric surgery in obese individuals, potentially guiding clinical decisions for improved outcomes.

High-density lipoprotein-binding protein (HDLBP), also called Vigilin, is a multifunctional RNA-binding protein with established roles in RNA transport and regulation, chromosome segregation, lipid homeostasis, and translational regulation. Frequently detected to be perturbed in phosphoproteome analysis, phosphorylation is indicated as a major mechanism in the regulation of HDLBP functions; however, its phosphorylation landscape remains unexplored. We performed a meta-phosphoproteome analysis of HDLBP to map site-specific functional and regulatory roles of its two most frequently detected phosphosites, S31 and S944. Co-occurrence analysis across multiple datasets indicated that they can be phosphorylated together, suggesting potential co-ordinated regulation. Site-specific co-regulation analysis revealed distinct phospho-regulatory networks, with upstream kinases identified exclusively for S944. Functional enrichment of co-regulated protein phosphosites (CPPs) highlighted its role in RNA metabolism, chromosome organization, and nucleoplasmic transport, while functional annotation of site-specific phosphorylation of CPPs indicates its involvement in cell cycle regulation, apoptosis, and carcinogenesis. Additionally, the potential role of CPPs in the lipid homeostasis network was explored. Furthermore, the differential expression of HDLBP phosphosites across multiple cancers was observed using UALCAN, suggesting a potential role for phospho-regulation of HDLBP in tumor-associated pathways. Together, these findings provide the first integrated view of HDLBP phosphorylation and could serve as a valuable framework for future targeted studies to elucidate the mechanistic roles of site-specific HDLBP phosphorylation in cellular and pathophysiological processes.

The initiation of gene expression during development, known as zygotic genome activation (ZGA), is accompanied by massive changes in chromosome organization. However, the earliest events of chromosome folding and their functional roles remain unclear. Using Hi-C on zebrafish embryos, we discovered that chromosome folding begins early in development with the formation of fountains, distinct elements of chromosome organization. Emerging preferentially at enhancers, fountains show an initial accumulation of cohesin, which later redistributes to CTCF sites at TAD borders. Knockouts of pioneer transcription factors driving ZGA enhancers cause a specific loss of fountains, establishing a causal link between enhancer activation and fountain formation. Polymer simulations demonstrate that fountains may arise as sites of facilitated cohesin loading, requiring two-sided but desynchronized loop extrusion, potentially caused by cohesin collisions with obstacles or internal switching. Moreover, we detected cohesin-dependent fountain patterns at enhancers in mouse cells and found them reemerging with cohesin loading after mitosis. Altogether, fountains represent enhancer-specific elements of chromosome organization and suggest that chromosome folding during development and after cell division starts with facilitated cohesin loading. Observations in multiple systems further support facilitated loading at enhancers as a widespread phenomenon.

Cartilaginous fishes are divided into holocephalans and elasmobranchs, and they offer valuable systems for analysing the genetic basis of adaptation to diverse habitats and the evolution of chromosomal organization. Genomic studies on cartilaginous fishes were initiated early with holocephalans because of their compact genomes, but have concentrated primarily on the family Callorhinchidae. Here, we focused on the most species-rich holocephalan family Chimaeridae and characterized the genome of its member, silver chimaera (Chimaera phantasma), in pursuit of genomic traces of adaptation to deep-sea vision. The resulting genome assembly exhibited high continuity and completeness, enabling the first chromosome-level comparison among holocephalans. They displayed substantial intragenomic variation in chromosome length, correlated with intron size, alongside a high degree of one-to-one chromosomal homology. Our search for silver chimaera photoreceptor genes revealed a shrunken set of opsin genes, including rhodopsin exhibiting a sequence signature typical of deep-sea adaptation. We also performed whole-genome resequencing of multiple silver chimaera individuals of both sexes, which identified a putative X-chromosome fragment. This is the first evidence of a holocephalan sex chromosome and suggests male heterogametic sex determination. Our findings contribute to a deeper understanding of vertebrate genome diversity and lay the groundwork for future genetic studies on this species.

The unique chlamydial developmental cycle comprises three stages: primary differentiation of infectious elementary bodies (EBs) into reticulate bodies (RBs), RB replication, and secondary differentiation into progeny EBs. Extensive chromosome remodeling during RB-to-EB differentiation is thought to be mediated by the histones HctA and HctB. Here, we used an inducible CRISPR interference system to repress hctA, hctB, or both genes during development in Chlamydia trachomatis. Surprisingly, repression of either histone gene alone or in combination caused only modest reductions in EB yield and did not prevent nucleoid condensation during the parental developmental cycle. In contrast, when progeny EBs generated under histone-repressing conditions were used to initiate secondary infections in the absence of inducer, histone deficiency during EB maturation profoundly impaired fitness in the next infection cycle. Secondary cultures initiated with HctA-deficient EBs exhibited a delayed onset of genome replication, consistent with inefficient primary EB-to-RB differentiation, whereas combined repression of hctA and hctB caused both delayed genome replication and persistently reduced genome accumulation, indicative of defects in RB formation and subsequent growth. Repression of hctB alone did not measurably affect genome replication in secondary cultures. Together, these findings reveal a transgenerational role for chlamydial histones and establish chromosome organization during EB maturation as a key determinant of developmental fitness across infection cycles.

Background/Objectives: Flea beetles (Coleoptera, Chrysomelidae: Alticinae) show extensive karyotypic diversity, yet cytogenetic and genomic data remain scarce for many taxa. Species of the genus Podagrica are characterized by unusually high chromosome numbers compared with the modal condition in Alticinae, suggesting a history of chromosomal fissions. This study aimed to characterize the karyotype and repetitive DNA composition of Podagrica fuscicornis, with special emphasis on the satellitome and its contribution to chromosome organization. Methods: Male specimens of P. fuscicornis collected in southern Spain were analyzed using conventional cytogenetic techniques, including Giemsa staining, DAPI staining, and C-banding. Fluorescence in situ hybridization was employed to map nucleolar organizer regions (NORs), telomeric repeats, and major satellite DNA (satDNA) families. The satellitome was characterized using Illumina short-read sequencing and analyzed with the RepeatExplorer2/TAREAN pipeline to identify satDNA families and estimate their genomic abundance and divergence. Results: The male karyotype of P. fuscicornis was 2n = 40 (38 + XY), with an Xyp sex chromosome system. Constitutive heterochromatin was mainly pericentromeric, and the Y chromosome was largely heterochromatic. NORs were located on a single autosomal pair, and the ancestral insect telomeric motif (TTAGG)n was detected at chromosome ends. The satellitome comprised at least 70 different satDNA families, representing 9.51% of the genome, some of them related to transposable elements. Ten of these 70 satDNAs are shared in other Alticinae species. The most abundant families were primarily localized in pericentromeric regions and showed differential distribution between autosomes and sex chromosomes. Conclusions: These results indicate that extensive chromosomal fissions and high satDNA dynamics could drive the high chromosome number and heterogeneous genome organization in P. fuscicornis, highlighting the role of repetitive DNA in karyotype evolution within Chrysomelidae.

Spinach (Spinacia oleracea L.) is a nutrient-dense leafy vegetable characterized by its rapid growth rate, high antioxidant content, and adaptability to various environmental conditions. The elucidation of the genetic regulatory networks of spinach, particularly the transcription factor families are important for stress responses and are essential for improving adaptability and sustainability. A genome-wide analysis identified 42 member families of the Ethylene Response Factor family gene product. Within each clade, they were classified into three major subclades (AP2, ERF and RAV) consistent with the composition of structural domains. Gene mapping showed an uneven number of SpoERF genes on six chromosomes, many of which were clustered together for an unclear purpose and suggests that tandem duplication is an important mechanism responsible for gene expansion. Gene structure and motif analysis revealed highly conserved AP2 domains but varied intron–exon patterns, which suggest functional diversification. Synteny analysis identified phylogeographically strongly related genes between spinach and Arabidopsis thaliana, probably due to ancient duplication events and the conserved functional elements of the essential ERF regulators. Promoter analysis showed extensive enrichment for many cis-acting elements (Abre, DRE, LTR, W-box, G-box) and revealed involvement of SpoERFs in hormone, developmental, and environmental stress responses among SpoERF family. The findings of this study systematically identify and characterize the AP2/ERF gene family in spinach, revealing their chromosomal organization, evolutionary relationships, conserved structural features, and nitrogen-responsive expression patterns, thereby providing candidate regulatory genes for future functional studies and molecular improvement of nitrogen-use efficiency in spinach.

Genome functions are regulated by chromatin and 3D chromosome organization. Dynamic condensation and relaxation of chromosomes during the cell cycle are largely controlled by the Condensin complexes. We mapped mutants in the Condensin II subunits SMC2A, CAP-D3 and CAP-H2 as hypersensitive to DNA-protein crosslink (DPC) inducers zebularine and ICRF-187. This suggested that Condensin II is required for resistance to genotoxic stress in Arabidopsis (Arabidopsis thaliana) and prompted us to explore the underlying phenotypes. We show that the role of Condensin II in resistance to zebularine is independent of DNA damage response signaling by SOG1 and homology-directed repair. Furthermore, we found that Arabidopsis Condensin II mutants have incompletely condensed mitotic chromosomes and show anaphase bridges. The anaphase bridges were more frequent upon treatment with zebularine or ICRF-187 and the duration of mitosis was prolonged. Altogether, we demonstrate that proper large-scale chromatin organization by Condensin II is important for resistance to DNA damage in Arabidopsis.

DNA bendability plays a critical role in stabilizing nucleosome assembly, yet its contribution to nucleosome dynamics in vivo remains poorly understood. Here, we applied chemical mapping to generate high-resolution nucleosome positioning maps at single-base-pair resolution from human interphase and metaphase chromosomes, revealing distinct patterns of nucleosome organization between the two states. Notably, we observed a unifying pattern of nucleosome positioning near euchromatic landmarks, including promoters, enhancers, and insulators, during mitosis. Interphase nucleosomes exhibited extensive repositioning, marked by increased nucleosome density, reduced spacing between nucleosomes, and the appearance of additional fragile nucleosomes compared to metaphase. Furthermore, our results show that metaphase nucleosomes display significantly higher DNA cyclizability around the dyad axis, whereas interphase nucleosomes, particularly those near regulatory regions, tend to position DNA with greater cyclizability at the edges of the nucleosome. Together, these findings highlight a dynamic interplay between DNA mechanics and nucleosome organization during the cell cycle.

Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these have mainly been observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is "secluded" from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. In polymer simulations, this contact pattern can only be explained by high loop extrusion activity within compartment S, combined with low extrusion elsewhere throughout the genome. This proposed targeting of loop extrusion is a novel phenomenon, not observed in vertebrate models, but we speculate may extend to more organisms, such as other insects. Overall, our study underscores how evolutionarily conserved mechanisms-compartmentalization and loop extrusion-can be repurposed to create new 3D genome architectures.

Genome folding is a key regulator of transcription, chromosome segregation, and genome stability. In Caenorhabditis elegans, chromatin folding strategies have diverged from those observed in mammals or flies, resulting in the absence of visible topologically associating domains (TADs) on autosomes. Here, condensin I, rather than cohesin, serves as the primary long-range loop extruder, while distinct cohesin isoforms specialize in mitotic cohesion and loop extrusion, forming enhancer-associated 'fountains' that modulate neuronal gene expression. On the X chromosome, dosage compensation depends on the dosage compensation complex, which incorporates a specialized condensin IDC to establishTADs, regulate chromatin states, and repress transcription. These multilayered mechanisms illustrate the evolutionary versatility of 3D genome organization and its intimate links to development, physiology, and lifespan, positioning C. elegans as a powerful model for dissecting structural maintenance of chromosomes-mediated genome regulation.

The cell nucleus is a dynamic environment where ATP-driven processes - like transcription, replication, and epigenetic modifications - continually drive the genome far from thermodynamic equilibrium. Recent interdisciplinary efforts combining cell biology and physics have introduced coarse-grained polymer models that reveal how these active processes shape chromosome organization in space and time. We review how these models have shed light on selected key features of nuclear function: the maintenance of epigenetic memory, the coupling between transcriptional activity and chromatin motion, and the emergence of replication factories. These approaches provide mechanistic insight and predictive power that are beyond experiments alone. We conclude by outlining future directions toward viewing the genome as an active polymer maintained far from equilibrium.

Understanding the molecular mechanisms underlying phenotypic novelties is fundamental to deciphering the evolution of biodiversity. As a pivotal driver of phenotypic divergence, gene regulation operates through multiple layers, including transcriptional dynamics and post-transcriptional modifications. Laryngeal echolocation, an evolutionary breakthrough enabling bats to occupy specialized nocturnal niches, has been instrumental in their global adaptive radiation. Here, we leverage a comparative framework of two laryngeal echolocating (Rhinolophus sinicus and Myotis pilosus) and two non-laryngeal echolocating bats (Cynopterus sphinx and Rousettus leschenaultii) to dissect the contributions of differential expression (DE) and alternative splicing (AS) in shaping this sophisticated sensory system. Integrating short-read RNA sequencing with long-read isoform-resolution data from cochlear tissues, we systematically identified differentially expressed genes (DEGs) and alternatively spliced genes (ASGs). Our multi-method validation revealed distinct regulatory signatures: Upregulated DEGs in laryngeal echolocating bats showed significant enrichment for neural function (synapse organization and neuron development), while ASGs are predominantly associated with epigenetic regulation (protein methylation, histone modification, and chromosome organization). Notably, cross-comparative analyses demonstrated a higher-than-expected overlap between DEGs and ASGs, with two key regulators (SRRM4 and MAP1B) consistently identified across all four interspecies comparisons. These conserved candidates exhibited dual regulatory modalities, suggesting their pleiotropic roles in coordinating transcriptional and post-transcriptional programs. Intriguingly, we detected varying levels of selection pressure acting on DEGs and ASGs, implying different evolutionary constraints on these regulatory layers. Overall, our findings establish that both DE and AS contribute to the molecular architecture of laryngeal echolocation, though their interplay-whether synergistic or independent-requires further mechanistic interrogation.

Compacting chromatin within the cellular nucleus presents a significant challenge for biology. Chromosomes must be both condensed and spatially organized to enable essential processes such as transcription and replication. Chromosome conformation capture experiments (e.g., Hi-C) provide valuable information about the spatial organization and, therefore, the connectivity between different genomic regions. These experiments inspired polymer models that describe the physical mechanism of the chromosomal energy landscape. The Full-Inversion Chromatin model (FI-Chrom), a data-driven approach for modeling genome organization, uses Hi-C contact maps to infer pairwise interaction potentials between all chromosomal loci. It combines Graphics Processing Unit (GPU)-accelerated simulations with efficient training of tens of millions of parameters derived from the maximum-entropy principle to determine 3D structures of chromosomes that accurately reproduce Hi-C-like data. FI-Chrom does not make any a priori assumptions regarding chromosome architecture, making it applicable to any chromosome conformation capture experiment. Its derived structural ensembles capture all essential features from the short- and long-range interactions of typical chromosome organization, such as segregated compartments, chromosome territories, and fully or partially formed loops. Although Hi-C contains only structural information, FI-Chrom extends these data by revealing an emergent dynamical mechanism encoded in the inferred energy landscape. For example, simulations show that chromatin loops are not static architectural features but rather transient structural elements. Statistical analyses further indicate that loops confined within a single compartment occur more frequently than those spanning multiple compartments, highlighting the dynamic and compartment-dependent nature of chromatin organization.

This paper examines the contrasting yet complementary approaches of the Constrained Disorder Principle (CDP) and Stefan Hell's deterministic optical nanoscopy for managing noise in complex systems. The CDP suggests that controlled disorder within dynamic boundaries is crucial for optimal system function, particularly in biological contexts, where variability acts as an adaptive mechanism rather than being merely a measurement error. In contrast, Hell's recent breakthrough in nanoscopy demonstrates that engineered diffraction minima can achieve sub-nanometer resolution without relying on stochastic (random) molecular switching, thereby replacing randomness with deterministic measurement precision. Philosophically, these two approaches are distinct: the CDP views noise as functionally necessary, while Hell's method seeks to overcome noise limitations. However, both frameworks address complementary aspects of information extraction. The primary goal of microscopy is to provide information about structures, thereby facilitating a better understanding of their functionality. Noise is inherent to biological structures and functions and is part of the information in complex systems. This manuscript achieves integration through three specific contributions: (1) a mathematical framework combining CDP variability bounds with Hell's precision measurements, validated through Monte Carlo simulations showing 15-30% precision improvements; (2) computational demonstrations with N = 10,000 trials quantifying performance under varying biological noise regimes; and (3) practical protocols for experimental implementation, including calibration procedures and real-time parameter optimization. The CDP provides a theoretical understanding of variability patterns at the system level, while Hell's technique offers precision tools at the molecular level for validation. Integrating these approaches enables multi-scale analysis, allowing for deterministic measurements to accurately quantify the functional variability that the CDP theory predicts is vital for system health. This synthesis opens up new possibilities for adaptive imaging systems that maintain biologically meaningful noise while achieving unprecedented measurement precision. Specific applications include cancer diagnostics through chromosomal organization variability, neurodegenerative disease monitoring via protein aggregation disorder patterns, and drug screening by assessing cellular response heterogeneity. The framework comprises machine learning integration pathways for automated recognition of variability patterns and adaptive acquisition strategies.

Dps is the most abundant nucleoid-associated protein in starved Escherichia coli with ∼180 000 copies per cell. Dps binds DNA and oxidizes iron, facilitating survival in harsh environments. Dps–DNA complexes can form crystalline structures, leading to the proposed model that Dps reorganizes the starved E. coli nucleoid into a compact liquid crystal, slowing chromosome dynamics, and limiting access of other proteins to DNA. In this work, we directly tested this model using live-cell super-resolution microscopy and Hi-C analysis. We found that after 96 h of starvation, Dps compacts the nucleoid, and increases short-range DNA–DNA interactions but does not affect chromosome accessibility to large protein nanocages or small restriction enzymes. We also report that chromosome dynamics and organization are primarily impacted by the bacterial growth phase; the effect of Dps is relatively minor. Our work clarifies the role of Dps in modulating nucleoid properties, and we propose an updated model for Dps–DNA interactions in which Dps binds, protects, and compacts DNA largely without influencing chromosome access, dynamics, and organization. Additionally, this work provides a general framework for assessing the impact of nucleoid-associated proteins on key aspects of chromosome function in live cells.

Ovulatory disorders are a major cause of infertility. Studies have shown that the renin-angiotensin system (RAS) plays a vital role in the female reproductive system. The angiotensin II type 1 receptor (AT1R), an important mediator of the RAS, may induce anovulation when activated. Previous studies have shown that the levels of AT1R autoantibody (AT1-AA) are significantly higher in the serum of infertile women and are negatively correlated with the oocyte maturation rate. However, systematic understanding of the changes of AT1-AA associated with female ovulatory dysfunction remains limited. In this study, participants were divided into three groups: healthy controls, tubal obstruction group, and ovulatory disorders group. The levels of AT1-AA in serum and follicular fluid were determined using ELISA. The results showed that AT1-AA levels were elevated in both serum and follicular fluid of the ovulatory disorders group compared to the tubal obstruction group. The levels of AT1-AA were negatively correlated with high-quality embryos in the ovulatory disorders group. Follicular fluid AT1-AA levels were an independent risk factor for developing ovulatory disorders. Furthermore, AT1-AA impeded mouse oocyte maturation in vitro, and this effect was suppressed by the second extracellular loop peptide of AT1R. Our findings indicate that follicular fluid AT1-AA is associated with ovulatory disorders and impaired oocyte maturation.

The cohesin complex plays essential roles in chromosome organization and gene regulation, yet how cohesin dynamics are controlled during cell-state transitions remains poorly understood. Here, we examined how cohesin regulation is remodeled during the differentiation of mouse embryonic stem cells (mESCs) into the cardiomyocyte lineage using an in vitro differentiation system. We found that core cohesin subunits remain broadly stable at the protein level. In contrast, the levels of cohesin regulators, including the cohesin removal protein WAPL and the cohesin stabilizing protein ESCO1, decline sharply despite modest transcript-level changes. The cohesion maintenance factor Sororin was also reduced. To better understand the net effect of these changes on cohesin dynamics, we use live-cell FRAP of RAD21, which revealed increased cohesin mobility in differentiated cells without a change in recovery kinetics, consistent with reduced stable chromatin engagement or redistribution into a chromatin-unbound nuclear pool. To test functional consequences, we generated homozygous degron alleles for Wapl and Esco1 and induced acute degradation using a dTAG-based system. Loss of WAPL altered cell-cycle dynamics in stem cells and produced a characteristic “vermicelli” chromosome phenotype, consistent with abnormally high and lethal cohesin retention on chromatin. Surprisingly, depletion of ESCO1 had no clear impact on viability and cell cycle progression. Notably, despite loss of detectable WAPL protein in the differentiated cell population, we find that WAPL remains functionally required to maintain a viable interphase chromosome organization. Together, these findings identify cohesin regulators, rather than cohesin abundance, as central drivers of changes in cohesin dynamics during differentiation. They further show that even very low levels of WAPL continue to provide critical structural plasticity of chromosomes following cell cycle exit and lineage commitment.