Comprehensive mapping of long-range interactions reveals folding principles of the human genome

Closing the loops: chromatin loop dynamics after DNA damage

Chromatin is a dynamic polymer in constant motion. These motions are heterogeneous between cells and within individual cell nuclei and are profoundly altered in response to DNA damage. The shifts in chromatin motions following genomic insults depend on the temporal and physical scales considered. They are also distinct in damaged and undamaged regions. In this review, we emphasize the role of chromatin tethering and loop formation in chromatin dynamics, with the view that pulsing loops are key contributors to chromatin motions. Chromatin tethers likely mediate micron-scale chromatin coherence predicted by polymer models and measured experimentally, and we propose that remodeling of the tethers in response to DNA breaks enables uncoupling of damaged and undamaged chromatin regions.

Leveraging strain competition to address antimicrobial resistance with microbiota therapies

The enteric microbiota is an established reservoir for multidrug-resistant organisms that present urgent clinical and public health threats. Observational data and small interventional studies suggest that microbiome interventions, such as fecal microbiota products and characterized live biotherapeutic bacterial strains, could be an effective antibiotic-sparing prevention approach to address these threats. However, bacterial colonization is a complex ecological phenomenon that remains understudied in the context of the human gut. Antibiotic resistance is one among many adaptative strategies that impact long-term colonization. Here we review and synthesize evidence of how bacterial competition and differential fitness in the context of the gut present opportunities to improve mechanistic understanding of colonization resistance, therapeutic development, patient care, and ultimately public health.

Unravelling early hematoendothelial development through the chick model: Insights and future perspectives

The chicken embryo has been an important model in advancing our understanding of early hematoendothelial development, particularly in the formation of hematopoietic stem cells (HSCs) and the endothelial-to-hematopoietic transition (EHT). The accessibility and ease of manipulation of chicken embryos have made them an invaluable tool for researching development of blood and endothelial cells. Early research using this model provided pivotal insights, demonstrating that intra-embryonic regions, such as the dorsal aorta (DA), are primary sources of HSCs, rather than the yolk sac (YS), as previously believed. The identification of intra-aortic hematopoietic clusters (IAHCs) and the process of EHT in the chicken embryo laid the foundation for similar discoveries in other vertebrate species, including mice and zebrafish. Recent advances in genetic tools, such as transgenic chickens expressing fluorescent proteins, have further enhanced the precision of cell lineage tracing and real-time imaging of dynamic cellular processes. This review highlights both historical contributions and contemporary advancements facilitated by the chicken model, underscoring its continued relevance in developmental biology. By examining key findings and methodological innovations, we aim to demonstrate the importance of the chicken embryo as a model system for understanding hematoendothelial development and its potential for informing therapeutic applications in regenerative medicine and blood disorders. Finally, we will underscore potential applications of the chicken model for comparative and omics-level studies in conjunction with other model systems and what future directions lie ahead.

Cardiac enhancers: Gateway to the regulatory mechanisms of heart regeneration

The adult mammalian heart has limited regenerative capacity. Cardiac injury, such as a myocardial infarction (MI), leads to permanent scarring and impaired heart function. In contrast, neonatal mice and zebrafish possess the ability to repair injured hearts. Cardiac regeneration is driven by profound transcriptional changes, which are controlled by gene regulatory elements, such as tissue regeneration enhancer elements (TREEs). Here, we review recent studies on cardiac injury/regeneration enhancers across species. We further explore regulatory mechanisms governing TREE activities and their associated binding regulators. We also discuss the potential of TREE engineering and how these enhancers can be utilized for heart repair. Decoding the regulatory logic of cardiac regeneration enhancers presents a promising avenue for understanding heart regeneration and advancing therapeutic strategies for heart failure.

Epigenetics in the modern era of crop improvements

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

Bridging spatial and temporal scales of developmental gene regulation

The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue organization during development is crucial for explaining the remarkable reproducibility of complex organisms. This review explores how chromatin-encoded information is transduced from localized transcriptional events to global gene expression patterns, highlighting the challenge of bridging these scales. We discuss recent experimental findings and theoretical frameworks, emphasizing polymer physics as a tool for describing the relationship between chromatin structure and dynamics across scales. By integrating these perspectives, we aim to clarify how gene regulation is coordinated across levels of biological organization and suggest strategies for future experimental approaches.

Three-dimensional genome architecture in intrahepatic cholangiocarcinoma

PURPOSE

Intrahepatic cholangiocarcinoma (ICC) is a common primary hepatic tumors with a 5-year survival rate of less than 20%. Therefore, it is crucial to elucidate the molecular mechanisms of ICC. Recently, the advance of high-throughput chromosome conformation capture (Hi-C) technology help us look insight into the three-dimensional (3D) genome structure variation during tumorigenesis. However, its function in ICC pathogenesis remained unclear.

METHODS

Hi-C and RNA-sequencing were applied to analyze 3D genome structures and gene expression in ICC and adjacent noncancerous hepatic tissue (ANHT). Furthermore, the dysregulated genes due to 3D genome changes were validated via quantitative real-time PCR and immunohistochemistry.

RESULTS

Primarily, the intrachromosomal interactions of chr1, chr2, chr3, and chr11 and the interchromosomal interactions of chr1-chr10, chr13-chr21, chr16-chr19, and chr19-chr22 were also significantly distinct between ANHT and ICC, which may potentially contribute to the activation of cell migration and invasion via the upregulation of WNT10A, EpCAM, S100A3/A6, and MAPK12. Interestingly, 56 compartment regions from 23 chromosomes underwent A to B or B to A transitions during ICC oncogenesis, which attenuated the complement pathway through the downregulation of C8A/C8B, F7, F10, and F13B. Notably, topologically associated domain (TAD) rearrangements were identified in the region containing HOPX (chr4: 57,514,154-57,522,688) and ACVR1 (chr2:158,592,958-158,732,374) in ICC, which may contribute to the hijacking of remote enhancers that were previously outside the TAD and increased expression of HOPX and ACVR1.

CONCLUSIONS

This study reveals relationship between 3D genome structural variations and gene dysregulation during ICC tumorigenesis, indicating the molecular mechanisms and potential biomarkers.

Generative inpainting of incomplete Euclidean distance matrices of trajectories generated by a fractional Brownian motion

Fractional Brownian motion (fBm) exhibits both randomness and strong scale-free correlations, posing a challenge for generative artificial intelligence to replicate the underlying stochastic process. In this study, we evaluate the performance of diffusion-based inpainting methods on a specific dataset of corrupted images, which represent incomplete Euclidean distance matrices (EDMs) of fBm across various memory exponents (H). Our dataset reveals that, in the regime of low missing ratios, data imputation is unique, as the remaining partial graph is rigid, thus providing a reliable ground truth for inpainting. We find that conditional diffusion generation effectively reproduces the inherent correlations of fBm paths across different memory regimes, including sub-diffusion, Brownian motion, and super-diffusion trajectories, making it a robust tool for statistical imputation in cases with high missing ratios. Moreover, while recent studies have suggested that diffusion models memorize samples from the training dataset, our findings indicate that diffusion behaves qualitatively differently from simple database searches, allowing for generalization rather than mere memorization of the training data. As a biological application, we utilize our fBm-trained diffusion model to impute microscopy-derived distance matrices of chromosomal segments (FISH data), which are incomplete due to experimental imperfections. We demonstrate that our inpainting method outperforms standard bioinformatic methods, suggesting a novel physics-informed generative approach for the enrichment of high-throughput biological datasets.

3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback

DNA within the nucleus is organised into a well-regulated three-dimensional (3D) structure. However, how such 3D genome structures influence speciation processes remains largely elusive. Recent studies have shown that 3D genome structures influence mutation rates, including the occurrence of chromosomal rearrangement. For example, breakpoints of chromosomal rearrangements tend to be located at topologically associating domain (TAD) boundaries. Here, we hypothesised that TAD structures may constrain the location of chromosomal inversions and thereby shape the genomic landscape of divergence between species with ongoing gene flow, given that inversions can act as barriers to gene flow. To test this hypothesis, we used a pair of Japanese stickleback species, Gasterosteus nipponicus (Japan Sea stickleback) and G. aculeatus (three-spined stickleback). We first constructed chromosome-scale genome assemblies of both species using high fidelity long reads and high-resolution proximity ligation data and identified several chromosomal inversions. Second, via population genomic analyses, we revealed higher genetic differentiation in inverted regions than in colinear regions and no gene flow within inversions, which contrasts with the significant gene flow in colinear regions. Third, using Hi-C data, we revealed 3D genome structures of sticklebacks, delineated by A/B compartments and TADs. Finally, we found that inversion breakpoints tend to be located at TAD boundaries. Thus, our study demonstrates that the 3D genome constrains breakpoints of inversions that can act as barriers to gene flow in the stickleback. Further integration of 3D genome analyses with population genomics could provide novel insights into how the 3D genome influences speciation.

TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation

Cis-regulatory elements (CREs) direct precise gene expression for development and environmental response, yet their spatial organization in crops is largely unknown. We introduce transposase-accessible chromosome conformation capture (TAC-C), a method integrating ATAC-seq and Hi-C to capture fine-scale chromatin interactions in four major crops: rice, sorghum, maize, and wheat. TAC-C reveals a strong association between chromatin interaction frequency and gene expression, particularly emphasizing the conserved roles of chromatin interaction hub anchors and hub genes across crop species. Integrating chromatin structure with population genetics data highlights that chromatin loops connect distal regulatory elements to phenotypic variation. In addition, asymmetrical open chromatin interactions among subgenomes, driven by transposon insertions and sequence variations, contribute to biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related genes through chromatin interactions, with enhanced photosynthetic efficiency and starch content in Taspl7&15 mutant. TAC-C provides insights into the spatial organization of regulatory elements in crops, especially for SPL-mediated photosynthesis regulation in wheat.

Chromosome-level assemblies of the White bream Parabramis pekinensis

White bream Parabramis pekinensis is an omnivorous fish belong to Cyprinidae that is widespread in Asia. In this study, we presented chromosome-level genome assemblies of P. pekinensis by using PacBio HiFi long reads and Hi-C technology. We assembled high-quality genome of 1.03 Gb with scaffold N50 length of 40.04 Mb, and a total of 98.31% of the assembled sequences were anchored to 24 chromosomes. BUSCO analysis revealed that the genome assembly has a high-level completeness of 98.35% gene coverage. A total of 26,542 protein-coding genes were predicted, of which 92.61% were functionally annotated. The phylogenetic analysis indicated that the lineage leading to P. pekinensis was diverged from the lineage to Megalobrama amblycephala approximately 7.6 million years ago. The high-quality genome assembly provide valuable resources for evolutionary study and genetic breeding of genus Parabramis.

Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation

The three-dimensional (3D) chromatin structure of Epstein-Barr virus (EBV) within host cells and the underlying mechanisms of chromatin interaction and gene regulation, particularly those involving EBV's noncoding RNAs (ncRNAs), have remained incompletely characterized. In this study, we employed state-of-the-art techniques of 3D genome mapping, including protein-associated chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), RNA-associated chromatin interaction technique (RDD), and super-resolution microscopy, to delineate the spatial architecture of EBV in human lymphoblastoid cells. We systematically analyzed EBV-to-EBV (E-E), EBV-to-host (E-H), and host-to-host (H-H) interactions linked to host proteins and EBV RNAs. Our findings reveal that EBV utilizes host CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) to form distinct chromatin contact domains (CCDs) and RNAPII-associated interaction domains (RAIDs). The anchors of these chromatin domains serve as platforms for extensive interactions with host chromatin, thus modulating host gene expression. Notably, EBV ncRNAs, especially Epstein-Barr-encoded RNAs (EBERs), target and interact with less accessible regions of host chromatin to repress a subset of genes via the inhibition of RNAPII-associated chromatin loops. This process involves the cofactor nucleolin (NCL) and its RNA recognition motifs, and depletion of either NCL or EBERs alters expression of genes crucial for host infection control, immune response, and cell cycle regulation. These findings unveil a sophisticated interplay between EBV and host chromatin.

Integrated analysis of differential intra-chromosomal community interactions: A study of breast cancer

It is challenging to analyze the dynamics of intra-chromosomal interactions when considering multiple high-dimensional epigenetic datasets. A computational approach, differential network analysis in intra-chromosomal community interaction (DNAICI), was proposed here to elucidate these dynamics by integrating Hi-C data with other epigenetic data. DNAICI utilized a novel hyperparameter tuning method, for optimizing the network clustering, to identify valid intra-chromosomal community interactions at different resolutions. The approach was first trained on Hi-C data and other epigenetic data in an untreated and one hour estrogen (E2)-treated breast cancer cell line, MCF7, and uncovered two major types of valid intra-chromosomal community interactions (active/repressive) that resembles the properties of A/B compartments (or open/closed chromatin domains). It was further tested on the breast cancer cell line MCF7 and its corresponding tamoxifen-resistant (TR) derivative, MCF7TR, and identified 515 differentially interacting and expressed genes (DIEGs) within intra-chromosomal community interactions. In silico analysis of these DIEGs revealed that endocrine resistance is among the top biological pathways, suggesting an interacting/looping-mediated mechanism in regulating breast cancer tamoxifen resistance. This novel integrated network analysis approach offers a broad application in diverse biological systems for identifying a biological-context-specific differential community interaction.

MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures

The genome is organized into distinct chromatin compartments with at least two main classes, a transcriptionally active A and an inactive B compartment, broadly corresponding to euchromatin and heterochromatin. Chromatin regions within the same compartment preferentially interact with each other over regions in the opposite compartment. A/B compartments are traditionally identified from ensemble Hi-C contact frequency matrices using principal component analysis of their covariance matrices. However, defining compartments at the single-cell level from sparse single-cell Hi-C data is challenging, especially since homologous copies are often not resolved. To address this, we present MaxComp, an unsupervised method, for inferring single-cell A/B compartments based on 3D geometric considerations in single-cell chromosome structures-derived either from multiplexed FISH-omics imaging or 3D structure models derived from Hi-C data. By representing each 3D chromosome structure as an undirected graph with edge-weights encoding structural information, MaxComp reformulates compartment prediction as a variant of the Max-cut problem, solved using semidefinite graph programming (SPD) to optimally partition the graph into two structural compartments. Our results show that the population average of MaxComp single-cell compartment annotations closely matches those derived from ensemble Hi-C principal component analysis, demonstrating that compartmentalization can be recovered from geometric principles alone, using only the 3D coordinates and nuclear microenvironment of chromatin regions. Our approach reveals widespread cell-to-cell variability in compartment organization, with substantial heterogeneity across genomic loci. When applied to multiplexed FISH imaging data, MaxComp also uncovers relationships between compartment annotations and transcriptional activity at the single-cell level. In summary, MaxComp offers a new framework for understanding chromatin compartmentalization in single cells, connecting 3D genome architecture, and transcriptional activity with the cell-to-cell variations of chromatin compartments.

Unfolding neural diversity: how dynamic three-dimensional genome architecture regulates brain function and disease

The advent of single cell multi-omic technologies has ushered in a revolution in how we study the impact of three-dimensional genome organization on brain cellular composition and function. Transcriptomic and epigenomic studies reveal enormous cellular diversity that is present in mammalian nervous systems, raising the question, "how does this diversity arise and for what is its use?" Advances in the field of three-dimensional nuclear architecture have illuminated our understanding of how genome folding gives rise to dynamic gene expression programs important in healthy brain function and in disease. In this review we highlight recent work defining how neuronal identity, maturation, and plasticity are shaped by genome architecture. We discuss how newly identified genetic variations influence genome architecture and contribute to the evolution of species-unique neuronal and behavioral functional traits. We include examples for both humans and model organisms in which maladaptive genomic architecture is a causal agent in disease. Finally, we make conclusions and address future perspectives of dynamic three-dimensional genome (4D nucelome) research.

3D genome organization shapes DNA damage susceptibility to platinum-based drugs

Platinum (Pt) drugs are widely utilized in cancer chemotherapy. Although cytotoxic and resistance mechanisms of Pt drugs have been thoroughly explored, it remains elusive what factors affect the receptiveness of DNA to drug-induced damage in nuclei. Here, we demonstrate that nuclear locations of chromatin play a key role in Pt drug-induced DNA damage susceptibility in vivo. By integrating data from damage-seq experiments with 3D genome structure information, we show that nuclear locations of chromatin relative to specific nuclear bodies and compartments explain patterns of cisplatin DNA damage susceptibility. This aligns with observations of cisplatin enrichment in biomolecular condensates at certain nuclear bodies. Finally, 3D structure mapping of DNA damage reveals characteristic differences between nuclear distributions of oxaliplatin-induced DNA damage in drug resistant versus sensitive cells. DNA damage increases in gene-poor chromatin at the nuclear periphery, while it decreases in gene-rich regions located at nuclear speckles. This suggests a strategic redistribution of Pt drug-induced damage in nuclei during chemoresistance development.

Binder and monomer valencies determine the extent of collapse and reswelling of chromatin

Multivalent DNA-bridging protein-mediated collapse of chromatin polymers have long been established as one of the driving factors in chromatin organization inside cells. These multivalent proteins can bind to distant binding sites along the chromatin backbone and bring them together in spatial proximity, leading to collapsed conformations. Recently, it has been suggested that these proteins not only drive the collapse of the chromatin polymer but also reswelling at higher concentrations. In this study, we investigate the physical mechanisms underlying this unexpected reswelling behavior. We use the Langevin dynamics simulation of a coarse-grained homopolymer to investigate the effects of the valencies of both the binders and the monomers on the polymer conformations. We find that while the extent of collapse of the polymer is strongly dependent on the binder valency, the extent of reswelling is largely determined by the monomer valency. Furthermore, we also discovered two different physical mechanisms that drive the reswelling of the polymer-excluded volume effects and loss of long-range loops. Finally, we obtain a classification map to determine the regimes in which each of these mechanisms is the dominant factor leading to polymer reswelling.

scHiCSRS: a self-representation smoothing method with Gaussian mixture model for imputing single cell Hi-C data

BACKGROUND

Single cell Hi-C (scHi-C) techniques make it possible to study cell-to-cell variability, but excess of zeros are makes scHi-C matrices extremely sparse and difficult for downstream analyses. The observed zeros are a combination of two events: structural zeros for which two loci never interact due to underlying biological mechanisms, or dropouts (sampling zeros) where two loci interact but not captured due to insufficient sequencing depth. Although data quality improvement approaches have been proposed, little has been done to differentiate these two types of zeros, even though such a distinction can greatly benefit downstream analysis such as clustering.

RESULTS

We propose scHiCSRS, a self-representation smoothing method that improves data quality, and a Gaussian mixture model that identifies structural zeros among observed zeros. scHiCSRS not only takes spatial dependencies of a scHi-C data matrix into account but also borrows information from similar single cells. Through an extensive set of simulation studies, we demonstrate the ability of scHiCSRS for identifying structural zeros with high sensitivity and for accurate imputation of dropout values in sampling zeros. Downstream analyses for three experimental datasets show that data improved from scHiCSRS yield more accurate clustering of cells than simply using observed data or improved data from comparison methods.

CONCLUSION

In summary, scHiCSRS provides a valuable tool for identifying structural zeros and imputing dropouts. The resulted data are improved for downstream analysis, especially for understanding cell-to-cell variation through subtype clustering.

Differential genome organization revealed by comparative topological analysis of Mycobacterium tuberculosis strains H37Rv and H37Ra

Recent studies have shown that three-dimensional architecture of bacterial chromatin plays an important role in gene expression regulation. However, genome topological organization in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, remains unknown. On the other hand, the exact mechanism of differential pathogenesis in the canonical strains of M. tuberculosis H37Rv and H37Ra remains poorly understood in terms of their raw sequences. In this context, a detailed contact map from a Hi-C experiment is a candidate for what bridges the gap. Here, we present the first comprehensive report on genome-wide contact maps between regions of H37Rv and H37Ra genomes. We tracked differences between the genome architectures of H37Rv and H37Ra, which could possibly explain the virulence attenuation in H37Ra. We confirm the existence of a differential organization between the two strains most significantly a higher chromosome interaction domain (CID) size in the attenuated H37Ra strain. CID boundaries are also found enriched with highly expressed genes and with higher operon density in H37Rv. Furthermore, most of the differentially expressed PE/PPE genes were present near the CID boundaries in H37Rv and not in H37Ra. We also found a systemic reorganization of CIDs in both virulent H37Rv and avirulent H37Ra strains after hypoxia induction. Collectively, our study proposes a differential genomic topological pattern between H37Rv and H37Ra, which could explain the virulence attenuation in H37Ra.IMPORTANCEGenome organization studies using chromosome conformation capture techniques have proved to be useful in establishing a three-dimensional (3D) landscape of bacterial chromatin. The sequence-based studies failed to unveil the exact mechanism for virulence attenuation in one of the Mycobacterium tuberculosis strains H37Ra. Moreover, as of today, no study investigated the 3D structure of the M. tuberculosis genome and how 3D genome organization affects transcription in M. tuberculosis. We investigated the genome topology in virulent and attenuated strains of M. tuberculosis using Hi-C. Our study demonstrated that virulent and attenuated M. tuberculosis strains exhibit distinct topological features that correlate with higher gene expression of virulence genes in the virulent H37Rv strain.

DDX5 super-enhancer promotes vasculogenic mimicry formation and metastasis in nasopharyngeal carcinoma by enhancing ADAM10 transcription

Anti-angiogenic therapies (AATs) exhibit limited efficacy, as most patients with cancer inevitably develop resistance to them. In this study, data generated using a nasopharyngeal carcinoma orthotopic mouse model, combined with clinical data, reveal compensatory vasculogenic mimicry (VM) formation during AAT treatment and the association of VM with poor prognosis in nasopharyngeal carcinoma. Additionally, data-independent acquisition mass spectrometry-based proteomics shows that upregulation of a disintegrin And metalloprotease 10 (ADAM10) contributes to VM. Mechanistically, epigenetic and high-resolution chromatin interaction landscape analyses demonstrate that although ADAM10 does not interact with either the proximal or distal enhancers, DEAD-box helicase 5 (DDX5), a transcription factor of ADAM10, is regulated by long-range looping enhancer-promoter interactions. Further analyses identify transcription factors binding to critical constituents of the DDX5 super-enhancer. Ingenol mebutate, which docks excellently with DDX5, reverses ADAM10-mediated gene expression changes, thereby effectively suppressing compensatory VM formation and metastasis and improving prognosis. Collectively, these findings provide insights into the clinical application of AATs.

RNA polymerase I is essential for driving the formation of 3D genome in early embryonic development in mouse, but not in human

BACKGROUND

Three-dimensional (3D) chromatin architecture undergoes dynamic reorganization during mammalian gametogenesis and early embryogenesis. While mouse studies have shown species-specific patterns as well as mechanisms underlying de novo organization, these remain poorly characterized in humans. Although RNA polymerases II and III have been shown to regulate chromatin structure, the potential role of RNA polymerase I (Pol I), which drives ribosomal RNA production, in shaping 3D genome organization during these developmental transitions has not been investigated.

METHODS

We employed a modified low-input in situ Hi-C approach to systematically compare 3D genome architecture dynamics from gametogenesis through early embryogenesis in human and mouse. Complementary Smart-seq2 for low-input transcriptomics, CUT&Tag for Pol I profiling, and Pol I functional inhibition assays were performed to elucidate the mechanisms governing chromatin organization.

RESULTS

Our study revealed an extensive reorganization of the 3D genome from human oogenesis to early embryogenesis, displaying significant differences with the mouse, including dramatically attenuated topologically associating domains (TADs) at germinal vesicle (GV) stage oocytes. The 3D genome reconstruction timing is a fundamental difference between species. In human, reconstruction initiates at the 4-cell stage embryo in human, while in mouse, it commences at the 2-cell stage embryo. We discovered that Pol I is crucial for establishing the chromatin structures during mouse embryogenesis, but not in human embryos. Intriguingly, the absence of Pol I transcription weakens TAD structure in mouse female germline stem cells, whereas it fortifies it in human counterparts.

CONCLUSIONS

These observed interspecies distinctions in chromatin organization dynamics provide novel insights into the evolutionary divergence of chromatin architecture regulation during early mammalian development. Our findings provide mechanistic insights into species-specific chromatin organization during germ cell and embryonic development and have potential implications for fertility preservation and birth defect prevention.

RobusTAD: reference panel based annotation of nested topologically associating domains

Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests a hierarchical organization of TADs. Accurately annotating nested TADs from Hi-C data remains challenging, both in terms of the precise identification of boundaries and the correct inference of hierarchies. While domain boundary is relatively well conserved across cells, few approaches have taken advantage of this fact. Here, we present RobusTAD to annotate TAD hierarchies. It incorporates additional Hi-C data to refine boundaries annotated from the study sample. RobusTAD outperforms existing tools at boundary and domain annotation across several benchmarking tasks.

Enhancers in Plant Development, Adaptation and Evolution

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants. This review provides an overview of how enhancers function to control gene regulation, methods to predict DNA sequences that may have enhancer activity, methods utilized to functionally validate enhancers and the current knowledge of enhancers in plants, including how they impact plant development, response to environment and evolutionary adaptation.

CREATE: cell-type-specific cis-regulatory element identification via discrete embedding

Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are predominantly sequence-based and typically focus on individual CRE types, limiting insights into their cell-type-specific functions and regulatory dynamics. Here, we present CREATE, a multimodal deep learning framework based on Vector Quantized Variational AutoEncoder, tailored for comprehensive CRE identification and characterization. CREATE integrates genomic sequences, chromatin accessibility, and chromatin interaction data to generate discrete CRE embeddings, enabling accurate multi-class classification and robust characterization of CREs. CREATE excels in identifying cell-type-specific CREs, and provides quantitative and interpretable insights into CRE-specific features, uncovering the underlying regulatory codes. By facilitating large-scale prediction of CREs in specific cell types, CREATE enhances the recognition of disease- or phenotype-associated biological variabilities of CREs, thus advancing our understanding of gene regulatory landscapes and their roles in health and disease.

Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development

Elucidating the regulatory mechanisms underlying the development of different brain regions in humans is essential for understanding advanced cognition and neuropsychiatric disorders. However, the spatiotemporal organization of three-dimensional (3D) chromatin structure and its regulatory functions across different brain regions remain poorly understood. Here, we generated an atlas of high-resolution 3D chromatin structure across six developing human brain regions, including the prefrontal cortex (PFC), primary visual cortex (V1), cerebellum (CB), subcortical corpus striatum (CS), thalamus (TL), and hippocampus (HP), spanning gestational weeks 11-26. We found that the spatial and temporal dynamics of 3D chromatin organization play a key role in regulating brain region development. We also identified H3K27ac-marked super-enhancers as key contributors to shaping brain region-specific 3D chromatin structures and gene expression patterns. Finally, we uncovered hundreds of neuropsychiatric GWAS SNP-linked genes, shedding light on critical molecules in various neuropsychiatric disorders. In summary, our findings provide important insights into the 3D chromatin regulatory mechanisms governing brain region-specific development and can serve as a valuable resource for advancing our understanding of neuropsychiatric disorders.

Mapping chromatin interactions at melanoma susceptibility loci uncovers distant cis-regulatory gene targets

Genome-wide association studies (GWASs) of melanoma risk have identified 68 independent signals at 54 loci. For most loci, specific functional variants and their respective target genes remain to be established. Capture-HiC is an assay that links fine-mapped risk variants to candidate target genes by comprehensively mapping chromatin interactions. We performed a melanoma GWAS region-focused capture-HiC assay in human primary melanocytes to identify physical interactions between fine-mapped risk variants and potential causal melanoma-susceptibility genes. Overall, chromatin-interaction data alone nominated potential causal genes for 61 of the 68 melanoma risk signals, identifying many candidates beyond those reported by previous studies. We further integrated these data with epigenomic (chromatin state, accessibility), gene expression (expression quantitative trait locus [eQTL]/transcriptome-wide association study [TWAS]), DNA methylation (methylation QTL [meQTL]/methylome-wide association study [MWAS]), and massively parallel reporter assay (MPRA) data generated from melanoma-relevant cell types to prioritize potentially cis-regulatory variants and their respective candidate gene targets. From the set of fine-mapped variants across these loci, we identified 140 prioritized credible causal variants linked to 195 candidate genes at 42 risk signals. In addition, we developed an integrative scoring system to facilitate candidate gene prioritization, integrating melanocyte and melanoma datasets. Notably, at several GWAS risk signals, we observed long-range chromatin connections (500 kb to >1 Mb) with distant candidate target genes. We validated several such cis-regulatory interactions using CRISPR inhibition, providing evidence for known cancer driver genes MDM4 and CBL, as well as the SRY-box transcription factor SOX4, as likely melanoma risk genes.

Regulation of pericentromeric DNA loop size via Scc2-cohesin interaction

Cohesin exhibits DNA loop extrusion when bound to the ATPase activator Scc2 (NIPBL in humans), which has been proposed to organize higher-order chromosome folding. In budding yeast, most chromosome-bound cohesins lack Scc2. How the Scc2-cohesin interaction is regulated on the chromosome and its physiological consequences remain unclear. Here, we show that the deletion of both ECO1 and WPL1, two known cohesin regulators, but not either alone, caused Scc2-cohesin co-localization in metaphase, particularly around centromeres, using calibrated chromatin immunoprecipitation sequencing (ChIP-seq). Eco1's mitotic activity was required to prevent this co-localization in Δwpl1. We also demonstrate that Scc2-cohesin co-localization enlarged pericentromeric DNA loops, linking centromeres to genome sites hundreds of kilobases away, and delayed mitotic chromosome segregation. These findings suggest that Wpl1 and Eco1 cooperatively regulate Scc2-cohesin interaction, restrict pericentromeric DNA loop size, and facilitate chromosome segregation.

Nanoscale DNA tracing reveals the self-organization mechanism of mitotic chromosomes

How genomic DNA is folded during cell division to form the characteristic rod-shaped mitotic chromosomes essential for faithful genome inheritance is a long-standing open question in biology. Here, we use nanoscale DNA tracing in single dividing cells to directly visualize how the 3D fold of genomic DNA changes during mitosis at scales from single loops to entire chromosomes. Our structural analysis reveals a characteristic genome scaling minimum of 6-8 megabases in mitosis. Combined with data-driven modeling and molecular perturbations, we can show that very large and strongly overlapping loops formed by condensins are the fundamental structuring principle of mitotic chromosomes. These loops compact chromosomes locally and globally to the limit set by chromatin self-repulsion. The characteristic length, density, and increasingly overlapping structure of mitotic loops we observe in 3D fully explain how the rod-shaped mitotic chromosome structure emerges by self-organization during cell division.

A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs

BACKGROUND

Topologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries can lead to aberrant expression of neighboring genes. In our study, we analyzed high-throughput chromatin conformation capture (Hi-C) datasets from publicly available sources, integrating 71 datasets across five tissues in six pig breeds.

RESULTS

Our comprehensive analysis revealed 65,843 TADs in pigs, and we found that TAD boundaries are enriched for expression Quantitative Trait Loci (eQTL), splicing Quantitative Trait Loci (sQTL), Loss-of-Function variants (LoFs), and other regulatory variants. Genes within conserved TADs are associated with fundamental biological functions, while those in dynamic TADs may have tissue-specific roles. Specifically, we observed differential expression of the NCOA2 gene within dynamic TADs. This gene is highly expressed in adipose tissue, where it plays a crucial role in regulating lipid metabolism and maintaining energy homeostasis. Additionally, differential expression of the BMPER gene within dynamic TADs is associated with its role in modulating the activities of bone morphogenetic proteins (BMPs)-critical growth factors involved in bone and cartilage development.

CONCLUSION

Our investigations have shed light on the pivotal roles of TADs in governing gene expression and even influencing traits. Our study has unveiled a holistic interplay between chromatin interactions and gene regulation across various tissues and pig breeds. Furthermore, we anticipate that incorporating markers, such as structural variants (SVs), and phenotypes will enhance our understanding of their intricate interactions.

The evolving role of histone H1 in shaping chromatin and epigenetic landscapes

Histone H1, long recognized for its fundamental role in stabilizing nucleosomes and compacting chromatin, is now emerging as a highly dynamic and versatile regulator essential for diverse nuclear processes. This review synthesizes recent advancements that move beyond H1's canonical structural functions, illuminating its intricate, often context-dependent, control over epigenetic modifications, gene expression, and 3D genome organization across eukaryotes. H1's ability to modulate chromatin accessibility and architecture, influenced by its local density, variant composition, and dynamic binding, dictates its species- and locus-specific impacts. H1 critically shapes DNA methylation landscapes and the deposition of key histone marks H3K27me3, often by affecting enzyme accessibility and inter-pathway dynamics. Its transcriptional impact transcends canonical transposable element silencing, extending to the selective fine-tuning of gene expression, with certain H1 variants even functioning as direct transcriptional activators. Regarding 3D genome organization, while H1's local density drives compartmentalization and influences epigenetic states in mammals, in Arabidopsis, it exhibits more complex, locus-specific roles including modulating telomere clustering, interstitial telomeric repeat insulation, and facilitating phase separation for heterochromatin foci assembly. Collectively, these findings establish histone H1 not merely as a structural backbone, but as a sophisticated regulator that intricately links chromatin's physical state to its functional outputs, profoundly impacting genome integrity, gene regulation, and cellular identity.

Hidden origami in Trypanosoma cruzi nuclei highlights its non-random 3D genomic organization

The protozoan Trypanosoma cruzi is the causative agent of Chagas disease and is known for its polycistronic transcription, with about 50% of its genome consisting of repetitive sequences, including coding (primarily multigenic families) and non-coding regions (such as ribosomal DNA, spliced leader [SL], and retroelements, etc). Here, we evaluated the genomic features associated with higher-order chromatin organization in T. cruzi (Brazil A4 strain) by extensive computational processing of high-throughput chromosome conformation capture (Hi-C). Through the mHi-C pipeline, designed to handle multimapping reads, we demonstrated that applying canonical Hi-C processing, which overlooks repetitive DNA sequences, results in a loss of DNA-DNA contacts, misidentifying them as chromatin-folding (CF) boundaries. Our analysis revealed that loci encoding multigenic families of virulence factors are enriched in chromatin loops and form shorter and tighter CF domains than the loci encoding core genes. We uncovered a non-random three-dimensional (3D) genomic organization in which nonprotein-coding RNA loci (transfer RNAs [tRNAs], small nuclear RNAs, and small nucleolar RNAs) and transcription termination sites are preferentially located at the boundaries of the CF domains. Our data indicate 3D clustering of tRNA loci, likely optimizing transcription by RNA polymerase III, and a complex interaction between spliced leader RNA and 18S rRNA loci, suggesting a link between RNA polymerase I and II machineries. Finally, we highlighted a group of genes encoding virulence factors that interact with SL-RNA loci, suggesting a potential regulatory role. Our findings provide insights into 3D genome organization in T. cruzi, contributing to the understanding of supranucleosomal-level chromatin organization and suggesting possible links between 3D architecture and gene expression.IMPORTANCEDespite the knowledge about the linear genome sequence and the identification of numerous virulence factors in the protozoan parasite Trypanosoma cruzi, there has been a limited understanding of how these genomic features are spatially organized within the nucleus and how this organization impacts gene regulation and pathogenicity. By providing a detailed analysis of the three-dimensional (3D) chromatin architecture in T. cruzi, our study contributed to narrowing this gap. We deciphered part of the origami structure hidden in the T. cruzi nucleus, showing the unidimensional genomic features are non-randomly 3D organized in the nuclear organelle. We uncovered the role of nonprotein-coding RNA loci (e.g., transfer RNAs, spliced leader RNA, and 18S RNA) in shaping genomic architecture, offering insights into an additional epigenetic layer that may influence gene expression.

Variant-to-function approaches for adipose tissue: Insights into cardiometabolic disorders

Genome-wide association studies (GWASs) have identified thousands of genetic loci associated with cardiometabolic disorders. However, the functional interpretation of these loci remains a daunting challenge. This is particularly true for adipose tissue, a critical organ in systemic metabolism and the pathogenesis of various cardiometabolic diseases. We discuss how variant-to-function (V2F) approaches are used to elucidate the mechanisms by which GWAS loci increase the risk of cardiometabolic disorders by directly influencing adipose tissue. We outline GWAS traits most likely to harbor adipose-related variants and summarize tools to pinpoint the putative causal variants, genes, and cell types for the associated loci. We explain how large-scale perturbation experiments, coupled with imaging and multi-omics, can be used to screen variants' effects on cellular phenotypes and how these phenotypes can be tied to physiological mechanisms. Lastly, we discuss the challenges and opportunities that lie ahead for V2F research and propose a roadmap for future studies.

Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci

The "holy grail" of chromatin research would be to follow the chromatin configuration in individual live cells over time. One way to achieve this goal would be to track the positions of multiple loci arranged along the chromatin polymer with fluorescent labels. Using distinguishable labels would define each locus uniquely in a microscopic image but would restrict the number of loci that could be observed simultaneously due to experimental limits to the number of distinguishable labels. Using the same label for all loci circumvents this limitation but requires a (currently lacking) framework for how to establish each observed locus identity, i.e., to which genomic position it corresponds. Here, we analyze theoretically, using simulations of Rouse model polymers, how single-particle tracking of multiple identically labeled loci enables the determination of loci identity. We show that the probability of correctly assigning observed loci to genomic positions converges exponentially to unity as the number of observed loci configurations increases. The convergence rate depends only weakly on the number of labeled loci, so that even large numbers of loci can be identified with high fidelity by tracking them across about eight independent chromatin configurations. In the case of two distinct labels that alternate along the chromatin polymer, we find that the probability of the correct assignment converges faster than for same-labeled loci, requiring observation of fewer independent chromatin configurations to establish loci identities. Finally, for a modified Rouse model polymer, which realizes a population of dynamic loops, we find that the success probability also converges to unity exponentially as the number of observed loci configurations increases, albeit slightly more slowly than for a classical Rouse model polymer. Altogether, these results establish particle tracking of multiple identically or alternately labeled loci over time as a feasible way to infer temporal dynamics of the coarse-grained configuration of the chromatin polymer in individual living cells.

Divergent 3D genome organization in livers of cave and surface morphs of Astyanax mexicanus as a potential driver of unique metabolic adaptations in cave environment

The cave morphs of Astyanax mexicanus have evolved a suite of distinct adaptations to life in perpetual darkness, including the loss of eyes and pigmentation loss, as well as profound metabolic changes such as hyperphagia and starvation resilience, traits that sharply contrast with those of their river-dwelling surface counterparts. While changed gene expression is a primary driver of these adaptations, the underlying role of 3D genome organization - a key regulator of gene expression - remains unexplored. Here, we investigate the 3D genome architecture of the livers of surface fish and two cavefish morphs (Pachón and Tinaja) using Hi-C, performing the first comparative 3D genomic analysis in this species. We analyzed and identified cave-specific 3D genomic features, such as genomic compartments and loops, which were conserved in both the cave populations but absent in surface fish. Integrating the 3D genome data with transcriptomic and epigenetic datasets, linked these changes to differential expression of metabolically relevant genes, such as Arhgef19 and Endog . Additionally, our study also uncovered genomic inversions unique to cavefish, potentially tied to cave adaptation. Our findings suggest that 3D genome organization contributes to transcriptomic shifts underlying cavefish phenotypes, providing a novel intra-species and morph specific perspective on 3D chromatin evolution. This study establishes a foundation for exploring how genome architecture potentially facilitates adaptation to new environments. Comparison of morphs within the same species also establishes a foundation for better understanding of how 3D genome reorganization may drive speciation and phenotypic diversity.

FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data

Sequential Oligopaints DNA FISH is an imaging technique that measures higher-order genome folding at single-allele resolution via multiplexed, probe-based tracing. Currently there is a paucity of algorithms to identify 3D genome features in sequential Oligopaints data. Here, we present FISHnet, a graph theory method based on optimization of network modularity to detect chromatin domains in pairwise distance matrices. FISHnet sensitively and specifically identifies domains and boundaries in both simulated and real single-allele imaging data and provides statistical tests for the identification of cell-type-specific domains-like folding patterns. Application of FISHnet across multiple published Oligopaints datasets confirms that nested domains consistent with TADs and subTADs are not an emergent property of ensemble Hi-C data but also observable on single alleles. We make FISHnet code freely available to the scientific community, thus enabling future studies aiming to elucidate the role of single-allele folding variation on genome function.

Epigenetic perspectives on wheat speciation, adaptation, and development

Bread wheat (Triticum aestivum) has undergone a complex evolutionary history shaped by polyploidization, domestication, and adaptation. Recent advances in multiomics approaches have shed light on the role of epigenetic mechanisms, including DNA methylation, histone modification, chromatin accessibility, and noncoding RNAs, in regulating gene expression throughout these processes. Epigenomic reprogramming contributes to genome stability and subgenome differentiation and modulates key agronomic traits by influencing flowering time, environmental responses, and developmental programs. This review synthesizes current insights into epigenetic regulation of wheat speciation, adaptation, and development, highlighting their potential applications in crop improvement. A deeper understanding of these mechanisms will facilitate targeted breeding strategies leveraging epigenetic variations to enhance wheat resilience and productivity in the face of changing environments.

Integrating Arabidopsis and crop species gene discovery for crop improvement

Genome sequence assemblies form a durable and precise framework supporting nearly all areas of biological research, including evolutionary biology, taxonomy and conservation science, pathogen population diversity, crop domestication, and biochemistry. In the early days of plant genomics, resources were limited to a handful of tractable genomes, leading to a tension between focus on discovering mechanisms in experimental species such as Arabidopsis thaliana (Arabidopsis) and on trait analyses in crop species. This tension arose from challenges in translating knowledge of gene function across the large evolutionary distances between Arabidopsis and diverse crop species in the absence of comparative genome support. For some time, these clashing interests influenced funding priorities in plant science that limited both the acquisition of knowledge of mechanisms in Arabidopsis and the timely development of the capacity of crop science to incorporate emerging knowledge of genes and their mechanisms. In this review we show how advances in genomics analysis technologies are revealing a high degree of conservation of molecular mechanisms between evolutionarily distant plant species. This progress is bridging the model-species-to-crop barrier, resulting in ever-increasing unification of plant science that is now accelerating progress in understanding mechanisms underlying diverse traits in crops and improving their performance. We lay out some examples of important priorities and outcomes arising from these new opportunities.

Toward decoding the mechanisms that shape sub-megabase-scale genome organization

Understanding genome organization at the kilobase to megabase scale is critical, as it encompasses genes and regulatory elements. Improvements in the resolution of experimental techniques have revealed novel structural motifs at this scale, including micro-compartments, nucleosome clutches, microdomains, and packing domains. Here we review recent progress on developing theories to explain these observations. Key advances include elucidating the role of nucleosome positioning and epigenetic modifications, the role and mechanisms of compartmentalization in local structure, and the interplay between loop extrusion and phase separation. This work has revealed probable mechanisms by which the observed structures emerge, but it remains unclear how these factors act together in the cell. To this end, recent studies have used chromatin conformation capture data in concert with diverse genomics datasets to create native-like models of chromatin at nucleosome resolution and below. While several roadblocks remain, this strategy promises to decode how molecular forces sum to shape chromatin structure and ultimately regulate transcription.

Sickle cell disease induces chromatin introversion and ferroptosis in CD8+ T cells to suppress anti-tumor immunity

Understanding how genetic disorders affect CD8+ T cells in the tumor microenvironment is key to improving cancer immunotherapy. Individuals with sickle cell disease (SCD), the most prevalent inherited blood disorder, have a higher risk of developing certain cancers than the general population, but the mechanisms driving this increased risk remain unclear. Our study revealed that SCD altered CD8+ T cell 3D genome architecture, triggering ferroptosis and weakening anti-tumor immunity, thereby promoting tumor growth. Using murine and humanized SCD models, we found that disrupted chromosomal interactions in CD8+ T cells reduced the expression of anti-ferroptotic genes, including SLC7A11 and hydrogen sulfide (H2S) biogenesis genes, thereby increasing susceptibility to ferroptosis. Therapeutic restoration of H2S concentration in SCD mice rescued SLC7A11 expression, mitigated ferroptosis, and enhanced immune and anti-tumor responses. These findings highlight the impact of inherited disorders on cancer immunity and suggest precision immunotherapy strategies for affected individuals.

Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants

BACKGROUND

Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type-whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs).

METHODS

We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy.

RESULTS

Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases.

CONCLUSIONS

Through several case studies, we demonstrate how Exo-C's multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.

Native nucleosomes intrinsically encode genome organization principles

The eukaryotic genome is packed into nucleosomes of 147 base pairs around a histone core and is organized into euchromatin and heterochromatin, corresponding to the A and B compartments, respectively1,2. Here we investigated whether individual nucleosomes contain sufficient information for 3D genomic organization into compartments, for example, in their biophysical properties. We purified native mononucleosomes to high monodispersity and used physiological concentrations of polyamines to determine their condensability. The chromosomal regions known to partition into A compartments have low condensability and those for B compartments have high condensability. Chromatin polymer simulations using condensability as the only input, without any trans factors, reproduced the A/B compartments. Condensability is also strongly anticorrelated with gene expression, particularly near the promoters and in a cell type-dependent manner. Therefore, mononucleosomes have biophysical properties associated with genes being on or off. Comparisons with genetic and epigenetic features indicate that nucleosome condensability is an emergent property, providing a natural axis on which to project the high-dimensional cellular chromatin state. Analysis using various condensing agents or histone modifications and mutations indicates that the genome organization principle encoded into nucleosomes is mostly electrostatic in nature. Polyamine depletion in mouse T cells, resulting from either knocking out or inhibiting ornithine decarboxylase, results in hyperpolarized condensability, indicating that when cells cannot rely on polyamines to translate the biophysical properties of nucleosomes to 3D genome organization, they accentuate condensability contrast, which may explain the dysfunction observed with polyamine deficiency3-5.

Chromatin loops are an ancestral hallmark of the animal regulatory genome

In bilaterian animals, gene regulation is shaped by a combination of linear and spatial regulatory information. Regulatory elements along the genome are integrated into gene regulatory landscapes through chromatin compartmentalization1,2, insulation of neighbouring genomic regions3,4 and chromatin looping that brings together distal cis-regulatory sequences5. However, the evolution of these regulatory features is unknown because the three-dimensional genome architecture of most animal lineages remains unexplored6,7. To trace the evolutionary origins of animal genome regulation, here we characterized the physical organization of the genome in non-bilaterian animals (sponges, ctenophores, placozoans and cnidarians)8,9 and their closest unicellular relatives (ichthyosporeans, filastereans and choanoflagellates)10 by combining high-resolution chromosome conformation capture11,12 with epigenomic marks and gene expression data. Our comparative analysis showed that chromatin looping is a conserved feature of genome architecture in ctenophores, placozoans and cnidarians. These sequence-determined distal contacts involve both promoter-enhancer and promoter-promoter interactions. By contrast, chromatin loops are absent in the unicellular relatives of animals. Our findings indicate that spatial genome regulation emerged early in animal evolution. This evolutionary innovation introduced regulatory complexity, ultimately facilitating the diversification of animal developmental programmes and cell type repertoires.

How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice

Large genomic rearrangements, such as chromosomal inversions, can play a key role in evolution, but the mechanisms by which these rearrangements arise remain poorly understood. To study the origins of inversions, we generated chromosome-level de novo genome assemblies for four subspecies of the deer mouse (Peromyscus maniculatus) with known inversion polymorphisms. We identified ∼8,000 inversions, including 47 megabase-scale inversions, that together affect ∼30% of the genome. Analysis of inversion breakpoints suggests that while most small (<1 Mb) inversions arose via ectopic recombination between retrotransposons, large (>1 Mb) inversions are primarily associated with segmental duplications (SDs). Large inversion breakpoints frequently occur near centromeres, which may be explained by an accumulation of retrotransposons in pericentromeric regions driving SDs. Additionally, multiple large inversions likely arose from ectopic recombination between near-identical centromeric satellite arrays located megabases apart, suggesting that centromeric repeats may also facilitate inversions. Together, our results illuminate how repeats give rise to massive shifts in chromosome architecture.

Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences

BACKGROUND

The lower Dipteran fungus gnat, Bradysia (aka Sciara) coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during male meiosis I and both maternal X sister chromatids are retained in male meiosis II. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. In addition, there is gene amplification in larval polytene chromosomes, and the X polytene chromosome folds back on itself mediated by extremely long-range interactions between three loci. These developmentally normal events present opportunities to study chromosome behaviors that are unusual in other systems. Moreover, little is known about the centromeric and telomeric sequences of lower Dipterans in general, and there are recent claims of horizontally-transferred genes in fungus gnats. Overall, there is a pressing need to learn more about the fungus gnat chromosome sequences.

RESULTS

We produced the first chromosome-scale models of the X and autosomal chromosomes where each somatic chromosome is represented by a single scaffold. Extensive analysis supports the chromosome identity and structural accuracy of the scaffolds, demonstrating they are co-linear with historical polytene maps, consistent with evolutionary expectations, and have accurate centromere positions, chromosome lengths, and copy numbers. The positions of alleged horizontally-transferred genes in the nuclear chromosomes were broadly confirmed by genomic analyses of the chromosome scaffolds using Hi-C and single-molecule long-read datasets. The chromosomal context of repeats shows family-specific biases, such as retrotransposons correlated with the centromeres. Moreover, scaffold termini were enriched with arrays of retrotransposon-related sequence as well as nucleosome-length (~ 175 bp) satellite repeats. Finally, the Hi-C data captured Mb-scale physical interactions on the X chromosome that are seen in polytene spreads, and we characterize these interesting "fold-back regions" at the sequence level for the first time.

CONCLUSIONS

The chromosome scaffolds were shown to be of exceptional quality, including loci harboring horizontally-transferred genes. Repeat analyses demonstrate family-specific biases and telomere repeat candidates. Hi-C analyses revealed the sequences of ultra-long-range interactions on the X chromosome. The chromosome-scale scaffolds pave the way for further studies of the unusual chromosome movements in Bradysia coprophila.

Chromosome-level genome assembly of the synanthropic fly Chrysomya megacephala: insights into oviposition location

The oriental latrine fly, Chrysomya megacephala (Diptera: Calliphoridae), is a medically important synanthropic blow fly species characterized by its necrophagy and coprophagy, often observed near carrion and animal feces. Notably, C. megacephala always arrives at carcass earlier than other species. To elucidate the underlying mechanisms behind the host choice in C. megacephala, we present the chromosome-scale genome assembly for this species. The genome size is 816.79 Mb, with a contig N50 of 1.60 Mb. The Hi-C data were anchored to six chromosomes, accounting for 99.93% of the draft assembled genome. Comparative genomic analysis revealed significant expansions in pathways of ligand-gated ion channel activity, passive transmembrane transporter activity, and protein methyltransferase activity, which may be closely associated with host localization and oviposition. After identifying 69 odor-binding proteins (OBPs) in the assembled genome, phylogenetic analysis showed that DmelOBP99b and CmegOBP99b exhibited high homology. Transcriptome analysis demonstrated that the relative expression of CmegOBP99b was consistently the highest during the metamorphosis, and RT-qPCR further confirmed the similar results. Additionally, CmegOBP99b exhibited a strong binding affinity to DMDS (dimethyl disulfide) as determined by molecular docking. To determine the protein expression level of CmegOBP99b in various body parts, we prepared recombinant CmegOBP99b protein and anti-CmegOBP99b polyclonal antibodies. Western blot analysis showed that CmegOBP99b was significantly expressed in the female's head compared to other parts, which is consistent with RT-qPCR results. Therefore, CmegOBP99b may be the primary odor-binding protein responsible for olfactory recognition and the behavioral coordination of C. megacephala. This study not only provides valuable insights into the molecular mechanisms of oviposition localization in C. megacephala but also facilitates further research into the genetic diversity and phylogeny of the Calliphoridae family.

BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries

As crucial chromatin structures, hierarchical TADs play important roles in epigenetic organization, transcriptional activity, gene regulation, and cell differentiation. Currently, it remains a highly challenging task to accurately identify hierarchical TADs in a computational manner. The key bottleneck for existing TAD callers lies in the difficulty in the prediction of precise TAD boundaries. We solve this problem by introducing a novel algorithm, called BINDER, which conducts a boundary consensus approach, and then precisely locate hierarchical TAD boundaries by developing a multifaceted boundary characterization strategy. In comparison with other leading TAD callers, BINDER shows significant improvement in identifying hierarchical TADs and exhibits the strongest robustness with ultrasparse data, which supports the importance of boundary identification in calling hierarchical TADs. Applying BINDER to experimental data and mouse hematopoietic cases, we find that the hierarchical TADs identified by BINDER show strong biological relevance in their epigenetic organization, transcriptional activity, DNA motifs, and coregulation during cellular differentiation. BINDER discovers differences in the enrichment of two specific transcription factors, CHD1 and CHD2, at TAD boundaries with different hierarchies. It also observes variations in the gene expression of TADs with different hierarchies during cellular differentiation.

H3K27me3 and the PRC1-H2AK119ub pathway cooperatively maintain heterochromatin and transcriptional silencing after the loss of H3K9 methylation

BACKGROUND

Heterochromatin is a fundamental component of eukaryotic chromosome architecture, crucial for genome stability and cell type-specific gene regulation. In mammalian nuclei, heterochromatin forms condensed B compartments, distinct from the transcriptionally active euchromatic A compartments. Histone H3 lysine 9 and lysine 27 trimethylation (H3K9me3 and H3K27me3) are two major epigenetic modifications that enrich constitutive and facultative heterochromatin, respectively. Previously, we found that the redistribution of H3K27me3 following the loss of H3K9 methylation contributes to heterochromatin maintenance, while the simultaneous loss of both H3K27me3 and H3K9 methylation induces heterochromatin decondensation in mouse embryonic fibroblasts. However, the spatial positioning of B compartments largely persists, suggesting additional mechanisms are involved.

RESULTS

In this study, we investigated the role of H2AK119 monoubiquitylation (uH2A), a repressive chromatin mark deposited by Polycomb Repressive Complex 1 (PRC1), in maintaining heterochromatin structure following the loss of H3K9 and H3K27 methylation. We observed that uH2A and H3K27me3 are independently enriched in B compartments after H3K9 methylation loss. Despite the absence of H3K9me3 and H3K27me3, uH2A remained localized and contributed to heterochromatin retention. These results suggest that PRC1-mediated uH2A functions independently and cooperatively with H3K27me3 to maintain heterochromatin organization originally created by H3K9 methylation.

CONCLUSION

Our findings highlight a compensatory role for uH2A in preserving heterochromatin structure after the loss of other repressive chromatin modifications. The PRC1-uH2A pathway plays a critical role in maintaining the integrity of B compartments and suggests that heterochromatin architecture is supported by a network of redundant epigenetic mechanisms in mammalian cells.

Examining the dynamics of three-dimensional genome organization with multitask matrix factorization

Three-dimensional (3D) genome organization, which determines how the DNA is packaged inside the nucleus, has emerged as a key component of the gene regulation machinery. High-throughput chromosome conformation data sets, such as Hi-C, have become available across multiple conditions and time points, offering a unique opportunity to examine changes in 3D genome organization and link them to phenotypic changes in normal and disease processes. However, systematic detection of higher-order structural changes across multiple Hi-C data sets remains a major challenge. Existing computational methods either do not model higher-order structural units or cannot model dynamics across more than two conditions of interest. We address these limitations with tree-guided integrated factorization (TGIF), a generalizable multitask nonnegative matrix factorization (NMF) approach that can be applied to time series or hierarchically related biological conditions. TGIF can identify large-scale changes at the compartment or subcompartment levels, as well as local changes at boundaries of topologically associated domains (TADs). Based on benchmarking in simulated and real Hi-C data, TGIF boundaries are more accurate and reproducible across differential levels of noise and sources of technical artifacts, and are more enriched in CTCF. Application to three multisample mammalian data sets shows that TGIF can detect differential regions at compartment, subcompartment, and boundary levels that are associated with significant changes in regulatory signals and gene expression enriched in tissue-specific processes. Finally, we leverage TGIF boundaries to prioritize sequence variants for multiple phenotypes from the NHGRI GWAS catalog. Taken together, TGIF is a flexible tool to examine 3D genome organization dynamics across disease and developmental processes.

A 3D Genome Atlas of Genetic Variants and Their Pathological Effects in Cancer

The hierarchical organization of the eukaryotic genome is crucial for nuclear activities and cellular development. Genetic aberrations can disrupt this 3D genomic architecture, potentially driving oncogenesis. However, current research often lacks a comprehensive perspective, focusing on specific mutation types and singular 3D structural levels. Here, pathological changes from chromosomes to nucleotides are systematically cataloged, including 10 789 interchromosomal translocations (ICTs), 18 863 structural variants (SVs), and 162 769 single nucleotide polymorphisms (SNPs). The multilayered analysis reveals that fewer than 10% of ICTs disrupt territories via potent 3D interactions, and only a minimal fraction of SVs disrupt compartments or intersect topologically associated domain structures, yet these events significantly influence gene expression. Pathogenic SNPs typically show reduced interactions within the 3D genomic space. To investigate the effects of variants in the context of 3D organization, a two-phase scoring algorithm, 3DFunc, is developed to evaluate the pathogenicity of variant-gene pairs in cancer. Using 3DFunc, IGHV3-23's critical role in chronic lymphocytic leukemia is identified and it is found that three pathological SNPs (rs6605578, rs7814783, rs2738144) interact with DEFA3. Additionally, 3DGAtlas is introduced, which provides a highly accessible 3D genome atlas and a valuable resource for exploring the pathological effects of genetic mutations in cancer.