3D Genome Structure Research Articles

Three-Dimensional Organization of Chicken Genome Provides Insights into Genetic Adaptation to Extreme Environments.

The high-throughput chromosome conformation capture (Hi-C) technique is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. However, the knowledge of the 3D genome structure and its dynamics during extreme environmental adaptations remains poor. Here, we characterized 3D genome architectures using the Hi-C technique for chicken liver cells. Upon comparing Lindian chicken (LDC) liver cells with Wenchang chicken (WCC) liver cells, we discovered that environmental adaptation contributed to the switching of A/B compartments, the reorganization of topologically associated domains (TADs), and TAD boundaries in both liver cells. In addition, the analysis of the switching of A/B compartments revealed that the switched compartmental genes (SCGs) were strongly associated with extreme environment adaption-related pathways, including tight junction, notch signaling pathway, vascular smooth muscle contraction, and the RIG-I-like receptor signaling pathway. The findings of this study advanced our understanding of the evolutionary role of chicken 3D genome architecture and its significance in genome activity and transcriptional regulation.

Structural variants drive context-dependent oncogene activation in cancer.

Higher-order chromatin structure is important for the regulation of genes by distal regulatory sequences1,2. Structural variants (SVs) that alter three-dimensional (3D) genome organization can lead to enhancer-promoter rewiring and human disease, particularly in the context of cancer3. However, only a small minority of SVs are associated with altered gene expression4,5, and it remains unclear why certain SVs lead to changes in distal gene expression and others do not. To address these questions, we used a combination of genomic profiling and genome engineering to identify sites of recurrent changes in 3D genome structure in cancer and determine the effects of specific rearrangements on oncogene activation. By analysing Hi-C data from 92 cancer cell lines and patient samples, we identified loci affected by recurrent alterations to 3D genome structure, including oncogenes such as MYC, TERT and CCND1. By using CRISPR-Cas9 genome engineering to generate de novo SVs, we show that oncogene activity can be predicted by using 'activity-by-contact' models that consider partner region chromatin contacts and enhancer activity. However, activity-by-contact models are only predictive of specific subsets of genes in the genome, suggesting that different classes of genes engage in distinct modes of regulation by distal regulatory elements. These results indicate that SVs that alter 3D genome organization are widespread in cancer genomes and begin to illustrate predictive rules for the consequences of SVs on oncogene activation.

Insights into the cell fate decision-making processes from chromosome structural reorganizations.

The cell fate decision-making process, which provides the capability of a cell transition to a new cell type, involves the reorganizations of 3D genome structures. Currently, the high temporal resolution picture of how the chromosome structural rearrangements occur and further influence the gene activities during the cell-state transition is still challenging to acquire. Here, we study the chromosome structural reorganizations during the cell-state transitions among the pluripotent embryonic stem cell, the terminally differentiated normal cell, and the cancer cell using a nonequilibrium landscape-switching model implemented in the molecular dynamics simulation. We quantify the chromosome (de)compaction pathways during the cell-state transitions and find that the two pathways having the same destinations can merge prior to reaching the final states. The chromosomes at the merging states have similar structural geometries but can differ in long-range compartment segregation and spatial distribution of the chromosomal loci and genes, leading to cell-type-specific transition mechanisms. We identify the irreversible pathways of chromosome structural rearrangements during the forward and reverse transitions connecting the same pair of cell states, underscoring the critical roles of nonequilibrium dynamics in the cell-state transitions. Our results contribute to the understanding of the cell fate decision-making processes from the chromosome structural perspective.

MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.

Abstract A069: Hi-C analysis in patient-derived organoids reveals the impact of three-dimensional chromatin structures on pancreatic cancer transcriptional subtypes

Abstract Three-dimensional (3D) chromatin structures connect genes to regulatory elements, thereby contributing to cell-type-specific gene regulation. However, its role in pancreatic cancer remains unclear. Inspired by our previous finding that open chromatin profiles analyzed by ATAC-seq well characterize the biological features and transcriptional status of pancreatic neoplasms, we hereby demonstrate the previously overlooked impact of 3D epigenetic regulation in pancreatic cancers. Through integrative analysis of Hi-C, ChIP-seq, and RNA-seq using patient-derived organoids, 3D genome modules, including compartments, topologically associating domains, and enhancer-promoter loops were found to play important roles in characterizing pancreatic tumors. Interestingly, intraductal papillary mucinous neoplasm (IPMN) lineages tended to have unique 3D chromatin structure profiles. We further found that transcriptional subtypes in pancreatic cancer, either classical/progenitor-like or basal/squamous-like, were largely underpinned by 3D structures. Compartment was responsible for supporting many subtype-specific genes, by synchronously activating genes that were in the vicinity, as represented by CYP2C family genes. Meanwhile, enhancer-promoter loop fine-tuned some key subtype genes, such as GATA6. By exploring the driving forces behind these 3D structures, we found that HNF1B, a transcription factor implicated in the progenitor subtype, was sufficient to induce subtype switch, together with their underlying 3D genome structure alterations. We demonstrate that HNF1B overexpression in squamous-type pancreatic cancer organoids induced the upregulation and downregulation of genes associated with the progenitor and squamous subtype, respectively. Mechanistically, these dynamic transcriptional and 3D structural modulation were accompanied by HNF1B-induced long-range genomic interactions and H3K27ac modification at HNF1B bound sites, implying HNF1B as a driving force. We also provide evidence suggesting that this HNF1B-induced subtype switch was mediated through the phase-separating property of HNF1B, which was enabled by its intrinsically disordered region (IDR). Induction of mutant HNF1B, whose IDR was either deleted (HNF1B-dIDR) or substituted by transcriptional phase-separation forming IDR from another peptide AKAP95 (HNF1B-AKAP95), showed that subtype switching effects of HNF1B were diminished by HNF1B-dIDR or recapitulated by HNF1B-AKAP95. Thus, HNF1B contributes to the transcriptional subtype formation in pancreatic cancers through its phase-separating structural ability. Collectively, the mapping of 3D structural changes induced by transcription factors, such as HNF1B, is useful for further understanding the features of pancreatic cancers. Our study may imply the potential of 3D structures to effectively suppress or unwind the malignant transformation process and to discover subtype-specific therapeutic targets. Citation Format: Hiroyuki Kato, Dosuke Iwadate, Keisuke Yamamoto, Hiroaki Fujiwara, Hideaki Ijichi, Mitsuhiro Fujishiro, Keisuke Tateishi. Hi-C analysis in patient-derived organoids reveals the impact of three-dimensional chromatin structures on pancreatic cancer transcriptional subtypes [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A069.

Comparative Analysis of Genome-Scale Gene Regulatory Networks in Human Hematopoietic Stem and Myeloid Progenitor Fractions

Background: Dynamic remodelling of gene regulatory networks (GRN) guides cell state changes during differentiation to establish and maintain cell identity and gene expression. We previously described combinatorial binding of 7 transcription factors (TF (heptad: FLI1, ERG, GATA2, RUNX1, TAL1, LYL1 and LMO2)) which form an autoregulatory network in human hematopoietic stem and progenitor cells (HSPC: Beck et al Blood 2013, Thoms et al Blood 2021). Here we mapped genome-wide binding of TFs and chromatin regulators and explored their roles in establishing and maintaining cell type specific GRNs across human hematopoietic stem cell (HSC) differentiation. Methods: We flow sorted cryopreserved CD34+ LIN- cells collected by apheresis into HSCs (CD38loCD45RA-), common myeloid progenitors (CMP: CD38hiCD45RA-CD123+), granulocyte monocyte progenitors (GMP: CD38hiCD45RA+CD123+) and megakaryocyte erythroid progenitors (MEP: CD38hiCD45RA-CD123-). Active regulatory regions (Fig A) were identified by a) chromatin immunoprecipitation (ChIP)/ChIPmentation for genome wide identification of active (H3K27ac, H3K4me3) and inactive (H3K27me3) histone marks, and TF and co-factor (heptad, PU.1, STAG2, CTCF) binding, b) HiC to broadly classify high order 3D genome structures and c) H3K27ac HiChIP at 5kb. Results: Combinatorial binding of heptad TFs in all cell types was confirmed, with the most overrepresented pattern being co-binding of all 7 factors. However, certain multifactor combinations were identified in restricted cell types or associated with lineage specific gene promoters. For example, the master erythroid TF GATA1 showed combinatorial binding in CMPs and MEPs, while the myeloid TF MPO showed combinatorial binding in CMPs and GMPs. Chromatin looping was highly variable across the four cell types, although high order genome architecture was conserved. We first focussed on HiChIP interactions involving promoters of the heptad genes and observed chromatin looping patterns consistent with an interconnected circuit. Promoter looping patterns were dynamic across cell types, and we found multiple distal regions, each with specific patterns of TF binding, connected to each heptad promoter (Fig B). Many of the distal regions were previously undescribed and may constitute novel regulators of heptad genes. To further understand the role of heptad TFs in regulating cell type specific gene expression, we used our HiChIP data to link promoters to candidate distal regulatory regions and focussed on promoter-regulator pairs with differential heptad binding across the cell types. In general, differential binding was accompanied by differential gene expression. Genes with high heptad binding in MEPs were enriched for pathways related to erythroid cells (e.g., ferroptosis signalling) while genes with high heptad binding in GMPs were enriched for pathways related to myeloid cells (e.g., TREM1 signalling). We then focussed on promoter-regulator pairs corresponding to genes expressed in mature erythroid and myeloid cells and observed cell specific patterns of TF binding. At erythroid genes we saw increasing GATA2/TAL1/LYL1/LMO2 binding and decreasing ERG binding along the HSC to MEP trajectory, while at myeloid genes we saw high GATA2/LYL1/LMO2 binding and low TAL1 binding along the HSC to GMP trajectory. To conduct an unbiased genome wide analysis of HSPC GRNs we used our data to annotate and cluster the 85,100 accessible chromatin regions present in HSPCs (Corces et al Nature Genetics 2016). Accessible regions clustered broadly as promoters, regulatory regions, or CTCF-bound. Regions with high heptad binding in either MEPs or GMPs were located in different subclusters, suggesting dynamic reorganisation of heptad TFs across the genome as HSCs proceed along differentiation trajectories. Taken together our data strongly supports a mechanistic link between differential heptad TF binding and cell type specific expression patterns and provides insight into how expression of multiple genes is coordinated during cell state transitions. Conclusion: This study provides a comprehensive characterisation of the gene regulatory landscape in rare subpopulations of human HSPCs and will be a key resource for understanding adult hematopoiesis. Our work provides a framework for analysing aberrant regulatory networks in leukemic cells and leveraging these to devise novel therapeutic strategies. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Subtype-specific 3D genome alteration in acute myeloid leukaemia.

Acute myeloid leukaemia (AML) represents a set of heterogeneous myeloid malignancies, and hallmarks include mutations in epigenetic modifiers, transcription factors and kinases1-5. The extent to which mutations in AML drive alterations in chromatin 3D structure and contribute to myeloid transformation is unclear. Here we use Hi-C and whole-genome sequencing to analyse 25 samples from patients with AML and 7 samples from healthy donors. Recurrent and subtype-specific alterations in A/B compartments, topologically associating domains and chromatin loops were identified. RNA sequencing, ATAC with sequencing and CUT&Tag for CTCF, H3K27ac and H3K27me3 in the same AML samples also revealed extensive and recurrent AML-specific promoter-enhancer and promoter-silencer loops. We validated the role of repressive loops on their target genes by CRISPR deletion and interference. Structural variation-induced enhancer-hijacking and silencer-hijacking events were further identified in AML samples. Hijacked enhancers play a part in AML cell growth, as demonstrated by CRISPR screening, whereas hijacked silencers have a downregulating role, as evidenced by CRISPR-interference-mediated de-repression. Finally, whole-genome bisulfite sequencing of 20 AML and normal samples revealed the delicate relationship between DNA methylation, CTCF binding and 3D genome structure. Treatment of AML cells with a DNA hypomethylating agent and triple knockdown of DNMT1, DNMT3A and DNMT3B enabled the manipulation of DNA methylation to revert 3D genome organization and gene expression. Overall, this study provides a resource for leukaemia studies and highlights the role of repressive loops and hijacked cis elements in human diseases.

DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes.

In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions. Discriminating the loops from genome-wide contact interactions is crucial for dissecting three-dimensional(3D) genome structure and function. Here, we present a deep learning method to predict genome-wide chromatin loops, called DLoopCaller, by combining accessible chromatin landscapes and raw Hi-C contact maps. Some available orthogonal data ChIA-PET/HiChIP and Capture Hi-C were used to generate positive samples with a wider contact matrix which provides the possibility to find more potential genome-wide chromatin loops. The experimental results demonstrate that DLoopCaller effectively improves the accuracy of predicting genome-wide chromatin loops compared to the state-of-the-art method Peakachu. Moreover, compared to two of most popular loop callers, such as HiCCUPS and Fit-Hi-C, DLoopCaller identifies some unique interactions. We conclude that a combination of chromatin landscapes on the one-dimensional genome contributes to understanding the 3D genome organization, and the identified chromatin loops reveal cell-type specificity and transcription factor motif co-enrichment across different cell lines and species.

Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation

Immunocytes dynamically reprogram their gene expression profiles during differentiation and immunoresponse. However, the underlying mechanism remains elusive. Here, we develop a single-cell Hi-C method and systematically delineate the 3D genome and dynamic epigenetic atlas of macrophages during these processes. We propose “degree of disorder” to measure genome organizational patterns inside topologically-associated domains, which is correlated with the chromatin epigenetic states, gene expression, and chromatin structure variability in individual cells. Furthermore, we identify that NF-κB initiates systematic chromatin conformation reorganization upon Mycobacterium tuberculosis infection. The integrated Hi-C, eQTL, and GWAS analysis depicts the atlas of the long-range target genes of mycobacterial disease susceptible loci. Among these, the SNP rs1873613 is located in the anchor of a dynamic chromatin loop with LRRK2, whose inhibitor AdoCbl could be an anti-tuberculosis drug candidate. Our study provides comprehensive resources for the 3D genome structure of immunocytes and sheds insights into the order of genome organization and the coordinated gene transcription during immunoresponse.

Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi.

Single-cell Hi-C (scHi-C) technologies can probe three-dimensional (3D) genome structures in individual cells. However, existing scHi-C analysis methods are hindered by the data quality and complex 3D genome patterns. The lack of computational scalability and interpretability poses further challenges for large-scale analysis. Here, we introduce Fast-Higashi, an ultrafast and interpretable method based on tensor decomposition and partial random walk with restart, enabling joint identification of cell identities and chromatin meta-interactions from sparse scHi-C data. Extensive evaluations demonstrate the advantage of Fast-Higashi over existing methods, leading to improved delineation of rare cell types and continuous developmental trajectories. Fast-Higashi can directly identify 3D genome features that define distinct cell types and help elucidate cell-type-specific connections between genome structure and function. Moreover, Fast-Higashi can generalize to incorporate other single-cell omics data. Fast-Higashi provides a highly efficient and interpretable scHi-C analysis solution that is applicable to a broad range of biological contexts.

Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells

Uncovering an informative feature of 3D genome structure, Guo etal. (2022) describe chromatin jets in quiescent murine thymocytes: 1-2 Mb structures formed by targeted cohesin loading at narrow accessible chromatin regions and visible as prominent off-diagonal stripes on contact maps.

Dynamics of Viral and Host 3D Genome Structure upon Infection.

Eukaryotic chromatin is highly organized in the 3D nuclear space and dynamically regulated in response to environmental stimuli. This genomic organization is arranged in a hierarchical fashion to support various cellular functions, including transcriptional regulation of gene expression. Like other host cellular mechanisms, viral pathogens utilize and modulate host chromatin architecture and its regulatory machinery to control features of their life cycle, such as lytic versus latent status. Combined with previous research focusing on individual loci, recent global genomic studies employing conformational assays coupled with high-throughput sequencing technology have informed models for host and, in some cases, viral 3D chromosomal structure re-organization during infection and the contribution of these alterations to virus-mediated diseases. Here, we review recent discoveries and progress in host and viral chromatin structural dynamics during infection, focusing on a subset of DNA (human herpesviruses and HPV) as well as RNA (HIV, influenza virus and SARS-CoV-2) viruses. An understanding of how host and viral genomic structure affect gene expression in both contexts and ultimately viral pathogenesis can facilitate the development of novel therapeutic strategies.

ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data

BackgroundThe three-dimensional (3D) structure of chromatin has a massive effect on its function. Because of this, it is desirable to have an understanding of the 3D structural organization of chromatin. To gain greater insight into the spatial organization of chromosomes and genomes and the functions they perform, chromosome conformation capture (3C) techniques, particularly Hi-C, have been developed. The Hi-C technology is widely used and well-known because of its ability to profile interactions for all read pairs in an entire genome. The advent of Hi-C has greatly expanded our understanding of the 3D genome, genome folding, gene regulation and has enabled the development of many 3D chromosome structure reconstruction methods.ResultsHere, we propose a novel approach for 3D chromosome and genome structure reconstruction from Hi-C data using Particle Swarm Optimization (PSO) approach called ParticleChromo3D. This algorithm begins with a grouping of candidate solution locations for each chromosome bin, according to the particle swarm algorithm, and then iterates its position towards a global best candidate solution. While moving towards the optimal global solution, each candidate solution or particle uses its own local best information and a randomizer to choose its path. Using several metrics to validate our results, we show that ParticleChromo3D produces a robust and rigorous representation of the 3D structure for input Hi-C data. We evaluated our algorithm on simulated and real Hi-C data in this work. Our results show that ParticleChromo3D is more accurate than most of the existing algorithms for 3D structure reconstruction.ConclusionsOur results also show that constructed ParticleChromo3D structures are very consistent, hence indicating that it will always arrive at the global solution at every iteration. The source code for ParticleChromo3D, the simulated and real Hi-C datasets, and the models generated for these datasets are available here: https://github.com/OluwadareLab/ParticleChromo3D

MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification.

The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way chromatin interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell-cycle-associated genes. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure.

Genome architecture plasticity underlies DNA replication timing dynamics in cell differentiation.

During the S-phase of eukaryotic cell cycle, DNA is replicated in a dedicatedly regulated temporal order, with regions containing active and inactive genes replicated early and late, respectively. Recent advances in sequencing technology allow us to explore the connection between replication timing (RT), histone modifications, and three-dimensional (3D) chromatin structure in diverse cell types. To characterize the dynamics during cell differentiation, corresponding sequencing data for human embryonic stem cells and four differentiated cell types were collected. By comparing RT and its extent of conservation before and after germ layer specification, the human genome was partitioned into distinct categories. Each category is then subject to comparisons on genomic, epigenetic, and chromatin 3D structural features. As expected, while constitutive early and late replication regions showed active and inactive features, respectively, dynamic regions with switched RT showed intermediate features. Surprisingly, although early-to-late replication and late-to-early replication regions showed similar histone modification patterns in hESCs, their structural preferences were opposite. Specifically, in hESCs, early-to-late replication regions tended to appear in the B compartment and large topologically associated domains, while late-to-early replication regions showed the opposite. Our results uncover the coordinated regulation of RT and 3D genome structure that underlies the loss of pluripotency and lineage commitment and indicate the importance and potential roles of genome architecture in biological processes.

3D genome alterations in T cells associated with disease activity of systemic lupus erythematosus

ObjectivesThree-dimensional (3D) genome alterations can dysregulate gene expression by rewiring physical interactions within chromosomes in a tissue-specific or cell-specific manner and lead to diseases. We aimed to elucidate the 3D...

Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation.

Innate lymphoid cells (ILCs) are well-characterized immune cells that play key roles in host defense and tissue homeostasis. Yet, how the three-dimensional (3D) genome organization underlies the development and functions of ILCs is unknown. Herein, we carried out an integrative analysis of the 3D genome structure, chromatin accessibility and gene expression in mature ILCs. Our results revealed that the local 3D configuration of the genome is rewired specifically at loci associated with ILC biology to promote their development and functional differentiation. Importantly, we demonstrated that the ontogenesis of ILC2s and the progression of allergic airway inflammation are determined by a unique local 3D configuration of the region containing the ILC-lineage-defining factor Id2, which is characterized by multiple interactions between the Id2 promoter and distal regulatory elements bound by the transcription factors GATA-3 and RORα, unveiling the mechanism whereby the Id2 expression is specifically controlled in group 2 ILCs.

Constricted migration is associated with stable 3D genome structure differences in cancer cells.

To spread from a localized tumor, metastatic cancer cells must squeeze through constrictions that cause major nuclear deformations. Since chromosome structure affects nucleus stiffness, gene regulation, and DNA repair, here, we investigate the relationship between 3D genome structure and constricted migration in cancer cells. Using melanoma (A375) cells, we identify phenotypic differences in cells that have undergone multiple rounds of constricted migration. These cells display a stably higher migration efficiency, elongated morphology, and differences in the distribution of Lamin A/C and heterochromatin. Hi-C experiments reveal differences in chromosome spatial compartmentalization specific to cells that have passed through constrictions and related alterations in expression of genes associated with migration and metastasis. Certain features of the 3D genome structure changes, such as a loss of B compartment interaction strength, are consistently observed after constricted migration in clonal populations of A375 cells and in MDA-MB-231 breast cancer cells. Our observations suggest that consistent types of chromosome structure changes are induced or selected by passage through constrictions and that these may epigenetically encode stable differences in gene expression and cellular migration phenotype.

475 High resolution chromatin loops associate with gene targets for psoriasis susceptibility regions

There are over 80 psoriasis-associated loci identified, with a majority playing regulatory roles; however, their gene targets are yet to be identified. Chromatin loops play an important role in gene regulation, and can be detected by chromosome conformation capture techniques like Hi-C. In this study, we deep sequenced Hi-C libraries (∼1 billion reads/reaction) to generate nine PBMC-derived subsets from 2 individuals (∼50,000 cells each): 4 unstimulated CD3+CD45RO+ memory T cells (CD4+CLA-, CD4+CLA+, CD8+CLA-, CD8+CLA+); the same 4 subsets after 24 hours of CD3/CD28 stimulation of CD1c- cells (primarily T cells); and mDC. Using a 5k-10k contact map resolution, we identified 13,186 ± 2,857 Hi-C loops per library, ranging from 30 to 1,980 kb long, using Mustache. Notably, we found that ∼50% of the identified loops have at least one end overlapping a transcription start site, providing a unique resource for mapping long-range promoter interactions in immunocytes. We identified 27 ± 6 loops per library that linked to promoters and whose loop ends could also be mapped to known psoriasis signals, defined by the 95% credible intervals generated from a recent transethnic GWAS (HGG Adv 2022). Of 47 target genes involved in such loops, we found 8 previously suggested gene targets for psoriasis: ANXA6, ELMO1, ETS1, FASLG, MBD2, IFI44, PTGER4 and STARD6. Among them, ANXA6, ETS1, FASLG and IFI44 were present only in T cells, while the rest presented in both T cells and mDC. We further revealed other psoriasis gene candidates including KAT5, NHLRC3/PROSER1, and SUCO, which were linked to known psoriasis signals through loops in multiple Hi-C libraries for both individuals and in both T cells and mDC. This study provides complementary support for known psoriasis-related genes at the level of 3D genome structure, and nominates other genes of interest for future studies.

Chromatin accessibility shapes meiotic recombination in mouse primordial germ cells through assisting double-strand breaks and loop formation

Meiotic recombination is a driver of evolution, and aberrant recombination is a major contributor to aneuploidy in mammals. Mechanism of recombination remains elusive yet. Here, we present a computational analysis to explore recombination-related dynamics of chromatin accessibility in mouse primordial germ cells (PGCs). Our data reveals that: (1) recombination hotspots which get accessible at meiosis-specific DNase I-hypersensitive sites (DHSs) only when PGCs enter meiosis are located preferentially in intronic and distal intergenic regions; (2) stable DHSs maintained stably across PGC differentiation are enriched by CTCF motifs and CTCF binding and mediate chromatin loop formation; (3) compared with the specific DHSs aroused at meiotic stage, stable DHSs are largely encoded in DNA sequence and also enriched by epigenetic marks; (4) PRDM9 is likely to target nucleosome-occupied hotspot regions and remodels local chromatin structure to make them accessible for recombination machinery; and (5) cells undergoing meiotic recombination are deficient in TAD structure and chromatin loop arrays are organized regularly along the axis formed between homologous chromosomes. Taken together, by analyzing DHS-related DNA features, epigenetic marks and 3D genome structure, we revealed some specific roles of chromatin accessibility in recombination, which would expand our understanding of recombination mechanism.