Neural tube defects (NTDs) are one of the most common congenital malformations. Folic acid deficiency in pregnant women increases the risk of developing NTDs; however, the underlying etiology and mechanisms remain elusive. In this study, the role of DNA double-strand breaks (DSBs) in 3D genome organization in NTDs with folate deficiency is reported. The NTD mouse model is burdened with abundant DSBs associated with the disruption of 3D genome organization. DSBs occurring in active genes lead to the stalling of RNA polymerase II (Pol II) and formation of R-loops in the 3D genome. The DSB ratios of the genomic regions negatively correlated with the distance from the transcription start sites of the gene. The DSB ratios of the proximal and distal enhancers are significantly higher and induce the displacement of loops with busy anchors. Furthermore, DSB-associated dysregulation of chromatin loops occurs in neural tube closure-associated genes that are abnormally expressed in human NTDs. Taken together, excessive DSB-associated 3D genome organization disruption within NTDs with folate deficiency contributes to the dysregulation of neural tube closure-associated genes.

BACKGROUND:Recent research has indicated a close connection between the three-dimensional (3D) structure of chromatin and early embryo development, with precise higher-order chromatin folding playing a significant role in mediating gene expression. However, the specific role of 3D genomic hierarchical structure and its dynamics in early embryo development remains largely unknown. RESULTS:In this study, we examined the hierarchical topological association domain (TAD) during early embryo development and its relationship with zygotic gene activation (ZGA), gene expression, and chromatin accessibility to gain a better understanding of the dynamics of TAD nesting levels during this developmental stage. Our findings show that ZGA precedes the establishment of hierarchical TAD, leading to widespread gene expression, an increase in the percentage of high-level TAD structures, and enhanced chromatin accessibility at higher hierarchical levels. Additionally, we utilized a deep neural network to investigate the formation of TAD boundaries and found that histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine trimethylation (H3K27me3) are key features in the establishment of TAD boundaries. Furthermore, we observed heterogeneous dynamics of hierarchical TAD among different species. CONCLUSIONS:Overall, our study sheds light on the folding dynamics of hierarchical TADs during early embryo development and underscores their close relationship with transcriptional programs.

Cancer is rarely the straightforward consequence of an abnormality in a single gene, but rather reflects a complex interplay of many genes, represented as gene modules. Here, we leverage the recent advances of model-agnostic interpretation approach and develop CGMega, an explainable and graph attention-based deep learning framework to perform cancer gene module dissection. CGMega outperforms current approaches in cancer gene prediction, and it provides a promising approach to integrate multi-omics information. We apply CGMega to breast cancer cell line and acute myeloid leukemia (AML) patients, and we uncover the high-order gene module formed by ErbB family and tumor factors NRG1, PPM1A and DLG2. We identify 396 candidate AML genes, and observe the enrichment of either known AML genes or candidate AML genes in a single gene module. We also identify patient-specific AML genes and associated gene modules. Together, these results indicate that CGMega can be used to dissect cancer gene modules, and provide high-order mechanistic insights into cancer development and heterogeneity.

BackgroundPancreatic ductal adenocarcinoma (PDAC) is frequently diagnosed in advanced stages, necessitating pancreaticoduodenectomy (PD) as a primary therapeutic approach. However, PD surgery can engender intricate complications. Thus, understanding the factors influencing postoperative complications documented in electronic medical records and their impact on survival rates is crucial for improving overall patient outcomes.MethodsA total of 749 patients were divided into two groups: 598 (79.84%) chose the RPD (Robotic pancreaticoduodenectomy) procedure and 151 (20.16%) chose the LPD (Laparoscopic pancreaticoduodenectomy) procedure. We used correlation analysis, survival analysis, and decision tree models to find the similarities and differences about postoperative complications and prognostic survival.ResultsPancreatic cancer, known for its aggressiveness, often requires pancreaticoduodenectomy as an effective treatment. In predictive models, both BMI and surgery duration weigh heavily. Lower BMI correlates with longer survival, while patients with heart disease and diabetes have lower survival rates. Complications like delayed gastric emptying, pancreatic fistula, and infection are closely linked post-surgery, prompting conjectures about their causal mechanisms. Interestingly, we found no significant correlation between nasogastric tube removal timing and delayed gastric emptying, suggesting its prompt removal post-decompression.ConclusionThis study aimed to explore predictive factors for postoperative complications and survival in PD patients. Effective predictive models enable early identification of high-risk individuals, allowing timely interventions. Higher BMI, heart disease, or diabetes significantly reduce survival rates in pancreatic cancer patients post-PD. Additionally, there’s no significant correlation between DGE incidence and postoperative extubation time, necessitating further investigation into its interaction with pancreatic fistula and infection.

In mammals, during the post-fertilization pre-implantation phase, the expression of cell type-specific genes is crucial for normal embryonic development, which is regulated by cis-regulatory elements (CREs). TFs control gene expression by interacting with CREs. Research shows that transcription factor binding sites (TFBSs) reflect the general characteristics of the regulatory genome. Here, we identified TFBSs from chromatin accessibility data in five stages of early human embryonic development, and quantified transcription factor binding sites-clustered regions (TFCRs) and their complexity (TC). Assigning TC values to TFCRs has made it possible to assess the functionality of these regulatory elements in a more quantitative way. Our findings reveal a robust correlation between TFCR complexity and gene expression starting from the 8Cell stage, which is when the zygotic genome is activated in humans. Furthermore, we have defined long-range TFCRs (LR-TFCRs) and conjecture that LR-TFCRs may regulate gene expression through phase-separation mechanisms during the early stages of human embryonic development.

Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription. TAD hierarchy demonstrates cell-to-cell variability, leading to the development of numerous callers. Here, authors present a comprehensive benchmark of TAD hierarchy callers and introduce the 'air conditioner' model to illustrate TAD hierarchy's role in transcription.

Advances in chromatin mapping have exposed the complex chromatin hierarchical organization in mammals, including topologically associating domains (TADs) and their substructures, yet the functional implications of this hierarchy in gene regulation and disease progression are not fully elucidated. Our study delves into the phenomenon of shared TAD boundaries, which are pivotal in maintaining the hierarchical chromatin structure and regulating gene activity. By integrating high-resolution Hi-C data, chromatin accessibility, and DNA double-strand breaks (DSBs) data from various cell lines, we systematically explore the complex regulatory landscape at high-level TAD boundaries. Our findings indicate that these boundaries are not only key architectural elements but also vibrant hubs, enriched with functionally crucial genes and complex transcription factor binding site-clustered regions. Moreover, they exhibit a pronounced enrichment of DSBs, suggesting a nuanced interplay between transcriptional regulation and genomic stability. Our research provides novel insights into the intricate relationship between the 3D genome structure, gene regulation, and DNA repair mechanisms, highlighting the role of shared TAD boundaries in maintaining genomic integrity and resilience against perturbations. The implications of our findings extend to understanding the complexities of genomic diseases and open new avenues for therapeutic interventions targeting the structural and functional integrity of TAD boundaries.

BackgroundDNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation.ResultsHere, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation.ConclusionsOur study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.

During early mammalian embryo development, different epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code in a spatiotemporal manner remains difficult to analyze, markedly limiting scientific and clinical research. Here, we present dbEmbryo, an integrated and interactive multi-omics database for human and mouse early embryos. dbEmbryo integrates data on gene expression, DNA methylation, histone modifications, chromatin accessibility, and higher-order chromatin structure profiles for human and mouse early embryos. It incorporates customized analysis tools, such as “multi-omics visualization,” “Gene&Peak annotation,” “ZGA gene cluster,” “ cis -regulation,” “synergistic regulation,” “promoter signal enrichment,” and “3D genome.” Users can retrieve gene expression and epigenetic profile patterns to analyze synergistic changes across different early embryo developmental stages. We showed the uniqueness of dbEmbryo among extant databases containing data on early embryo development and provided an overview. Using dbEmbryo, we obtained a phase-separated model of transcriptional control during early embryo development. dbEmbryo offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryo development.

Endometrial cancer (EC) is one of the three fatal tumors of the female reproductive system. Epigenetic alterations have been reported to be important in tumorigenesis, especially the chromatin accessibility changes and transcription factor binding differences. However, the regulatory mechanism underlying epigenetic alterations in EC development remains unclear. Here, we identified and characterized transcription factor binding site clustered regions (TFCRs) by integrating chromatin accessibility and transcription factor binding information. We totally identified 78,820 TFCRs and explored the relationship between TFCRs and regulatory elements, gene expression and mutation. Finally, we constructed a bioinformatic framework to identify candidate oncogenes and screened 13 candidate key genes, which may serve as potential diagnostic markers or therapeutic targets of EC.

Recent studies have shown that the three-dimensional (3D) structure of chromatin is associated with cancer progression. However, the roles of the 3D genome structure and its dynamics in cancer remains largely unknown. In this study, we investigated hierarchical topologically associating domain (TAD) structures in cancers and defined a “TAD hierarchical score (TH score)” for genes, which allowed us to assess the TAD nesting level of all genes in a simplified way. We demonstrated that the TAD nesting levels of genes in a tumor differ from those in normal tissue. Furthermore, the hierarchical TAD level dynamics were related to transcriptional changes in cancer, and some of the genes in which the hierarchical level was altered were significantly related to the prognosis of cancer patients. Overall, the results of this study suggest that the folding dynamics of TADs are closely related to transcriptional abnormalities in cancers, emphasizing that the function of hierarchical chromatin organization goes beyond simple chromatin packaging efficiency.

目的:探究哺乳动物早期胚胎发育过程中基因表达调控信息的变化规律.方法:收集小鼠早期胚胎发育各时期的RNA-seq,ATAC-seq,MethylC-Seq和H3K4me3 ChIP-seq数据进行整合分析,观察小鼠早期胚胎发育各时期转录因子表达量的变化,计算各时期基因表达量与转录因子结合位点数量及染色质可及性的相关性,筛选各时期表达量前10％的基因,统计其表达量和转录因子占比,并进行启动子可及性分析.根据前期报道的转录因子三节点调控网络,对早期胚胎各时期转录因子调控网络的富集模式进行分析.根据多组学数据分析结果,推测早期胚胎发育调控过程中转录因子和表观遗传修饰信息的共调控模型.结果:转录因子数量和调控关系变化以及染色质可及性、DNA甲基化修饰、组蛋白修饰等表观遗传修饰共同调控早期胚胎发育各时期的基因表达,这些因素在不同时期发挥不同程度的调控作用.结论:转录因子和表观遗传修饰在早期胚胎发育过程中动态调控基因表达.