'; ?> geneimprint : Hot off the Press http://www.geneimprint.com/site/hot-off-the-press Daily listing of the most recent articles in epigenetics and imprinting, collected from the PubMed database. en-us Mon, 21 Apr 2025 00:21:55 EDT Mon, 21 Apr 2025 00:21:55 EDT jirtle@radonc.duke.edu james001@jirtle.com Epigenomic and proteomic analyses provide insights into early-life immune regulation and asthma development in infants. Li Y, Zhu Z, Camargo CA, Espinola JA, Hasegawa K, Liang L
Nat Commun (Apr 2025)

Infants with severe bronchiolitis (i.e., bronchiolitis requiring hospitalization) face increased risks of respiratory diseases in childhood. We conduct epigenome-wide association studies in a multi-ethnic cohort of these infants. We identify 61 differentially methylated regions in infant blood (<1 year of age) associated with recurrent wheezing by age 3 (170 cases, 318 non-cases) and/or asthma by age 6 (112 cases, 394 non-cases). These differentially methylated regions are enriched in the enhancers of peripheral blood neutrophils. Several differentially methylated regions exhibit interaction with rhinovirus infection and/or specific blood cell types. In the same blood samples, circulating levels of 104 proteins correlate with the differentially methylated regions, and many proteins show phenotypic association with asthma. Through Mendelian randomization, we find causal evidence supporting a protective role of higher plasma ST2 (also known as IL1RL1) protein against asthma. DNA methylation is also associated with ST2 protein level in infant blood. Taken together, our findings suggest the contribution of DNA methylation to asthma development through regulating early-life systemic immune responses.]]> Wed, 31 Dec 1969 19:00:00 EST Mom genes and dad genes: genomic imprinting in the regulation of social behaviors. O'Leary EM, Bonthuis PJ
Epigenomics (Apr 2025)

Genomic imprinting is an epigenetic phenomenon in mammals that affects brain development and behavior. Imprinting involves the regulation of allelic expression for some genes in offspring that depends on whether alleles are inherited from mothers compared to fathers, and is thought to provide parental control over offspring social behavior phenotypes. Imprinted gene expression is prevalent in the mammalian brain, and human imprinted gene mutations are associated with neurodevelopmental disorders and neurodivergent social behavior in Prader-Willi Syndrome, Angelman Syndrome, and autism. Here, we provide a review of the evidence that imprinted genes influence social behaviors across major neurodevelopmental stages in humans and mouse animal models that include parent-infant interactions, juvenile sociability, and adult aggression, dominance, and sexual behavior.]]> Wed, 31 Dec 1969 19:00:00 EST Epigenetic ageing clocks: statistical methods and emerging computational challenges. Teschendorff AE, Horvath S
Nat Rev Genet (May 2025)

Over the past decade, epigenetic clocks have emerged as powerful machine learning tools, not only to estimate chronological and biological age but also to assess the efficacy of anti-ageing, cellular rejuvenation and disease-preventive interventions. However, many computational and statistical challenges remain that limit our understanding, interpretation and application of epigenetic clocks. Here, we review these computational challenges, focusing on interpretation, cell-type heterogeneity and emerging single-cell methods, aiming to provide guidelines for the rigorous construction of interpretable epigenetic clocks at cell-type and single-cell resolution.]]> Wed, 31 Dec 1969 19:00:00 EST PlantEMS: A comprehensive database of epigenetic modification sites across multiple plant species. Dao F, Xie X, Zhang H, Guan Z, Wu C, Su W, Wei Y, Hong F, Luo X, Xie S, Lai H, Gao D, Yang Y, Zhang Y, Ning L, Li S, Hao Y, Lebeau B, Ling CCY, Huang J, Fullwood MJ, Lin H, Lv H
Plant Commun (Apr 2025)

In summary, PlantEMS is designed to advance plant epigenetics research by providing a comprehensive repository of multi-omics and multi-modification data. This resource enables detailed investigations into the epigenetic regulatory mechanisms underlying essential plant traits and responses, potentially informing innovative strategies for crop management, monitoring, and development.]]> Wed, 31 Dec 1969 19:00:00 EST On integrative analysis of multi-level gene expression data in Kidney cancer subgrouping. Jeyananthan P, W P N M, S M R
Urologia (May 2025)

Kidney cancer is one of the most dangerous cancer mainly targeting men. In 2020, around 430, 000 people were diagnosed with this disease worldwide. It can be divided into three prime subgroups such as kidney renal cell carcinoma (KIRC), kidney renal papilliary cell carcinoma (KIRP) and kidney chromophobe (KICH). Correct identification of these subgroups on time is crucial for the initiation and determination of proper treatment. On-time identification of this disease and its subgroup can help both the clinicians and patients to improve the situation. Hence, this study checks the possibility of using multi-omics data in the kidney cancer subgrouping, whether integrating multiple omics data will increase the subgrouping accuracy or not. Four different molecular data such as genomics, proteomics, epigenomics and miRNA from The Cancer Genome Atlas (TCGA) are used in this study. As the data is in a very high dimension world, this study starts with selecting the relevant features of the study using Pearson's correlation coefficient. Those selected features are used with three different classification algorithms such as k-nearest neighbor (KNN), supporting vector machines (SVMs) and random forest. Performances are compared to see whether the integration of multi-omics data can improve the accuracy of kidney cancer subgrouping. This study shows that integration of multi-omics data can improve the performance of the kidney cancer subgrouping. The highest performance (accuracy value of 0.98±0.03) is gained by top 400 features selected from integrated multi-omics data, with support vector machines.]]> Wed, 31 Dec 1969 19:00:00 EST TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data. Zhang G, Song C, Yin M, Liu L, Zhang Y, Li Y, Zhang J, Guo M, Li C
Nat Commun (Apr 2025)

It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of diseases. The use of large-scale multi-omics epigenomic data enables the representation of the complex epigenomic patterns of control of the regulatory elements and the regulators. Herein, we propose Transcription Regulator Activity Prediction Tool (TRAPT), a multi-modality deep learning framework, which infers regulator activity by learning and integrating the regulatory potentials of target gene cis-regulatory elements and genome-wide binding sites. The results of experiments on 570 TR-related datasets show that TRAPT outperformed state-of-the-art methods in predicting the TRs, especially in terms of forecasting transcription co-factors and chromatin regulators. Moreover, we successfully identify key TRs associated with diseases, genetic variations, cell-fate decisions, and tissues. Our method provides an innovative perspective on identifying TRs by using epigenomic data.]]> Wed, 31 Dec 1969 19:00:00 EST Developmental epigenomic effects of maternal financial problems. Holuka C, Menta G, Caro JC, Vögele C, D'Ambrosio C, Turner JD
Dev Psychopathol (May 2025)

Early-life adversity as neglect or low socioeconomic status is associated with negative physical/mental health outcomes and plays an important role in health trajectories through life. The early-life environment has been shown to be encoded as changes in epigenetic markers that are retained for many years.We investigated the effect of maternal major financial problems (MFP) and material deprivation (MD) on their children's epigenome in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Epigenetic aging, measured with epigenetic clocks, was weakly accelerated with increased MFP. In subsequent EWAS, MFP, and MD showed strong, independent programing effects on children's genomes. MFP in the period from birth to age seven was associated with genome-wide epigenetic modifications on children's genome visible at age 7 and partially remaining at age 15.These results support the hypothesis that physiological processes at least partially explain associations between early-life adversity and health problems later in life. Both maternal stressors (MFP/MD) had similar effects on biological pathways, providing preliminary evidence for the mechanisms underlying the effects of low socioeconomic status in early life and disease outcomes later in life. Understanding these associations is essential to explain disease susceptibility, overall life trajectories and the transition from health to disease.]]> Wed, 31 Dec 1969 19:00:00 EST Prenatal diagnosis of imprinted associated chromosome abnormalities identified by noninvasive prenatal testing (NIPT). Peng H, Wang D, Guo F, Hou Y, Hu T, Du Q, Yang J
Sci Rep (Apr 2025)

To explore the clinical value of noninvasive prenatal testing (NIPT) combined with chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq), methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), and fluorescence in situ hybridization (FISH) in the early screening of imprinted chromosome abnormalities. We retrospectively studied the prenatal diagnosis and pregnancy outcomes of 9 pregnant women with imprinted associated chromosome abnormalities via NIPT. All pregnant women received detailed genetic counselling and prenatal diagnosis. Karyotyping analysis, CNV-seq, CMA, FISH or MS-MLPA were performed on the amniotic fluid samples. We collected the intrauterine phenotypes via ultrasound and followed them up until the induction of labor or one year after birth. Six fetuses (6 out of 9) were diagnosed with regional abnormalities of Imprinting Disease. The most commonly diagnosed syndrome was 15q11-q13 duplication syndrome ( 3 out of 6), followed by mosaic trisomy 7 (2 out of 6) and Temple syndrome (1 out of 6). The other three fetuses (3 out of 9) were diagnosed with absence of heterozygosity (AOH). After genetic counselling, 4 pregnant women (4 out of 9) chose induced labor, 3 pregnant women (3 out of 9) chose spontaneous labor, and 2 pregnant women (2 out of 9) chose cesarean section. The widespread use of NIPT in prenatal screening provides more opportunities to detect rare chromosome aneuploidies (RCAs) and microdeletion/microduplication syndromes (MMSs) in mid-pregnancy. The combination of NIPT and other prenatal diagnostic technologies can help increase the possibility of detecting imprinting-related diseases with no phenotype or a late phenotype in utero.]]> Wed, 31 Dec 1969 19:00:00 EST Exploring omics solutions to reduce micro/nanoplastic toxicity in plants: A comprehensive overview. Arif SM, Khan I, Saeed M, Chaudhari SK, Ghorbanpour M, Hasan M, Mustafa G
Sci Total Environ (Apr 2025)

The proliferation of plastic waste, particularly in the form of microplastics (MPs) and nanoplastics (NPs), has emerged as a significant environmental challenge with profound implications for agricultural ecosystems. These pervasive pollutants accumulate in soil, altering its physicochemical properties and disrupting microbial communities. MPs/NPs can infiltrate plant systems, leading to oxidative stress and cytotoxic effects, which in turn compromise essential physiological functions such as water uptake, nutrient absorption, and photosynthesis. This situation threatens crop yield and health, while also posing risks to human health and food security through potential accumulation in the food chain. Despite increasing awareness of this issue, substantial gaps still remain in our understanding of the physiological and molecular mechanisms that govern plant responses to MP/NP stress. This review employs integrative omics techniques including genomics, transcriptomics, proteomics, metabolomics, and epigenomics to elucidate these responses. High-throughput methodologies have revealed significant genetic and metabolic alterations that enable plants to mitigate the toxicity associated with MPs/NPs. The findings indicate a reconfiguration of metabolic pathways aimed at maintaining cellular homeostasis, activation of antioxidant mechanisms, and modulation of gene expression related to stress responses. Additionally, epigenetic modifications suggest that plants adapt to prolonged plastics exposure, highlighting unexplored avenues for targeted research. By integrating various omics approaches, a comprehensive understanding of molecular interactions and their effects on plant systems can be achieved. This review underscores potential targets for biotechnological and agronomic interventions aimed at enhancing plant resilience by identifying key stress-responsive genes, proteins, and metabolites. Ultimately, this work addresses critical knowledge gaps and highlights the importance of multi-omics strategies in developing sustainable solutions to mitigate the adverse effects of MP/NP pollution in agriculture, thereby ensuring the integrity of food systems and ecosystems.]]> Wed, 31 Dec 1969 19:00:00 EST Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease. O'Sullivan J, Patel S, Leventhal GE, Fitzgerald RS, Laserna-Mendieta EJ, Huseyin CE, Konstantinidou N, Rutherford E, Lavelle A, Dabbagh K, DeSantis TZ, Shanahan F, Temko A, Iwai S, Claesson MJ
Gut Microbes (Dec 2025)

Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient's succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.]]> Wed, 31 Dec 1969 19:00:00 EST Unified molecular approach for spatial epigenome, transcriptome, and cell lineages. Huang YH, Belk JA, Zhang R, Weiser NE, Chiang Z, Jones MG, Mischel PS, Buenrostro JD, Chang HY
Proc Natl Acad Sci U S A (Apr 2025)

Spatial epigenomics and multiomics can provide fine-grained insights into cellular states but their widespread adoption is limited by the requirement for bespoke slides and capture chemistries for each data modality. Here, we present SPatial assay for Accessible chromatin, Cell lineages, and gene Expression with sequencing (SPACE-seq), a method that utilizes polyadenine-tailed epigenomic libraries to enable facile spatial multiomics using standard whole transcriptome reagents. Applying SPACE-seq to a human glioblastoma specimen, we reveal the state of the tumor microenvironment, extrachromosomal DNA copy numbers, and identify putative mitochondrial DNA variants.]]> Wed, 31 Dec 1969 19:00:00 EST Conservation of imprinted expression across genotypes is correlated with consistency of imprinting across endosperm development in maize. Higgins K, Nyabashi V, Anderson S
G3 (Bethesda) (Apr 2025)

Imprinted expression is an essential process for seed viability affecting hundreds of genes in Zea mays endosperm; however, most studies have examined just one time point for analysis. The focus on single time points can limit our ability to identify imprinted genes and our ability to draw conclusions for the role of imprinting in endosperm. In this study, we examine imprinted expression across 4 time points ranging from the transition to endoreduplication from mitotic division through the beginning of programmed cell death. Additionally, we assessed imprinting variation across 8 diverse maize lines, 6 of which have never before been assessed for imprinting. Through this analysis, we identify over 700 imprinted genes with varying consistency across time points including 255 genes imprinted at every time point and 105 genes displaying transient imprinting. We find a correlation between high consistency of imprinting across time and high conservation of parental bias across 8 diverse maize lines reciprocally crossed with B73. Additionally, we identify evidence of imprinting for 3 zein genes that are critical for nutrient accumulation in the endosperm, suggesting that imprinting may play a more important role in seed composition than previously thought. Taken together, this study provides a more holistic view of imprinting variation across time and across genotypes in maize and enables us to more thoroughly investigate the complex imprinting landscape.]]> Wed, 31 Dec 1969 19:00:00 EST Bidirectional disruption of transcripts causes broad methylation defects in pseudohypoparathyroidism type 1B. Iwasaki Y, Reyes M, Ryabets-Lienhard A, Gales B, Linglart A, Miller DE, Salusky IB, Bastepe M, Jüppner H
Proc Natl Acad Sci U S A (Apr 2025)

Pseudohypoparathyroidism type 1B (PHP1B) is a multihormone resistance disorder caused by aberrant methylation. Characteristic epigenetic changes at differentially methylated regions (DMRs), i.e., NESP, AS1, AS2, XL, and A/B, are associated with specific structural defects in different autosomal dominant PHP1B (AD-PHP1B) subtypes. However, mechanisms underlying abnormal methylation remain incompletely defined, largely because viable PHP1B mouse models are lacking. Using lymphoblastoid cells and induced pluripotent stem cells, we show that various methylation patterns in PHP1B reflect differential disruption of sense and antisense transcripts. In cases with broad methylation changes, loss of the maternal, sense-transcribed exon H/AS region impairs methylation of the AS1 DMR, which results in biallelic expression of an antisense transcript, , and NESP hypermethylation. In contrast, cases with normal AS1 methylation, including deletions, show monoallelic expression and normal NESP methylation. The roles of these transcripts were confirmed by a retrotransposon in intron 1, identified in an AD-PHP1B family. This insertion impaired exon H/AS transcription when located on the maternal allele, thus preventing the complete establishment of methylation at all maternal DMRs, leading to biallelic transcription. However, maternal transcription was profoundly attenuated, thus allowing only a small gain-of-methylation at NESP. Likewise, on the paternal allele, the retrotransposon attenuated transcription, thus preventing complete NESP methylation. Our findings support a model of bidirectional transcription-mediated regulation of methylation at DMRs and will help to refine systematic approaches for establishing molecular defects underlying different PHP1B subtypes.]]> Wed, 31 Dec 1969 19:00:00 EST Histone Modifications as Molecular Drivers of Cardiac Aging: Metabolic Alterations, Epigenetic Mechanisms, and Emerging Therapeutic Strategies. Alrumaihi F, Al-Doaiss AA, Ullah F, Alwanian WM, Alharbi HO, Alassaf FA, Alfifi SM, Alshabrmi FM, Aba Alkhay FF, Alatawi EA, Smith O
Curr Probl Cardiol (Apr 2025)

Cardiac aging represents a complex pathophysiological process characterized by progressive metabolic recombination and functional dedifferentiation of cardiac cellular components. Despite advancements in cardiovascular medicine, a critical research gap persists in understanding the precise epigenetic mechanisms that drive age-related cardiac dysfunction. This comprehensive review elucidates the pivotal role of histone modifications-including methylation, acetylation, and phosphorylation-in orchestrating the molecular landscape of cardiac aging. Significant gaps remain in our understanding of site-specific histone modification impacts on cardiac function, the intricate crosstalk between different histone marks, and their integration with metabolic alterations that characterize the aging myocardium. Current evidence reveals a dynamic epigenetic signature in aged cardiac tissue, typically featuring increased transcriptional activation markers alongside decreased repressive marks, though context-dependent variations exist. This review explores how histone modifications influence critical pathways governing mitochondrial dysfunction, DNA damage repair, inflammation, and fibrosis in aging hearts. Innovative therapeutic approaches targeting specific histone-modifying enzymes promise to mitigate age-related cardiac deterioration, potentially revolutionizing treatment paradigms for cardiovascular diseases in aging populations. Addressing these knowledge gaps requires multidimensional approaches that integrate epigenomics with functional assessment of cardiac performance.]]> Wed, 31 Dec 1969 19:00:00 EST Strengthening Rigor and Reproducibility in Epigenome-Wide Association Studies of Social Exposures and Brain-Based Health Outcomes. McKenna BG, Lussier AA, Suderman MJ, Walton E, Simpkin AJ, Hüls A, Dunn EC
Curr Environ Health Rep (Apr 2025)

Studies examining the effects of social factors on the epigenome have proliferated over the last two decades. Social epigenetics research to date has broadly demonstrated that social factors spanning childhood adversity, to neighborhood disadvantage, educational attainment, and economic instability are associated with alterations to DNA methylation that may have a functional impact on health. These relationships are particularly relevant to brain-based health outcomes such as psychiatric disorders, which are strongly influenced by social exposures and are also the leading cause of disability worldwide. However, social epigenetics studies are limited by the many challenges faced by both epigenome-wide association studies (EWAS) and the study of social factors.]]> Wed, 31 Dec 1969 19:00:00 EST Epigenetic timing effects on child developmental outcomes: a longitudinal meta-regression of findings from the Pregnancy And Childhood Epigenetics Consortium. Neumann A, Sammallahti S, Cosin-Tomas M, Reese SE, Suderman M, Alemany S, Almqvist C, Andrusaityte S, Arshad SH, Bakermans-Kranenburg MJ, Beilin L, Breton C, Bustamante M, Czamara D, Dabelea D, Eng C, Eskenazi B, Fuemmeler BF, Gilliland FD, Grazuleviciene R, HÃ¥berg SE, Herberth G, Holland N, Hough A, Hu D, Huen K, Hüls A, Jarvelin MR, Jin J, Julvez J, Koletzko BV, Koppelman GH, Kull I, Lu X, Maitre L, Mason D, Melén E, Merid SK, Molloy PL, Mori TA, Mulder RH, Page CM, Richmond RC, Röder S, Ross JP, Schellhas L, Sebert S, Sheppard D, Snieder H, Starling AP, Stein DJ, Tindula G, van IJzendoorn MH, Vonk J, Walton E, Witonsky J, Xu CJ, Yang IV, Yousefi PD, Zar HJ, Zenclussen AC, Zhang H, Tiemeier H, London SJ, Felix JF, Cecil C
Genome Med (Apr 2025)

DNA methylation (DNAm) is a developmentally dynamic epigenetic process; yet, most epigenome-wide association studies (EWAS) have examined DNAm at only one timepoint or without systematic comparisons between timepoints. Thus, it is unclear whether DNAm alterations during certain developmental periods are more informative than others for health outcomes, how persistent epigenetic signals are across time, and whether epigenetic timing effects differ by outcome.]]> Wed, 31 Dec 1969 19:00:00 EST Enhancing the neural differentiation capabilities of genetically asymmetric mouse F1 hybrid embryonic stem cell lines. Saito A, Kato H, Kiyosawa H
Exp Anim (Apr 2025)

Allele-specific, monoallelic expression in diploid organisms represents an extreme case of allelic imbalance resulting from incompatibility between cis- and trans-elements. Due to haploinsufficiency, such monoallelic expression can lead to sporadic genetic diseases. In mice, allelic imbalances can be introduced into F1 offspring from inbred strains. Previously, we established F1 hybrid embryonic stem (ES) cell lines derived from four different mouse strains, each belonging to a different subspecies with substantial genetic polymorphisms. In this study, we investigated the neural differentiation capacity of the established ES cell lines. By introducing different culture conditions, which kept the ES cells undifferentiated under various pluripotencies, we succeeded in differentiating the majority of ES cell lines (eight out of eleven) with our default neural differentiation paradigm. Still, three lines exhibited insufficient differentiation despite combining culture conditions promoting undifferentiated as well as differentiated status. In addition, Ube3a imprinting was seen in two lines. Our findings contribute to the methodological understanding of mouse ES cell pluripotency and lead to the practical utility of F1 hybrid ES cells as a model for studying phenotypes resulting from gene locus interactions.]]> Wed, 31 Dec 1969 19:00:00 EST Evolution of genome-wide methylation profiling technologies. Montano C, Timp W
Genome Res (Apr 2025)

In this mini-review, we explore the advancements in genome-wide DNA methylation profiling, tracing the evolution from traditional methods such as methylation arrays and whole-genome bisulfite sequencing to the cutting-edge single-molecule profiling enabled by long-read sequencing (LRS) technologies. We highlight how LRS is transforming clinical and translational research, particularly by its ability to simultaneously measure genetic and epigenetic information, providing a more comprehensive understanding of complex disease mechanisms. We discuss current challenges and future directions in the field, emphasizing the need for innovative computational tools and robust, reproducible approaches to fully harness the capabilities of LRS in molecular diagnostics.]]> Wed, 31 Dec 1969 19:00:00 EST METTL3-mediated m6A modification in sepsis: current evidence and future perspectives. Wu Z, Miao C, Zhang H
Epigenomics (Apr 2025)

Sepsis, a severe systemic inflammatory condition triggered by infection, is associated with high morbidity and mortality worldwide. While medical diagnosis and treatment have advanced in recent years, a specific therapy remains unavailable. Recently, significant progress has been made in studying the epigenetic RNA modification N6-methyladenosine (m6A) and its core methyltransferase METTL3. The role of m6A in sepsis has also been increasingly elucidated. This review aims to explore the pathological mechanisms of sepsis and its relationship with m6A, focusing on the role of the key m6A writer, METTL3, in sepsis.]]> Wed, 31 Dec 1969 19:00:00 EST Unveiling chromatin dynamics with virtual epigenome. Lin MY, Lo YC, Hung JH
Nat Commun (Apr 2025)

The three-dimensional organization of chromatin is essential for gene regulation and cellular function, with epigenome playing a key role. Hi-C methods have expanded our understanding of chromatin interactions, but their high cost and complexity limit their use. Existing models for predicting chromatin interactions rely on limited ChIP-seq inputs, reducing their accuracy and generalizability. In this work, we present a computational approach, EpiVerse, which leverages imputed epigenetic signals and advanced deep learning techniques. EpiVerse significantly improves the accuracy of cross-cell-type Hi-C prediction, while also enhancing model interpretability by incorporating chromatin state prediction within a multitask learning framework. Moreover, EpiVerse predicts Hi-C contact maps across an array of 39 human tissues, which provides a comprehensive view of the complex relationship between chromatin structure and gene regulation. Furthermore, EpiVerse facilitates unprecedented in silico perturbation experiments at the "epigenome-level" to unveil the chromatin architecture under specific conditions. EpiVerse is available on GitHub: https://github.com/jhhung/EpiVerse .]]> Wed, 31 Dec 1969 19:00:00 EST