'; ?> 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 Sat, 07 Feb 2026 03:46:38 EST Sat, 07 Feb 2026 03:46:38 EST jirtle@radonc.duke.edu james001@jirtle.com Dissecting methylation errors at imprinted genes in human spermatozoa: from molecular observations to clinical applications†. Marques CJ, Sousa M, Carvalho F, Barros A
Biol Reprod (Feb 2026)

Epigenetic modifications regulate chromatin conformation and transcription factor accessibility to regulatory regions of the genome, controlling gene expression without altering the DNA sequence itself, and being stably transmitted throughout cell divisions. One of the most well studied epigenetic marks is DNA methylation, which controls the monoallelic, parental-origin dependent expression of imprinted genes. Paternal imprinting marks are established in the male germ line, so that mature gametes - the spermatozoa - transmit correct imprints to the future embryo. Anomalies in the establishment and/or maintenance of imprinting marks can interfere with embryonic and placental development and/or result in the birth of children affected by imprinting syndromes, such as Silver-Russell (SRS) and Beckwith-Wiedemann (BWS). Here, we review the literature on the observations of imprinting errors in the male gamete, in the context of disturbances in spermatogenesis resulting in male infertility, focusing on the observations described by our group and others. We provide a clinical perspective on the implementation of sperm methylation analysis as a tool to improve diagnostic and therapeutic strategies in Assisted Reproduction Technologies (ART) and highlight the importance of understanding the molecular mechanisms underlying spermatogenic defects and male infertility.]]> Wed, 31 Dec 1969 19:00:00 EST Single-Cell Multimodal Profiling Highlights Persistent Aortic Smooth Muscle Cell Changes in Diabetic Mice Despite Glycemic Control. Tanwar VS, Malek V, Wang J, Luo Y, Malhi NK, Zhang H, Abdollahi M, Lanting L, Senapati P, Das S, Reddy MA, Zang C, Miller CL, Chen ZB, Natarajan R
Arterioscler Thromb Vasc Biol (Feb 2026)

Type 2 diabetes is associated with accelerated vascular complications such as hypertension and atherosclerosis. Phenotypic switching of vascular smooth muscle cells (SMCs), a major driver of these complications, is enhanced in diabetes. Despite adequate glycemic control, SMC dysfunction can persist due to metabolic memory of prior hyperglycemia. However, the mechanisms are unclear. Here, leveraging single-cell multiomics, we examined the effect of glucose normalization on transcriptomic and epigenomic changes associated with SMC phenotypic transition in type 2 diabetes mice.]]> Wed, 31 Dec 1969 19:00:00 EST A cell type enrichment analysis tool for brain DNA methylation data (CEAM). Müller J, Laroche VT, Imm J, Weymouth L, Harvey J, Reijnders RA, Smith AR, van den Hove D, Lunnon K, Cavill R, Pishva E
Epigenetics (Dec 2026)

DNA methylation (DNAm) signatures are highly cell type-specific, yet most epigenome-wide association studies (EWAS) are performed on bulk tissue, potentially obscuring critical cell type-specific patterns. Existing computational tools for detecting cell type-specific DNAm changes are often limited by the accuracy of cell type deconvolution algorithms. Here, we introduce CEAM (Cell-type Enrichment Analysis for Methylation), a robust and interpretable framework for cell type enrichment analysis in DNA methylation data. CEAM applies over-representation analysis with cell type-specific CpG panels from Illumina EPIC arrays derived from nuclei-sorted cortical post-mortem brains from neurologically healthy aged individuals. The constructed CpG panels were systematically evaluated using both simulated datasets and published EWAS results from Alzheimer's disease, Lewy body disease, and multiple sclerosis. CEAM demonstrated resilience to shifts in cell type composition, a common confounder in EWAS, and remained robust across a wide range of differentially methylated positions, when upstream modeling of cell type composition was modeled with sufficient accuracy. Application to existing EWAS findings generated in neurodegenerative diseases revealed enrichment patterns concordant with established disease biology, confirming CEAM's biological relevance. The workflow is publicly available as an interactive Shiny app (https://um-dementia-systems-biology.shinyapps.io/CEAM/) enabling rapid, interpretable analysis of cell type-specific DNAm changes from bulk EWAS.]]> Wed, 31 Dec 1969 19:00:00 EST Cell-free DNA epigenomic profiling enables noninvasive detection and monitoring of translocation renal cell carcinoma. Garinet S, Semaan K, Li J, Zhang Z, Konda P, Sadagopan A, Canniff J, Phillips N, Klega K, Pandey M, Savignano H, Davidsohn MP, Lyons K, Medda A, Khanna P, Achom M, Fortunato BJ, Nawfal R, El Hajj Chehade R, O'Toole J, Horst J, Freeman D, Trowbridge R, Chau CH, Figg WD, Berchuck JE, Crompton BD, Seo JH, Choueiri TK, Freedman ML, Baca SC, Viswanathan SR
J Clin Invest (Feb 2026)

TFE3 translocation renal cell carcinoma (tRCC), an aggressive kidney cancer driven by TFE3 gene fusions, is frequently misdiagnosed owing to morphologic overlap with other kidney cancer subtypes. Conventional liquid biopsy assays that detect tumor DNA via somatic mutations or copy number alterations are unsuitable for tRCC since it often lacks recurrent genetic alterations and because fusion breakpoints are highly variable between patients. We reasoned that epigenomic profiling could more effectively detect tRCC because the driver fusion constitutes an oncogenic transcription factor that alters gene regulation. By defining a TFE3-driven epigenomic signature in tRCC cell lines and detecting it in patient plasma using ChIP-seq, we distinguished tRCC from clear-cell RCC (AUC = 0.86) and samples of individuals without evidence of cancer (AUC = 0.92) at low tumor fractions (<1%). This work establishes a framework for noninvasive epigenomic detection, diagnosis, and monitoring of tRCC, with implications for other mutationally quiet, fusion-driven cancers.]]> Wed, 31 Dec 1969 19:00:00 EST : a computational suite for DNA methylation sequencing data analysis. Loyfer N, Rosenski J, Kaplan T
Life Sci Alliance (Apr 2026)

Next-generation methylation-aware sequencing of DNA sheds light on the fundamental role of methylation in cellular function in health and disease, increasing the number of covered CpG sites from hundreds of thousands in previous array-based approaches to tens of millions across the whole genome. While array-based approaches are limited to single-CpG resolution, next-generation sequencing allows for a more detailed, single-molecule fragment-level analysis; however, existing tools to fully use this capability are not yet well developed. Here, we present , an extensive computational suite tailored for methylation sequencing data. allows fast access and ultracompact anonymized representation of high-throughput methylome data, obtained through various library preparation and sequencing methods, with a custom epiread file format achieving a compression factor of over 100x from the input BAM file. In addition, contains state-of-the-art algorithms for genomic segmentation, biomarker identification, genetic and epigenetic data integration, and more. offers fragment-level analysis and informative visualizations, across multiple genomic regions and samples.]]> Wed, 31 Dec 1969 19:00:00 EST [Obesity and genetics: advances in understanding genetic factors and their clinical impact]. Gamero-de-Luna EJ, Capilla Díaz S, Yanes Rodríguez M
Semergen (Feb 2026)

Obesity is a complex chronic disease involving physiological, behavioural, and environmental factors, with a key role played by the gut microbiota. A narrative review was conducted using PubMed, Scopus, Web of Science, and EMBASE databases, including books, clinical practice guidelines, meta-analyses, observational studies, and reviews published in English or Spanish. Animal studies and publications prior to 2014 were excluded. A total of 15,074 publications were identified, of which 127 were selected for full-text review. Key findings include the lack of consensus on obesity classification, phenotypic variability that cannot be solely explained by genetic or epigenetic factors, and differences between monogenic, syndromic, and polygenic obesity. The implementation of genomic and epigenetic tools, such as biomarkers and personalized nutritional strategies, is crucial for precision medicine in obesity management. However, further research is needed for its widespread clinical application.]]> Wed, 31 Dec 1969 19:00:00 EST Synergistic integration of clinical and multi-omics data for early MCI diagnosis using an attention-based graph fusion network. Yu S, Zhao J, Ouyang J, Wang X, Kou P, Zhu K, Liu P
J Neurosci Methods (Apr 2026)

Mild cognitive impairment (MCI), a precursor to Alzheimer's disease (AD), requires precise early diagnosis. Single-omics approaches often miss disease complexity, motivating integrative and interpretable solutions.]]> Wed, 31 Dec 1969 19:00:00 EST Limitations and opportunities in multi-omics integration for neurodevelopmental, neurodegenerative and psychiatric disorders: A systematic review. Behrens LMP, Fernandes GDS, Gonçalves GF, Nunes FVM, Weimer RD, Moreira JCF, Dorn M
Neuroscience (Feb 2026)

Recent advances in high-throughput technologies have led to an increased generation of biological data across genomics, transcriptomics, proteomics, epigenomics, and metabolomics. However, a major challenge remains: effectively integrating these multi-omics datasets to allow a more holistic understanding of the complex, interconnected mechanisms underlying human diseases. Neurodevelopmental, neurodegenerative, and psychiatric disorders are particularly multifactorial and heterogeneous, making them candidates for multi-omics approaches. In this context, this systematic review assesses the current state of multi-omics integration in neurological research. Records retrieved from five major databases were processed, and 156 studies were included for further analysis. The most frequently studied conditions were Alzheimer's Disease, Depressive Disorder and Parkinson's Disease, with epigenomics-transcriptomics and metagenomics-metabolomics emerging as the most common omics pairings. The field remains dominated by studies integrating pairs of omics layers. Only a limited number of computational tools are currently being applied to the integration of more than two omics layers, highlighting a gap in comprehensive multi-omics modeling. Despite progress, key challenges persist, including data accessibility and the need for standardized frameworks to allow cross-study comparisons. Moreover, most computational findings lack experimental validation in wet-laboratory settings. Future research should address these challenges, develop scalable algorithms for integrating multi-omics data, and leverage large, open-access datasets. Integrating computational predictions with experimental validation could help researchers prioritize high-confidence biomarkers relevant to clinical applications. Collaborative efforts among bioinformaticians, clinicians, and experimentalists will be essential to translating these advances into clinically actionable solutions.]]> Wed, 31 Dec 1969 19:00:00 EST ‑folate axis as a modulator of the epigenetic landscape in autoimmune diseases (Review). Navarro-Rodríguez PM, Bajeca-Serrano RF, Turrubiates-Hernández FJ, Ceja-Gálvez HR, Hernández-Bello J, Hernández-Ramírez CO, Ramírez-de Los Santos S, Muñoz-Valle JF
Int J Mol Med (Mar 2026)

The one‑carbon metabolism pathway, regulated by the methylenetetrahydrofolate reductase (MTHFR) enzyme, represents a key nexus where genetic predisposition and nutrient status converge to shape the epigenetic landscape of autoimmune diseases. The objective of the present review is to synthesize evidence of how the ‑folate axis drives epigenomic patterns in these conditions. One of the main diseases involved is rheumatoid arthritis, where drug‑naïve patients show T‑cell and synovial hypomethylation with cytokine‑driven DNMT suppression, a process aggravated by reduced folate availability and polymorphisms that constrain S‑adenosylmethionine supply. Similarly, in systemic lupus erythematosus, CD4 T cells exhibit global hypomethylation with an interferon‑skewed signature (such as ), associated with impaired activity and a folate‑dependent SAM:SAH imbalance that further diminishes DNMT function. Finally, in celiac disease, intestinal differential methylation, including LINE‑1 hypomethylation, is observed, driven by gluten‑induced villous atrophy and folate malabsorption. Overall, impaired one‑carbon metabolism and ‑dependent methylation capacity may be key determinants of epigenomic dysfunction underlying autoimmune disease and its clinical severity.17.]]> Wed, 31 Dec 1969 19:00:00 EST Melatonin-enabled omics: understanding plant responses to single and combined abiotic stresses for climate-smart agriculture. Raza A, Li Y, Charagh S, Guo C, Zhao M, Hu Z
GM Crops Food (Dec 2026)

Climate change-driven single and combined abiotic stresses pose escalating threats to sustainable, climate-smart agriculture and global food security. Melatonin (MLT, a powerful plant biostimulant) has established noteworthy potential in improving stress tolerance by regulating diverse physiological, biochemical, and molecular responses. Therefore, this review delivers a comprehensive synopsis of MLT-enabled omics responses across genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics, phenomics, ionomics, and microbiomics levels that collectively regulate plant adaptation to multiple abiotic stresses. We also highlight the crosstalk between these omics layers and the power of integrated multi-omics (panomics) approaches to harness the complex regulatory networks underlying MLT-enabled stress tolerance. Lastly, we argue for translating these omics insights into actionable strategies through advanced genetic engineering and synthetic biology platforms to develop MLT-enabled, stress-smart crop plants.]]> Wed, 31 Dec 1969 19:00:00 EST Computational methods for spatial multi-omics integration. Geng A, Cui C, Luo Z, Xu J, Meng Y, Cui F, Wei L, Zou Q, Zhang Z
Biotechnol Adv (2026)

The rapid development of spatial multi-omics technologies has enabled the simultaneous acquisition of transcriptomic, proteomic, and epigenomic information from the same tissue section. However, substantial differences in distributional properties, data dimensionality, and noise levels across modalities, together with the inherent sparsity and incompleteness of spatial information, pose major challenges for data integration and modeling. In recent years, deep learning-based spatial multi-omics integration algorithms have emerged rapidly, offering new approaches for constructing unified latent representations and achieving cross-modal fusion. In this review, we systematically summarize existing spatial multi-omics integration methods for the first time, categorizing and comparing them from two perspectives. We not only systematically surveyed the datasets employed by these methods, but also highlighted the key downstream analytical tasks they support, and further summarized the major challenges currently faced in spatial multi-omics integration research. Furthermore, we compare the strengths and limitations of different approaches to assist researchers in selecting appropriate methods more efficiently, thereby advancing the application of spatial multi-omics in uncovering multilayer regulatory mechanisms of tissue microenvironments and disease processes.]]> Wed, 31 Dec 1969 19:00:00 EST Maternal adiposity and DNA methylation of TfR2 and HJV genes in early pregnancy: mediating role of inflammation and consequences for iron status. Demirdjian SP, Irwin RE, Thompson PD, Mulhern MS, Kerr MA, Ledwidge M, Rahman KL, Conway C, Rodriguez EP, McCann MT
J Nutr (Feb 2026)

Growing evidence shows that obesity influences iron status during pregnancy, however, it is unknown whether maternal obesity is associated with epigenetic changes in TfR2 and HJV.]]> Wed, 31 Dec 1969 19:00:00 EST Erythropoietin Expression and Regulation: Piecing Together Known Mechanisms and Emerging Insights. Idriss S, Hoogewijs D, Girodon F, Gardie B
Am J Hematol (Mar 2026)

Erythropoietin (EPO) is a circulating glycoprotein hormone essential for red blood cell production. The history of EPO stretches from early observations of hypoxia in the mid-19th century to its gene cloning and the clinical use of recombinant forms. Structurally, EPO's extensive glycosylation shapes stability, receptor binding, and therapeutic potential, inspiring engineered analogs with distinct pharmacokinetics. Developmentally, EPO expression shifts from embryonic neural crest and fetal hepatocytes to renal interstitial fibroblasts after birth. EPO gene regulation integrates hypoxia-inducible factors, transcriptional repressors, enhancers, with HIF-2α as the principal activator, and post-translational mechanisms. Recent findings reveal genetic variants within the EPO gene in patients with erythrocytosis. Isoelectric focusing profiles of EPO in these patients was similar to the hepatic-derived EPO profiles in premature newborns, highlighting a dynamic and context-dependent regulation. These findings suggest that reactivation of EPO expression in the liver could be therapeutically valuable, given that hepatic-derived EPO exhibits enhanced activity. Clinically, erythropoiesis-stimulating agents transformed anemia management but raised safety concerns, leading to refined guidelines. The recent introduction of hypoxia-inducible factor prolyl hydroxylase inhibitors represents a new strategy that restores endogenous EPO production and coordinates iron metabolism through transient HIF stabilization. Outstanding challenges include the absence of faithful human EPO-producing cell models and incomplete understanding of the full molecular mechanisms controlling EPO expression and production. Combining insights from developmental biology, genetics, and epigenomics may open new avenues for therapies targeting disorders of erythropoiesis and oxygen homeostasis.]]> Wed, 31 Dec 1969 19:00:00 EST ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species. Hossain M, Mojumder A, Rashid SMM, Islam ABMMK
BMC Bioinformatics (Feb 2026)

]]> Wed, 31 Dec 1969 19:00:00 EST CRISPR 2.0: Expanding the genome engineering Toolbox for epigenetics, RNA editing, and molecular diagnostics. Pradhan K, Anoop S
Gene (Feb 2026)

Non-canonical CRISPR systems adaptation has led to genome editing through nucleases, and the development of transcriptional and epigenetic regulation, transcriptome editing, and molecular diagnostics has resulted in a diversified set of tools-CRISPR 2.0. In this review, the author summarizes the mechanisms and recent engineering advances of (i) dCas9-based epigenetic effectors, (ii) RNA-targeting Cas13 systems and engineered RNA editors, (iii) DNA base editors and prime editors, and (iv) CRISPR-powered diagnostic platforms and their translational readiness. There is a critical comparison of the various approaches (e.g., RNAi/ASO versus Cas13-based methods; base editing versus prime editing) along with practical translational considerations such as delivery technologies, safety (off-target/edit windows, mosaicism), and regulatory pathways which are evaluated. Three concise case studies refer to map laboratory evidence to clinical or near-clinical outcomes and the ethical and governance discussion is widened to include global access, intellectual property and equity in deployment. Finally, the authors classify technologies according to their level of readiness - diagnostics and some ex-vivo therapeutic approaches are already in or very close to clinical use, chosen in-vivo editing methods are undergoing early trials, and AI-assisted nuclease design is still mostly theoretical but is getting better fast. This comprehensive viewpoint is intended to help researchers and physicians understand which CRISPR tools are most likely to be translated soon and where more validation is required.]]> Wed, 31 Dec 1969 19:00:00 EST Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat. Li R, Duan S, Deng Q, Ma W, Liu C, Gao P, Lu L, Yuan Y
Gigascience (Feb 2026)

The chromatin accessibility landscape is the basis of cell-specific gene expression. We generated a multi organ, single-nucleus chromatin accessibility landscape from the model organism Rattus norvegicus. For this single-cell atlas, we constructed 25 libraries via snATAC-seq from nine organs in the rat, with a total of over 110,000 cells. Cell classification integrating gene activity scores with known marker genes identified 77 cell types, which were strongly correlated with those in published mouse single-cell transcriptome atlases. We further investigated the enrichment of cell type- and organ-specific transcription factors (TFs), Shared and organ-specific features of endothelial and stromal cells, as well as cross-organ macrophage regulatory states, and the conservation and specificity of gene regulatory programs across species. Together, these findings provide a valuable foundation for dissecting tissue-specific regulatory logic and for advancing cross-organ and cross-species cell type annotation and functional inference in the rat model.]]> Wed, 31 Dec 1969 19:00:00 EST Genome-wide profiling of salivary promoter-region DNA methylation in periodontitis: the Tromsø study. Petrenya N, Jönsson B, Hadler-Olsen E, Larsson L, Flatberg A, BeisvÃ¥g V, Holde GE, Zykova SN, Asa'ad F
BMC Med Genomics (Feb 2026)

]]> Wed, 31 Dec 1969 19:00:00 EST ChIP happens: from biochemical origins to the modern omics toolbox for understanding steroid hormone receptors. Grimes TF, Pope J, Stenning J, Smith TE, Kent DG, Baker S, Brackenbury WJ, Willems LI, Holding AN
Biochem J (Feb 2026)

Nuclear steroid hormone receptors (SHRs) are ligand-activated transcription factors that mediate cellular responses to steroid hormones (SHs) through regulating gene expression. Understanding the SHR function is crucial for elucidating SH-driven physiology and pathology, including their roles in normal development, metabolism and reproduction, alongside their aberrant function in cancer, endocrine disorders and inflammatory diseases. Investigating the mechanisms that underscore SHR signalling and regulation is therefore essential for advancing our knowledge of both normal physiology and disease and is vital to the development of novel therapeutic strategies. In this review, we examine a range of methods for studying SHR interactions with chromatin and coregulator proteins, from classical biochemical assays to more advanced approaches such as PL-MS, RIME and ChIP. We also highlight potential future innovations in the field, including in situ Calling Cards and UV-induced photocross-linking RIME (UVXL-RIME), that may overcome current methodological limitations, in turn enabling the study of SHRs in increasingly physiologically relevant contexts.]]> Wed, 31 Dec 1969 19:00:00 EST Divergent epigenetic profile underlie pubertal disorders in MKRN3-associated central precocious puberty and Prader-Willi syndrome: insights from a frameshift variant. Jin YY, Wang X, Yang L, Mu J, Luo FH
World J Pediatr (Feb 2026)

MKRN3 gene loss-of-function mutations cause central precocious puberty (CPP), whereas its deletion in Prader-Willi syndrome (PWS) paradoxically leads to hypogonadism. The mechanistic basis for these opposing reproductive phenotypes remains largely unclear.]]> Wed, 31 Dec 1969 19:00:00 EST Digital Biomarkers for Precision Early Detection of Lung Cancer: Integrating AI-Driven Multi-Omics Into Clinical Pathways. Bu F, Ling ZQ
Cancer Med (Feb 2026)

Lung cancer remains the leading cause of cancer-related mortality worldwide, highlighting the urgent need for earlier detection within real-world screening and patient management pathways. Recent advances in multi-omics technologies have created new opportunities for identifying biomarkers associated with early-stage lung cancer, particularly in high-risk populations under clinical surveillance.]]> Wed, 31 Dec 1969 19:00:00 EST