geneimprint : Hot off the Press

'; ?> 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 Tue, 02 Sep 2025 14:04:17 EDT Tue, 02 Sep 2025 14:04:17 EDT jirtle@radonc.duke.edu james001@jirtle.com Placental DNA methylation key topics: sex- and cell-type specificity, mediation, multi-omics, and biomarker discovery. Cohen NJ, Lesseur C, Cardenas A, Ward-Caviness CK, Spring AC, Rager JE, Fry RC, Eaves LA
Epigenomics (Sep 2025)

The placenta is a dynamic organ that serves numerous purposes for fostering a successful pregnancy and the delivery of a healthy infant in humans. It performs critical functions in nutrient and oxygen transport, immune modulation, and hormonal regulation. DNA methylation, a key epigenetic mechanism of transcriptional regulation, plays a key role in the underlying etiologies of placenta-related health complications. Therefore, assessing placental DNA methylation is essential for understanding how adverse prenatal exposures may impact both short-term and long-term health outcomes in women and children. In this review, we summarize current knowledge on the effects of prenatal exposures on placental DNA methylation and their implications for maternal and child health, focused on human population studies. We also outline five critical directions for human placental DNA methylation research: (1) Investigating sex-specific DNA methylation patterns, (2) Assessing cell type-specific DNA methylation signatures, (3) Applying causal inference methods, (4) Integrating multi-omics approaches, and (5) Using DNA methylation as a biomarker for environmental exposures and developmental outcomes. Advancing research in these areas will enhance our understanding of the biological underpinnings of the developmental origins of health and disease (DOHaD) hypothesis and maximize the potential of placental samples to inform DOHaD-related research.]]> Wed, 31 Dec 1969 19:00:00 EST Generalist Malaria Parasites and Host Imprinting: Unveiling Transcriptional Memory. GarcÃa-Longoria L, Palinauskas V, AÅ¾elytÄ J, Marzal A, Ovelleiro D, Hellgren O
Mol Biol Evol (Sep 2025)

Generalist parasites must adapt to diverse host environments to ensure their survival and transmission. These adaptations can involve fixed genetic responses, transcriptional plasticity, or epigenetic mechanisms. The avian malaria parasite Plasmodium homocircumflexum offers an ideal model for studying transcriptional variation across hosts. We experimentally inoculated P. homocircumflexum into different bird species, bypassing the vector, to assess whether gene expression remains stable across hosts, resets in response to new environments, or reflects epigenetic inheritance. We tested two alternative hypotheses: (i) universal gene expression profile ("one key fits all"), where parasite expression remains consistent across hosts. Our outcomes revealed that gene expression differed significantly depending on the host species and time postinfection, rejecting this hypothesis. (ii) Transcriptional plasticity, where gene expression is determined by the recipient host. Contrary to this hypothesis, we observed that gene expression was primarily influenced by the donor at 8âd postinfection (dpi), whereas gene expression was more aligned with the recipient host at 16âdpi. We also explored two mechanisms to explain these patterns: (i) epigenetic inheritance, whereby early transcription reflects the donor environment but adjusts over time, and (ii) genetic differentiation selecting for specific haplotypes. Our data support mechanism (i): 2,647 differentially expressed genes (DEGs) were associated with the donor at 8âdpi, while only 271 DEGs were linked to the recipient at 16âdpi. Single Nucleotide Polymorphism analyses revealed low genetic differentiation, rejecting mechanism (ii). These findings suggest that P. homocircumflexum undergoes a shift from donor-dependent to recipient-dependent gene expression, likely driven by epigenetic regulation and transcriptional plasticity.]]> Wed, 31 Dec 1969 19:00:00 EST and are human placenta-specific imprinted genes associated with germline-inherited maternal DNA methylation. Daskeviciute D, Sainty B, Chappell-Maor L, Bone C, Russell S, Iglesias-Platas I, Arnaud P, Monteagudo-SÃ¡nchez A, Greenberg MVC, Chen K, Manerao-Azua A, Perez de Nanclares G, Lartey J, Monk D
Epigenetics (Dec 2025)

Genomic imprinting is the parent-of-origin specific monoallelic expression of genes that result from complex epigenetic interactions. It is often achieved by monoallelic 5-methylcytosine, resulting in the formation of differentially methylated regions (DMRs). These show a bias towards oocyte-derived methylation and survive reprogramming in the pre-implantation embryo. Imprinting is widespread in the human placenta. We have recently performed whole-genome screens for novel imprinted placenta-specific germline DMRs (gDMRs) by comparing methylomes of gametes, blastocysts and various somatic tissues, including placenta. We observe that, unlike conventional imprinting, for which methylation at gDMRs is observed in all tissues, placenta-specific imprinting is associated with transient gDMRs, present only in the pre-implantation embryo and extra-embryonic lineages. To expand the list of imprinted genes subject to placenta-specific imprinting, we reinvestigated our list of candidate loci and characterized two novel imprinted genes, and , both of which display polymorphic imprinting. Interrogation of placenta single-cell RNA-seq datasets, as well as cell-type methylation profiles, revealed complex cell-type specificity. We further interrogated their methylation and expression in placental samples from complicated pregnancies, but failed to identify differences between intrauterine growth restricted or pre-eclamptic samples and controls, suggesting they are not involved in these conditions.]]> Wed, 31 Dec 1969 19:00:00 EST Conservation epigenomics: integrating epigenetic mechanisms into species conservation. Hu Y, Zhou W, Wei F
Sci China Life Sci (Sep 2025)

]]> Wed, 31 Dec 1969 19:00:00 EST The myoblast methylome: multiple types of associations with chromatin and transcription. Sen S, Lacey M, Baribault C, Ponnaluri VKC, Esteve PO, Ehrlich KC, Meletta M, Pradhan S, Ehrlich M
Epigenetics (Dec 2025)

Epigenetic changes are implicated in development, repair, and physiology of postnatal skeletal muscle (SkM). We generated methylomes for human myoblasts (SkM progenitor cells) and determined myoblast differentially methylated regions (DMRs) for comparison to the epigenomics and transcriptomics of diverse cell types. Analyses were from global genomic and single-gene perspectives and included reporter gene assays. One atypical finding was the association of promoter-adjacent hypermethylation in myoblasts with transcription turn-on, but at downmodulated levels, for certain genes (., and ). In contrast, brain-specific was in repressed chromatin and silent in most cell types but linked to hypermethylated DMRs specifically in myoblasts. The -linked DMRs might be needed because of the overlapping or nearby binding of myogenic differentiation protein 1 (MYOD). We found genome-wide overlap of DMRs with MYOD or CCCTC-binding factor (CTCF) binding sites in myoblasts that is consistent with the importance of MYOD, as well as CTCF, in organizing myoblast transcription-enhancing chromatin interactions. We also observed some gene upregulation correlated with a special association of regional DNA hypomethylation with H3K36me3, H3K27ac, and H3K4me1 enrichment. Our study highlights unusual relationships between epigenetics and gene expression that illustrate the interplay between DNA methylation and chromatin epigenetics in the regulation of transcription.]]> Wed, 31 Dec 1969 19:00:00 EST The emerging role of multiomics in aging research. Ruden DM
Epigenomics (Sep 2025)

Aging is a complex biological process involving coordinated changes across multiple molecular systems. Traditional reductionist approaches, while valuable, are insufficient to capture the full scope of aging's systemic nature. Multiomics - integrating data from genomics, transcriptomics, epigenomics, proteomics, and metabolomics - provides a comprehensive framework to study aging as an interconnected network. In this Perspective, I explore how multiomic strategies, particularly those leveraging epigenomic and single-cell data, are reshaping our understanding of aging biology. Epigenetic alterations, including DNA methylation and histone modifications, are not only hallmarks but also powerful biomarkers of biological age. I discuss advances in multiomic aging clocks, cross-tissue atlases, and single-cell spatial technologies that decode aging at unprecedented resolution. I also build on a prior review I wrote with colleagues, Epigenomics. 2023;15(14):741-754, which introduced the concept of pathological epigenetic events that are reversible (PEERs) - epigenetic alterations linked to early-life exposures that predispose to aging and disease but may be therapeutically modifiable. This Perspective examines how PEERs and multiomics intersect to inform biomarkers, geroprotective interventions, and personalized aging medicine. Finally, I highlight integration challenges, ethical concerns, and the need for standardization to accelerate clinical translation. Together, these insights position multiomics as a central pillar in the future of aging research.]]> Wed, 31 Dec 1969 19:00:00 EST Differential methylation patterns in cord blood associated with prenatal exposure to neighborhood crime: an epigenome-wide association study and regional analysis. Martin CL, Chen J, D'Alessio AS, Ward-Caviness CK, Ye A, Lodge EK, Ghastine L, Dhingra R, Jima DD, Murphy SK, Hoyo C
Epigenetics (Dec 2025)

Exposure to prenatal social stressors during pregnancy is associated with adverse birth outcomes and has been linked to epigenetic changes in DNA methylation (DNAm); however, less understood is the effect of neighborhood-level stressors like crime during pregnancy on offspring DNAm. Using data from the Newborn Epigenetic Study, we conducted epigenome-wide and regional analyses of the association between exposure to neighborhood crime and DNAm in offspring cord blood using Illumina's HumanMethylation450k BeadChip among 185 mother-offspring pairs. Prenatal exposure to neighborhood crime at the census block group level was mapped to participants' residential addresses during the gestational window from the date of last menstrual period to delivery. Models for the epigenome-wide and regional analyses were adjusted for maternal age, race/ethnicity, education, smoking, cell-type composition, and offspring sex. Genetic influence and gene expression enrichment were assessed using methylation quantitative trait loci (mQTLs) and expression quantitative trait methylation (eQTMs) analyses. Functional enrichment was determined using Gene Ontology and KEGG databases. We did not find evidence of epigenome-wide associations between prenatal neighborhood crime exposure and DNAm; however, we identified nine differentially methylated regions (DMRs) comprising 51 CpG sites associated with neighborhood crime. CpG sites within significant differentially methylated regions were associated with mQTLs at birth and eQTMs upon further examination. KEGG analysis identified a significant Th1 and Th2 cell differentiation pathway. Our results suggest potential links between prenatal neighborhood crime exposure and offspring DNAm; however, additional research is needed in larger cohorts across wider geographic areas to confirm our results.]]> Wed, 31 Dec 1969 19:00:00 EST Gaining insights into epigenetic memories through artificial intelligence and omics science in plants. DobrÃ¡nszki J, Vassileva V, Agius DR, Moschou PN, Gallusci P, Berger MMJ, Farkas D, Basso MF, Martinelli F
J Integr Plant Biol (Sep 2025)

Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus-dependent decision-making circuits. Unlike animals, plant memory is uniquely rooted in cellular, molecular, and biochemical networks, lacking specialized organs for these functions. Consequently, plants can effectively learn and respond to diverse challenges, becoming used to recurring signals. Artificial intelligence (AI) and machine learning (ML) represent the new frontiers of biological sciences, offering the potential to predict crop behavior under environmental stresses associated with climate change. Epigenetic mechanisms, serving as the foundational blueprints of plant memory, are crucial in regulating plant adaptation to environmental stimuli. They achieve this adaptation by modulating chromatin structure and accessibility, which contribute to gene expression regulation and allow plants to adapt dynamically to changing environmental conditions. In this review, we describe novel methods and approaches in AI and ML to elucidate how plant memory occurs in response to environmental stimuli and priming mechanisms. Furthermore, we explore innovative strategies exploiting transgenerational memory for plant breeding to develop crops resilient to multiple stresses. In this context, AI and ML can aid in integrating and analyzing epigenetic data of plant stress responses to optimize the training of the parental plants.]]> Wed, 31 Dec 1969 19:00:00 EST use capsules, transporters, mobile genetic elements, and other evolutionary adaptations to survive antibiotics exposure in the absence of resistance genes. Mmatli M, Mbelle NM, Fourie B, Osei Sekyere J
Virulence (Dec 2025)

Whole-genome sequencing, transcriptomic profiling, and epigenomic analyses were performed. Phenotypic assays were used to evaluate the effects of various inhibitors on antibiotic susceptibility, while bioinformatic pipelines were used to characterize resistance determinants, virulence factors, and mobile genetic elements (MGEs).]]> Wed, 31 Dec 1969 19:00:00 EST Sex-stratified piRNA expression analysis reveals shared functional impacts of perinatal lead (Pb) exposure in murine hearts. Sala-Hamrick KE, Wang K, Perera BPU, Sartor MA, Svoboda LK, Dolinoy DC
Epigenetics (Dec 2025)

The landscape of PIWI-interacting RNA (piRNA) expression in the heart is poorly understood, particularly regarding sex differences. Altered piRNA expression has been reported in cardiovascular disease (CVD), and although exposure to the metal lead (Pb) is strongly associated with CVD risk, no studies have investigated Pb's effects on cardiac piRNAs. This study aimed to characterize piRNA expression in the murine heart and assess sex-specific effects of human-relevant maternal Pb exposure on adult offspring cardiac piRNA expression. piRNAs were identified from whole mouse hearts using sodium periodate exclusion of small RNA and subsequent sequencing. Control mice expressed 18,956 piRNAs in combined-sex analysis; sex-specific analyses revealed 9,231 piRNAs in female hearts and 5,972 piRNAs in male hearts. Genomic mapping showed 28-41% aligned to introns, while 12-28% mapped to exons. Comparing control and Pb-exposed hearts, we found more potential Pb-induced expression changes in females (847) compared to males (187) (p-valueâ<â0.05 and |logFC|â>â1). These piRNAs were significantly enriched near genes involved in biological processes related to heart function and CVD development, including mitochondrial function, energy metabolism, and cardiac muscle structure (FDRâ<â0.05). Overall, we characterized combined and sex-stratified piRNA expression in both control and Pb-exposed murine hearts. In addition to providing a foundation for sex-specific piRNA expression in the heart, these findings suggest a novel epigenetic mechanism by which developmental Pb exposure may impact CVD risk later in life. Future studies will link these sex-specific molecular changes to Pb-induced alterations in cardiac function.]]> 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 (54âCD; 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 4âyears of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.]]> Wed, 31 Dec 1969 19:00:00 EST High-throughput assessment of and methylation-based newborn screening using IsoPure and QIAcube HT systems. Cartagena C, Alshawsh M, Bui MQ, Gamage D, Thakor RP, Pitt J, Greaves RF, Wall M, Saffery R, Amor DJ, Godler DE
Epigenomics (Sep 2025)

This study compared methylation-specific quantitative melt analysis of FMR1 and SNRPN methylation (mDNA) using automated bisulfite conversion by the magnetic-bead-based IsoPure and column-based QIAcube HT systems.]]> Wed, 31 Dec 1969 19:00:00 EST Perfluoroalkyl substance pollutants disrupt microglia function and trigger transcriptional and epigenomic changes. Cheng Y, Li JR, Yu H, Li S, Tychhon B, Cheng C, Weng YL
Toxicology (Nov 2025)

Per- and polyfluoroalkyl substances (PFAS), commonly referred to as "forever chemicals", are widely utilized in various industries and consumer products worldwide. Their exposure has been associated with numerous diseases and malignancies, including neurodevelopmental and neurodegenerative disorders. However, the molecular mechanisms underlying PFAS-induced adverse effects on the central nervous system (CNS) remain poorly understood. In this study, we investigated the transcriptomic and epigenetic changes in microglia exposed to perfluorooctane sulfonate (PFOS), a prevalent PFAS compound. Our findings demonstrate that 24-hour PFOS exposure (25 and 50â¯ÂµM) disrupts the microglial transcriptome and compromises their homeostatic state, marked by increased inflammation and impaired actin cytoskeleton remodeling. Comparative analysis with in vivo transcriptional states revealed that PFOS-exposed microglia exhibit gene expression profiles resembling those of aged microglia. Additionally, profiling of active chromatin regions uncovered significant alterations in the H3K27ac landscape in PFOS-exposed microglia. Notably, these epigenetic disruptions persisted even after PFOS withdrawal, with a subset of H3K27ac-enriched regions remaining altered, suggesting the presence of lasting epigenetic scars. Furthermore, transcription factor analysis implicated the AP-1 and TEAD families as potential upstream regulators connecting the altered chromatin landscape to transcriptomic changes. Collectively, these findings provide mechanistic insights into how PFOS exposure disrupts microglial function and highlight its potential role in exacerbating neurodegenerative processes.]]> Wed, 31 Dec 1969 19:00:00 EST Deciphering sarcoidosis immunopathogenesis through systems biology. Jbeli AH, Crouser ED, Bhargava M
Curr Opin Pulm Med (Sep 2025)

Sarcoidosis is a complex, multisystem disease characterized by granulomatous inflammation and variable clinical outcomes. Its pathogenesis and progression are driven by intricate biological interactions, involving a complex interplay between patient-specific factors such as genetic background, sex, and environmental exposures, as well as epigenetic modifications that regulate gene expression and protein levels. These interconnected layers ultimately drive immune response to yet unidentified trigger(s), culminating in granuloma formation and, in some cases, with an aberrant repair response leading to irreversible organ dysfunction in some cases. In this review, we aim to synthesize recent multiomics research that unravels the underlying biological networks, offering a systems-level understanding of sarcoidosis.]]> Wed, 31 Dec 1969 19:00:00 EST Vigorous But Not Moderate Physical Activity Is Associated With Reduced Cardiovascular Disease Risk In Young Hispanic Men. Gattoni C, Bebe K, Bross R, Wang C, Swerdloff RS, Oudiz RJ, Kraus WE, Rossiter HB
Am J Cardiol (Sep 2025)

Physical Activity Guidelines for Americans recommend at least 150 min/week of moderate (MPA) to vigorous (VPA) physical activity to maintain health, regardless of cardiovascular disease (CVD) risk. This study assessed whether physical activity (PA) intensity distinguishes between low and high CVD risk in 196 lean and obese Hispanic men aged 18-40 from the Study of Male Reproductive Epigenomics. PA was measured for 7 days using triaxial accelerometry. The 30-year "full" Framingham Risk Score (FRS) was calculated. Diet quality was assessed using the Healthy Eating Index (HEI-2020). Mean age was 30 Â± 5 years with a median FRS of 14% (range: 3% to 85%). The high-risk group (n = 89) had a mean full FRS of 20.3% Â± 11.1%, compared to 7.0% Â± 3.6% in the low-risk group (n = 107; p <0.001). Both groups met guideline-recommended PA levels. However, the low-risk group performed more VPA (25 Â± 20 vs 12 Â± 12 min/day; p <0.001). Logistic regressions showed that each additional 1 min/day of VPA reduced the odds of high CVD risk by 4.4% (p = 0.007), adjusted for smoking, diet, age and Body Mass Index (BMI), while MPA did not significantly predict CVD risk (p = 0.823). Stepwise regressions showed that smoking status, BMI, VPA, and diet explained 47.8% of FRS variance (p <0.001), while MPA was excluded. In conclusion, VPA, but not MPA, significantly distinguished low from high CVD risk in young Hispanic men, highlighting the potential role of higher-intensity exercise to reduce CVD risk in this population.]]> Wed, 31 Dec 1969 19:00:00 EST Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools. Zhuang BC, Jude MS, Konwar C, Yusupov N, Ryan CP, Engelbrecht HR, Whitehead J, Halberstam AA, MacIsaac JL, Dever K, Tran TK, Korinek K, Zimmer Z, Lee NR, McDade TW, Kuzawa CW, Huffman KM, Belsky DW, Binder EB, Czamara D, Korthauer K, Kobor MS
Life Sci Alliance (Sep 2025)

The recently launched Illumina Infinium MethylationEPIC v2.0 (EPICv2), successor of MethylationEPIC v1.0 (EPICv1), retains most of the probes in EPICv1, while expanding coverage of regulatory elements. The concordance between the two EPIC versions in DNA methylation-based tools has not yet been investigated. To address this, DNA methylation was profiled on both versions using matched blood samples across four cohorts spanning early to late adulthood. High concordance between versions at the array level but variable agreement at the individual probe level was noted. A significant contribution of the EPIC version to DNA methylation variation was observed, though it was to a smaller extent compared with sample relatedness and cell-type composition. Modest but significant differences in DNA methylation-based estimates between versions were observed, irrespective of the data preprocessing method used. Adjustments for EPIC version or calculation of estimates separately for each version largely mitigated these version-specific discordances. This work emphasizes the importance of accounting for EPIC version differences in research scenarios, especially in meta-analyses and longitudinal studies that require data harmonization across versions.]]> Wed, 31 Dec 1969 19:00:00 EST Transcript profiling and gene regulation of the human pre-implantation embryo: parental effects and impact of ARTs. Ferreux L, Ducreux B, Firmin J, Chargui A, Pocate-Cheriet K, Maignien C, Santulli P, Borensztein M, Fauque P, Patrat C
Hum Reprod Update (Sep 2025)

Infertility is a growing global challenge, with ARTs significantly improving birth rates for infertile couples. However, ART conceptions are associated with a higher risk of negative obstetrical and perinatal outcomes, with potential long-term effects on offspring health. Many pre-implantation embryos exhibit abnormal morphokinetics, implantation failure, or arrested development. ART procedures and parental factors are suspected to perturb the embryonic transcriptome, potentially affecting molecular and epigenetic events during gametogenesis and early development. The timing and mechanisms of these perturbations remain unclear. Genome-wide transcriptomic misregulation in ART-conceived human pre-implantation embryos may provide important insights into observed differences between ART and naturally conceived offspring.]]> Wed, 31 Dec 1969 19:00:00 EST Insights into tissue- and cell type-specific effects of Grb10 on pig skeletal muscle growth by multi-omics analysis. Li M, Liu H, Lu T, Li S, Zhou X, Miao H, Zhang Y, Peng C, Chen K, He J, Yin Y, Zhao P, Han X
Sci China Life Sci (Sep 2025)

Domestic pigs are shaped by artificial and natural selection into obese and lean types that are closely related to muscle tissue. However, the key genes and regulatory mechanisms behind these developments remain largely unknown. Here, we pinpoint GRB10 specificity in muscle tissue and cells between obese and lean pigs by combining genomics, transcriptomics, epigenomics, and single-cell transcriptomics. GRB10 shows notable differences in divergent selection on haplotype blocks and expression levels between obese and lean pig breeds, with its expression profiles varying significantly by tissue and development stage. Notably, we identify a muscle-specific promoter of GRB10 and its transcription factor KLF15. This TF-promoter binding is verified by dual luciferase and chromatin immunoprecipitation (ChIP) assays, and is suggested to be conserved in humans. Single-nucleus RNA sequencing further highlights differential expression patterns of GRB10 between obese and lean pig breeds across various cell types. Type IIa myonuclei and TTN FAPs, which are more predominant in lean pigs, play a crucial role in myofibril assembly and muscle tissue development. These findings offer insights into the regulatory mechanisms controlling muscle growth. They highlight the tissue- and cell type-specific effects of GRB10 on muscle heterogeneity, which has potential applications in livestock breeding and human obesity research.]]> Wed, 31 Dec 1969 19:00:00 EST scPOEM: Robust Co-embedding of Peaks and Genes Revealing Peak-Gene Regulation. Zhong Y, Hou Y, Yang Y, Zheng X, Cai JJ
Bioinformatics (Sep 2025)

Identifying regulatory elements in various chromosomal regions that influence gene expression is a fundamental challenge in epigenomics, with profound implications for understanding gene regulation and disease mechanisms. The advent of paired single-cell RNA sequencing and single-cell ATAC sequencing has created unprecedented opportunities to address this challenge by enabling simultaneous profiling of gene expression and chromatin accessibility at single-cell resolution. However, the inherent signals between them are weak due to the highly sparse and noisy nature of data.]]> Wed, 31 Dec 1969 19:00:00 EST Mosaicism for Genome Wide Homozygosity Identified as an Incidental Finding in Two Apparently Healthy Pregnant Women. Haskell GT, Askree SH, Kline L, Hasadsri L, Cabral H, Gadi I, Schwartz S
Am J Med Genet A (Sep 2025)

Uniparental Disomy (UPD) occurs when both copies of a chromosome or chromosomal segment originate from only one parent. Mosaic genome-wide UPD (mos gwUPD) is typically identified in cases of fetal demise and placental dysplasia or in prenatal cases, where imprinting effects are associated with abnormal ultrasound findings. Children with mos gwUPD and clinical features due to UPD-associated imprinting effects (especially Beckwith-Wiedemann syndrome) have been reported; however, reports of adults with mos gwUPD are rare. Here we describe mos gwUPD in two apparently healthy pregnant adult women. Carrier testing noted variants with skewed allelic ratios outside of the normal heterozygous range, prompting further testing. Single nucleotide polymorphism (SNP) microarray identified mosaicism for gwUPD in both individuals, present at 85% and 90%, respectively, in blood, with varying percentages in other tissues. Neither woman displayed clinical features that would be expected with gwUPD at the time of testing, although retrospective careful personal history was consistent. Both women had uneventful pregnancies and delivered full-term healthy infants. These two cases demonstrate that mos gwUPD can be an incidental finding identified in apparently healthy adult women. Clinical follow-up is important for tumor monitoring, genetic counseling, and monitoring of future pregnancies due to mos gwUPD in the maternal endometrial tissue.]]> Wed, 31 Dec 1969 19:00:00 EST