'; ?> 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, 21 Jan 2025 11:36:06 EST Tue, 21 Jan 2025 11:36:06 EST jirtle@radonc.duke.edu james001@jirtle.com Single-cell transcriptomics and epigenomics point to CD58-CD2 interaction in controlling primary melanoma growth and immunity. Stubenvoll A, Schmidt M, Moeller J, Chango MAL, Schultz C, Antoniadou O, Loeffler-Wirth H, Bernhart S, Große F, Thier B, Paschen A, Anderegg U, Simon JC, Ziemer M, Schoeder CT, Binder H, Kunz M
Cancer Commun (Lond) (Jan 2025)

]]> Wed, 31 Dec 1969 19:00:00 EST MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model. Jeong Y, Gerhäuser C, Sauter G, Schlomm T, Rohr K, Lutsik P
Nat Commun (Jan 2025)

DNA methylation (DNAm) is a key epigenetic mark that shows profound alterations in cancer. Read-level methylomes enable more in-depth analyses, due to their broad genomic coverage and preservation of rare cell-type signals, compared to summarized data such as 450K/EPIC microarrays. Here, we propose MethylBERT, a Transformer-based model for read-level methylation pattern classification. MethylBERT identifies tumour-derived sequence reads based on their methylation patterns and local genomic sequence, and estimates tumour cell fractions within bulk samples. In our evaluation, MethylBERT outperforms existing deconvolution methods and demonstrates high accuracy regardless of methylation pattern complexity, read length and read coverage. Moreover, we show its applicability to cell-type deconvolution as well as non-invasive early cancer diagnostics using liquid biopsy samples. MethylBERT represents a significant advancement in read-level methylome analysis and enables accurate tumour purity estimation. The broad applicability of MethylBERT will enhance studies on both tumour and non-cancerous bulk methylomes.]]> Wed, 31 Dec 1969 19:00:00 EST Extensive epigenomic dysregulation is a hallmark of homologous recombination deficiency in triple-negative breast cancer. Chen Y, Salas LA, Marotti JD, Jenkins NP, Cheng C, Miller TW, Kettenbach AN, Christensen BC
Int J Cancer (Mar 2025)

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with substantial disease heterogeneity, limited treatment options, and dismal clinical outcomes. Some TNBCs display homologous recombination deficiency (HRD), a phenotype with elevated genomic burden and worse prognosis if left untreated but chemotherapeutic sensitivity. While the molecular landscape of TNBC is distinct from other breast cancer subtypes, the TNBC-specific link between HRD and epigenome-wide methylation has not been established. This study reports two independent cohorts of TNBC tumors (n = 32 and n = 58) with HRD and epigenomic landscapes measured by the Multiplex Ligation-dependent Probe Amplification assay and the Illumina MethylationEPIC arrays, respectively. Genome-wide copy number and methylation alterations were significantly higher in HRD (all p <.05). Methylation of genome-wide repeat element Alu and transcriptional regulatory regions were significantly lower in HRD (all p <.05). An age-adjusted epigenome-wide association study of the continuous HRD probability scores revealed significant loci (all FDR <0.05) that were depleted from the CpG-rich "island" regions often seen in gene promoters but enriched in the CpG-poor "open sea" regions localized to gene enhancers. The significant loci implicated well-known candidate genes involved in the epithelial-to-mesenchymal transition, Wnt signaling, and DNA damage response. Supervised machine learning of HRD with nucleotide-specific methylation as the input enabled clinically relevant tumor stratification. Taken together, this study provides novel biological and translational insights into HRD in TNBCs.]]> Wed, 31 Dec 1969 19:00:00 EST Applications of Nanotechnology for Spatial Omics: Biological Structures and Functions at Nanoscale Resolution. Wang R, Hastings WJ, Saliba JG, Bao D, Huang Y, Maity S, Kamal Ahmad OM, Hu L, Wang S, Fan J, Ning B
ACS Nano (Jan 2025)

Spatial omics methods are extensions of traditional histological methods that can illuminate important biomedical mechanisms of physiology and disease by examining the distribution of biomolecules, including nucleic acids, proteins, lipids, and metabolites, at microscale resolution within tissues or individual cells. Since, for some applications, the desired resolution for spatial omics approaches the nanometer scale, classical tools have inherent limitations when applied to spatial omics analyses, and they can measure only a limited number of targets. Nanotechnology applications have been instrumental in overcoming these bottlenecks. When nanometer-level resolution is needed for spatial omics, super resolution microscopy or detection imaging techniques, such as mass spectrometer imaging, are required to generate precise spatial images of target expression. DNA nanostructures are widely used in spatial omics for purposes such as nucleic acid detection, signal amplification, and DNA barcoding for target molecule labeling, underscoring advances in spatial omics. Other properties of nanotechnologies include advanced spatial omics methods, such as microfluidic chips and DNA barcodes. In this review, we describe how nanotechnologies have been applied to the development of spatial transcriptomics, proteomics, metabolomics, epigenomics, and multiomics approaches. We focus on how nanotechnology supports improved resolution and throughput of spatial omics, surpassing traditional techniques. We also summarize future challenges and opportunities for the application of nanotechnology to spatial omics methods.]]> Wed, 31 Dec 1969 19:00:00 EST Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping. Margalit S, Tulpová Z, Detinis Zur T, Michaeli Y, Deek J, Nifker G, Haldar R, Gnatek Y, Omer D, Dekel B, Baris Feldman H, Grunwald A, Ebenstein Y
NAR Genom Bioinform (Mar 2025)

Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural variants (SVs) and copy number variations (CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping (OGM) and nanopore sequencing [Oxford Nanopore Technologies (ONT)] bridge this resolution gap and offer enhanced performance for cytogenetic applications. Additionally, both methods can capture epigenetic information as they profile native, individual DNA molecules. We compared the effectiveness of the two methods in characterizing the structural, copy number and epigenetic landscape of a clear cell renal cell carcinoma tumor. Both methods provided comparable results for basic karyotyping and CNVs, but differed in their ability to detect SVs of different sizes and types. ONT outperformed OGM in detecting small SVs, while OGM excelled in detecting larger SVs, including translocations. Differences were also observed among various ONT SV callers. Additionally, both methods provided insights into the tumor's methylome and hydroxymethylome. While ONT was superior in methylation calling, hydroxymethylation reports can be further optimized. Our findings underscore the importance of carefully selecting the most appropriate platform based on specific research questions.]]> Wed, 31 Dec 1969 19:00:00 EST Evolutionary lineage-specific genomic imprinting at the ZNF791 locus. Ahn J, Hwang IS, Park MR, Rosa-Velazquez M, Cho IC, Relling AE, Hwang S, Lee K
PLoS Genet (Jan 2025)

Genomic imprinting is an epigenetic process that results in parent-of-origin effects on mammalian development and growth. Research on genomic imprinting in domesticated animals has lagged due to a primary focus on orthologs of mouse and human imprinted genes. This emphasis has limited the discovery of imprinted genes specific to livestock. To identify genomic imprinting in pigs, we generated parthenogenetic porcine embryos alongside biparental normal embryos, and then performed whole-genome bisulfite sequencing and RNA sequencing on these samples. In our analyses, we discovered a maternally methylated differentially methylated region within the orthologous ZNF791 locus in pigs. Additionally, we identified both a major imprinted isoform of the ZNF791-like gene and an unannotated antisense transcript that has not been previously annotated. Importantly, our comparative analyses of the orthologous ZNF791 gene in various eutherian mammals, including humans, non-human primates, rodents, artiodactyls, and dogs, revealed that this gene is subjected to genomic imprinting exclusively in domesticated animals, thereby highlighting lineage-specific imprinting. Furthermore, we explored the potential mechanisms behind the establishment of maternal DNA methylation imprints in porcine and bovine oocytes, supporting the notion that integration of transposable elements, active transcription, and histone modification may collectively contribute to the methylation of embedded intragenic CpG island promoters. Our findings convey fundamental insights into molecular and evolutionary aspects of livestock species-specific genomic imprinting and provide critical agricultural implications.]]> Wed, 31 Dec 1969 19:00:00 EST Genomic imprinting and environmental epigenetics: Their influence on sheep reproductive traits across parities. Tavasolian F, Gholizadeh M, Hafezian H
Anim Reprod Sci (Feb 2025)

This study aimed to explore the impact of genomic imprinting on the genetic variance of composite reproductive traits across three parities in Baluchi sheep. The traits analyzed included litter mean weight per lamb born (LMWLB), litter mean weight per lamb weaned (LMWLW), total litter weight at birth (TLWB), and total litter weight at weaning (TLWW). We employed a univariate linear animal model for each trait, treating performance across parities as separate traits. Twenty-four animal models were assessed, incorporating direct additive genetic effects, maternal genetic effects, maternal permanent environmental effects, direct and maternal genetic covariances, as well as maternal and paternal imprinting. Model selection was based on Akaike's Information Criterion (AIC). Direct heritability estimates for the traits were generally low, ranging from 0.039 ± 0.017 for LMWLW to 0.085 ± 0.028 for TLWW. TLWB and TLWW exhibited higher heritability than LMWLB and LMWLW in their respective parities. In the best model (model 24), maternal imprinting heritability estimates from the first to third parity were 0.059 ± 0.016, 0.060 ± 0.013, and 0.085 ± 0.021 for TLWB, 0.075 ± 0.021, 0.068 ± 0.025, and 0.048 ± 0.016 for LMWLB, 0.051 ± 0.013, 0.065 ± 0.019, and 0.068 ± 0.020 for TLWW, and, 0.072 ± 0.012, 0.057 ± 0.018 and 0.054 ± 0.011 for LMWLW, respectively. Paternal imprinting heritability estimates were consistently lower than maternal imprinting estimates, with values across parities ranging from 0.001 ± 0.024 to 0.019 ± 0.032 for TLWB, 0.005 ± 0.022-0.010 ± 0.019 for LMWLB, 0.012 ± 0.05-0.017 ± 0.05 for TLWW and, 0.013 ± 0.01-0.016 ± 0.01 for LMWLW. In conclusion, imprinting effects should be included in breeding programs to increase the accuracy of genetic evaluation.]]> Wed, 31 Dec 1969 19:00:00 EST Functional Annotation of Bipolar Disorder 2 Risk Location Implicates Novel Susceptibility Genes. Can GŞ, Bakır E, Oktay Y
Neuropsychobiology (Jan 2025)

Bipolar 2 disorder (BD2) is an independent disease with specific familial aggregation, significant functional impairment, specific treatment challenges and several distinctive clinical features. However, unlike bipolar 1 disorder, studies investigating causal and functional genes are lacking. This study aims to identify and prioritize causal genetic variants and genes for BD2 by analyzing brain-specific gene expression markers, to improve the understanding of its genetic underpinnings and support advancements in diagnosis, treatment and prognosis.]]> Wed, 31 Dec 1969 19:00:00 EST Epigenetic Upregulation of Carotid Body Angiotensin Signaling Increases Blood Pressure. Zhu F, Wang Z, Davis K, McSwiggin H, Zyuzin J, Liu J, Yan W, Rehan VK, Jendzjowsky N
Hypertension (Feb 2025)

Epigenetic changes can be shaped by a wide array of environmental cues, maternal health, and behaviors. One of the most detrimental behaviors to the developing fetus is nicotine exposure. Perinatal nicotine exposure remains a significant risk factor for cardiovascular health and, in particular, hypertension. Increased basal carotid body (CB) activity and excitation are significant contributors to hypertension. This study investigated the epigenetic changes to CB activity induced by perinatal nicotine exposure resulting in CB-mediated hypertension.]]> 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 Clinical utility of regions of homozygosity (ROH) identified in exome sequencing: when to pursue confirmatory uniparental disomy testing for imprinting disorders? Huo X, Lu X, Lu D, Liu H, Liu Y, Zhao Q, Sun Y, Dai W, Qiu W, Yu Y, Fan Y
Clin Chem Lab Med (Jan 2025)

Regions of homozygosity (ROH) could implicate uniparental disomy (UPD) on specific chromosomes associated with imprinting disorders. Though the algorithms for ROH detection in exome sequencing (ES) have been developed, optimal reporting thresholds and when to pursue confirmatory UPD testing for imprinting disorders remain in ambiguity. This study used a data-driven approach to assess optimal reporting thresholds of ROH in clinical practice.]]> Wed, 31 Dec 1969 19:00:00 EST Epigenetic Regulation of Innate and Adaptive Immune Cells in Salt-Sensitive Hypertension. Mutchler AL, Haynes AP, Saleem M, Jamison S, Khan MM, Ertuglu L, Kirabo A
Circ Res (Jan 2025)

Access to excess dietary sodium has heightened the risk of cardiovascular diseases, particularly affecting individuals with salt sensitivity of blood pressure. Our research indicates that innate antigen-presenting immune cells contribute to rapid blood pressure increases in response to excess sodium intake. Emerging evidence suggests that epigenetic reprogramming, with subsequent transcriptional and metabolic changes, of innate immune cells allows these cells to have a sustained response to repetitive stimuli. Epigenetic mechanisms also steer T-cell differentiation in response to innate immune signaling. Immune cells respond to environmental and nutritional cues, such as salt, promoting epigenetic regulation changes. This article aims to identify and discuss the role of epigenetic mechanisms in the immune system contributing to salt-sensitive hypertension.]]> Wed, 31 Dec 1969 19:00:00 EST Generation of live mice from haploid ESCs with germline-DMR deletions or switch. Ma Y, Yan M, Xie Z, Zhang H, Li Z, Li Y, Yang S, Zhang M, Li W, Li J
Cell Discov (Jan 2025)

Genomic imprinting is required for sexual reproduction and embryonic development of mammals, in which, differentially methylated regions (DMRs) regulate the parent-specific monoallelic expression of imprinted genes. Numerous studies on imprinted genes have highlighted their critical roles in development. However, what imprinting network is essential for development is still unclear. Here, we establish a stepwise system to reconstruct a development-related imprinting network, in which diploid embryonic stem cells (ESCs) are derived by fusing between parthenogenetic (PG)- and androgenetic (AG)-haploid embryonic stem cells (haESCs) with different DMR deletions (termed Ha-Ha-fusion system), followed by tetraploid complementation to produce all-haESC fetuses. Diploid ESCs fused between PG-haESCs carrying 8 maternally-derived DMR deletions and AG-haESCs with 2 paternally-derived DMR deletions give rise to live pups efficiently, among which, one lives to weaning. Strikingly, diploid ESCs derived from the fusion of PG-haESCs with 7 maternal DMR deletions and AG-haESCs with 2 paternal DMR deletions and maternal Snrpn-DMR deletion also support full-term embryonic development. Moreover, embryos reconstructed by injection of AG-haESCs with hypomethylated H19-DMR into oocytes with H19-DMR deletion develop into live mice sustaining inverted allelic gene expression. Together, our findings indicate that restoration of monoallelic expression of 10 imprinted regions is adequate for the full-term development of all-haESC pups, and it works irrespective of their parental origins. Meanwhile, Ha-Ha-fusion system provides a useful tool for deciphering imprinting regulation networks during embryonic development.]]> Wed, 31 Dec 1969 19:00:00 EST New Multiomic Studies Shed Light on Cellular Diversity and Neuronal Susceptibility in Parkinson's Disease. Liang M, Chu L, Yue Z
Mov Disord (Jan 2025)

Parkinson's disease is a complex neurodegenerative disorder characterized by degeneration of dopaminergic neurons, with patients manifesting varying motor and nonmotor symptoms. Previous studies using single-cell RNA sequencing in rodent models and humans have identified distinct heterogeneity of neurons and glial cells with differential vulnerability. Recent studies have increasingly leveraged multiomics approaches, including spatial transcriptomics, epigenomics, and proteomics, in the study of Parkinson's disease, providing new insights into pathogenic mechanisms. Continued advancements in experimental technologies and sophisticated computational tools will be essential in uncovering a network of neuronal vulnerability and prioritizing disease modifiers for novel therapeutics development. © 2025 International Parkinson and Movement Disorder Society.]]> Wed, 31 Dec 1969 19:00:00 EST Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3. Hure V, Piron-Prunier F, Yehouessi T, Vitte C, Kornienko AE, Adam G, Nordborg M, Déléris A
Genome Biol (Jan 2025)

The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammals, plants, and fungi. However, H3K27me3 can be recruited to many TEs in the absence of DNA/H3K9 methylation machinery and sometimes also co-occur with DNA methylation.]]> Wed, 31 Dec 1969 19:00:00 EST A Menu for Microbes: Unraveling Appetite Regulation and Weight Dynamics Through the Microbiota-Brain Connection Across the Lifespan. Ribeiro G, Schellekens H, Cuesta-Marti C, Maneschy I, Ismael S, Cuevas-Sierra A, Martínez JA, Silvestre MP, Marques C, Moreira-Rosário A, Faria A, Moreno LA, Calhau C
Am J Physiol Gastrointest Liver Physiol (Jan 2025)

Appetite, as the internal drive for food intake, is often dysregulated in a broad spectrum of conditions associated with over- and under-nutrition across the lifespan. Appetite regulation is a complex, integrative process comprising psychological and behavioral events, peripheral and metabolic inputs, and central neurotransmitter and metabolic interactions. The microbiota-gut-brain axis has emerged as a critical mediator of multiple physiological processes, including energy metabolism, brain function, and behavior. Therefore, the role of the microbiota-gut-brain axis in appetite and obesity is receiving increased attention. Omics approaches such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics in appetite and weight regulation offer new opportunities for featuring obesity phenotypes. Furthermore, gut microbiota-targeted approaches such as pre- pro- post- and synbiotic, personalized nutrition, and fecal microbiota transplantation are novel avenues for precision treatments. The aim of this narrative review is (1) to provide an overview of the role of the microbiota-gut-brain-axis in appetite regulation across the lifespan and (2) to discuss the potential of omics and gut microbiota-targeted approaches to deepen understanding of appetite regulation and obesity.]]> Wed, 31 Dec 1969 19:00:00 EST Assessing Metabolic Ageing via DNA Methylation Surrogate Markers: A Multicohort Study in Britain, Ireland and the USA. Xu K, Hernández B, Arpawong TE, Camuzeaux S, Chekmeneva E, Crimmins EM, Elliott P, Fiorito G, Jiménez B, Kenny RA, McCrory C, McLoughlin S, Pinto R, Sands C, Vineis P, Lau CE, Robinson O
Aging Cell (Jan 2025)

Metabolomics and epigenomics have been used to develop 'ageing clocks' that assess biological age and identify 'accelerated ageing'. While metabolites are subject to short-term variation, DNA methylation (DNAm) may capture longer-term metabolic changes. We aimed to develop a hybrid DNAm-metabolic clock using DNAm as metabolite surrogates ('DNAm-metabolites') for age prediction. Within the UK Airwave cohort (n = 820), we developed DNAm metabolites by regressing 594 metabolites on DNAm and selected 177 DNAm metabolites and 193 metabolites to construct 'DNAm-metabolic' and 'metabolic' clocks. We evaluated clocks in their age prediction and association with noncommunicable disease risk factors. We additionally validated the DNAm-metabolic clock for the prediction of age and health outcomes in The Irish Longitudinal Study of Ageing (TILDA, n = 488) and the Health and Retirement Study (HRS, n = 4018). Around 70% of DNAm metabolites showed significant metabolite correlations (Pearson's r: > 0.30, p < 10) in the Airwave test set and overall stronger age associations than metabolites. The DNAm-metabolic clock was enriched for metabolic traits and was associated (p < 0.05) with male sex, heavy drinking, anxiety, depression and trauma. In TILDA and HRS, the DNAm-metabolic clock predicted age (r = 0.73 and 0.69), disability and gait speed (p < 0.05). In HRS, it additionally predicted time to death, diabetes, cardiovascular disease, frailty and grip strength. DNAm metabolite surrogates may facilitate metabolic studies using only DNAm data. Clocks built from DNAm metabolites provided a novel approach to assess metabolic ageing, potentially enabling early detection of metabolic-related diseases for personalised medicine.]]> Wed, 31 Dec 1969 19:00:00 EST Insights into the molecular underpinning of type 2 diabetes complications. Singh A, Bocher O, Zeggini E
Hum Mol Genet (Jan 2025)

Type 2 diabetes (T2D) complications pose a significant global health challenge. Omics technologies have been employed to investigate these complications and identify the biological pathways involved. In this review, we focus on four major T2D complications: diabetic kidney disease, diabetic retinopathy, diabetic neuropathy, and cardiovascular complications. We discuss advancements in omics research, summarizing findings from genetic, epigenomic, transcriptomic, proteomic, and metabolomic studies across different ancestries and disease-relevant tissues. We stress the importance of integrating multi-omics techniques to elucidate the biological mechanisms underlying T2D complications and advocate for ancestrally diverse studies. Ultimately, these insights will improve risk prediction for T2D complications and inform translation strategies.]]> Wed, 31 Dec 1969 19:00:00 EST Non-canonical imprinting, manifesting as post-fertilization placenta-specific parent-of-origin dependent methylation, is not conserved in humans. Daskeviciute D, Chappell-Maor L, Sainty B, Arnaud P, Iglesias-Platas I, Simon C, Okae H, Arima T, Vassena R, Lartey J, Monk D
Hum Mol Genet (Jan 2025)

Genomic imprinting is the parent-of-origin dependent monoallelic expression of genes often associated with regions of germline-derived DNA methylation that are maintained as differentially methylated regions (gDMRs) in somatic tissues. This form of epigenetic regulation is highly conserved in mammals and is thought to have co-evolved with placentation. Tissue-specific gDMRs have been identified in human placenta, suggesting that species-specific imprinting dependent on unorthodox epigenetic establishment or maintenance may be more widespread than previously anticipated. Non-canonical imprinting, reliant on differential allelic H3K27me3 enrichment, has been reported in mouse and rat pre-implantation embryos, often overlapping long terminal repeat (LTR)-derived promoters. These non-canonical imprints lose parental allele-specific H3K27me3 specificity, subsequently gaining DNA methylation on the same allele in extra-embryonic tissues resulting in placenta-specific, somatically acquired maternal DMRs. To determine if similar non-canonical imprinting is present in the human placenta, we interrogated allelic DNA methylation for a selected number of loci, including (i) the human orthologues of non-canonical imprinted regions in mouse and rat, (ii) promoters of human LTR-derived transcripts, and (iii) CpG islands with intermediate placenta-specific methylation that are unmethylated in gametes and pre-implantation embryos. We failed to identify any non-canonical imprints in the human placenta whole villi samples. Furthermore, the assayed genes were shown to be biallelically expressed in human pre-implantation embryos, indicating they are not imprinted at earlier time points. Together, our work reiterates the continued evolution of placenta-specific imprinting in mammals, which we suggest is linked to epigenetic differences during the maternal-to-embryo transition and species-specific integration of retrotransposable elements.]]> Wed, 31 Dec 1969 19:00:00 EST Developmental and molecular effects of pure-tone sine wave exposure on early zebrafish embryo development: Implications for reproductive health. Zuo Y, Bai Z, Yang K, Lin Z, Hu X, Sun H
Ecotoxicol Environ Saf (Jan 2025)

Noise pollution has become a significant concern for human health, yet its effects on early embryonic development remain underexplored. Specifically, data on the impact of sine wave noise on newly fertilized embryos is limited. This study aimed to address this gap by using zebrafish embryos at the 1-cell stage as a model to assess the toxicity of sine waves, following OECD Test No. 236. We exposed embryos to sound levels of 90 decibels (dB) and above, observing increased deformity rates, delayed development, and reductions in body length, heart rate and brain size. To elucidate the molecular mechanisms underlying these effects, we employed transcriptomics, metabolomics, and epigenomics (m6A-MeRIP-seq). KEGG enrichment analysis revealed significant alterations in arachidonic acid metabolism, axon guidance, and ubiquitin-mediated proteolysis. In conclusion, our findings demonstrate that high levels of sine wave noise adversely affect early embryo development. These results provide crucial insights for developing strategies to mitigate noise pollution and protect early developmental stages.]]> Wed, 31 Dec 1969 19:00:00 EST