'; ?> 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, 25 Sep 2021 15:39:24 EDT Sat, 25 Sep 2021 15:39:24 EDT jirtle@radonc.duke.edu james001@jirtle.com A comprehensive integrated post-GWAS analysis of Type 1 diabetes reveals enhancer-based immune dysregulation. Kim SS, Hudgins AD, Yang J, Zhu Y, Tu Z, Rosenfeld MG, DiLorenzo TP, Suh Y
PLoS One (2021)

Type 1 diabetes (T1D) is an organ-specific autoimmune disease, whereby immune cell-mediated killing leads to loss of the insulin-producing β cells in the pancreas. Genome-wide association studies (GWAS) have identified over 200 genetic variants associated with risk for T1D. The majority of the GWAS risk variants reside in the non-coding regions of the genome, suggesting that gene regulatory changes substantially contribute to T1D. However, identification of causal regulatory variants associated with T1D risk and their affected genes is challenging due to incomplete knowledge of non-coding regulatory elements and the cellular states and processes in which they function. Here, we performed a comprehensive integrated post-GWAS analysis of T1D to identify functional regulatory variants in enhancers and their cognate target genes. Starting with 1,817 candidate T1D SNPs defined from the GWAS catalog and LDlink databases, we conducted functional annotation analysis using genomic data from various public databases. These include 1) Roadmap Epigenomics, ENCODE, and RegulomeDB for epigenome data; 2) GTEx for tissue-specific gene expression and expression quantitative trait loci data; and 3) lncRNASNP2 for long non-coding RNA data. Our results indicated a prevalent enhancer-based immune dysregulation in T1D pathogenesis. We identified 26 high-probability causal enhancer SNPs associated with T1D, and 64 predicted target genes. The majority of the target genes play major roles in antigen presentation and immune response and are regulated through complex transcriptional regulatory circuits, including those in HLA (6p21) and non-HLA (16p11.2) loci. These candidate causal enhancer SNPs are supported by strong evidence and warrant functional follow-up studies.]]> Wed, 31 Dec 1969 19:00:00 EST Understanding environmental epigenomics in autism spectrum disorder: an interview with Farah R Zahir. Zahir FR
Epigenomics (Sep 2021)

In this interview, Dr Farah R Zahir speaks with Storm Johnson, Commissioning Editor for , on her work to date in the field of epigenomics, autism and intellectual disability. Dr Farah R Zahir specializes in the identification of novel genetic and epigenetic causes for neurodevelopmental diseases. Her PhD, awarded in 2011 by the University of British Columbia (UBC), resulted in the characterization of new intellectual disability (ID) syndromes, as well as discovery of several new causative genes for the disorder. She was awarded the prestigious James Miller Memorial Prize for integrating basic and clinical science in 2010. Her PhD dissertation was nominated for the Governor General's gold medal - the highest possible accolade at UBC for doctoral research work. She then completed a postdoctoral tenure in Canada's premier Michael Smith Genome Sciences Centre, where she used whole-genome-sequencing methods to comprehensively assess genetic, molecular and structural causes for ID, employing several firsts for bioinformatic data mining in the field. During her postdoctorate she won three distinguished awards and was a fellow of the Canadian Institute of Health Research, ranking in the top 2% nationally. Dr Zahir was appointed an Assistant Professor at the Hamad Bin Khalifa University in 2016, where she led a group focused on neurogenomics and neuroepigenomics research. She was a founding member of the Precision and Genomics Medicine graduate program there. Currently she has rejoined UBC's department of Medical Genetics. Among her most significant achievements is the establishment of the novel Zahir Friedman syndrome, an intellectual disability/autism spectrum disorder syndrome that is caused by a major epigenomic regulator. Her current primary research interest is how epigenomics can be changed by environmental impacts and how these effects may be harnessed for neurodevelopmental disorders' prophylaxis and therapeutics.]]> Wed, 31 Dec 1969 19:00:00 EST Polymer Modeling of 3D Epigenome Folding: Application to Drosophila. Jost D
Methods Mol Biol (2022)

Mechanistic modeling in biology allows to investigate, based on first principles, if putative hypotheses are compatible with observations and to drive further experimental works. Along this line, polymer modeling has been instrumental in 3D genomics to better understand the impact of key mechanisms on the spatial genome organization. Here, I describe how polymer-based models can be practically used to study the role of epigenome in chromosome folding. I illustrate this methodology in the context of Drosophila epigenome folding.]]> Wed, 31 Dec 1969 19:00:00 EST KDM5A suppresses PML-RARα target gene expression and APL differentiation through repressing H3K4me2. Xu S, Wang S, Xing S, Yu D, Rong B, Gao H, Sheng M, Tan Y, Sun X, Wang K, Xue K, Shi Z, Lan F
Blood Adv (09 2021)

Epigenetic abnormalities are frequently involved in the initiation and progression of cancers, including acute myeloid leukemia (AML). A subtype of AML, acute promyelocytic leukemia (APL), is mainly driven by a specific oncogenic fusion event of promyelocytic leukemia-RA receptor fusion oncoprotein (PML-RARα). PML-RARα was reported as a transcription repressor through the interaction with nuclear receptor corepressor and histone deacetylase complexes leading to the mis-suppression of its target genes and differentiation blockage. Although previous studies were mainly focused on the connection of histone acetylation, it is still largely unknown whether alternative epigenetics mechanisms are involved in APL progression. KDM5A is a demethylase of histone H3 lysine 4 di- and tri-methylations (H3K4me2/3) and a transcription corepressor. Here, we found that the loss of KDM5A led to APL NB4 cell differentiation and retarded growth. Mechanistically, through epigenomics and transcriptomics analyses, KDM5A binding was detected in 1889 genes, with the majority of the binding events at promoter regions. KDM5A suppressed the expression of 621 genes, including 42 PML-RARα target genes, primarily by controlling the H3K4me2 in the promoters and 5' end intragenic regions. In addition, a recently reported pan-KDM5 inhibitor, CPI-455, on its own could phenocopy the differentiation effects as KDM5A loss in NB4 cells. CPI-455 treatment or KDM5A knockout could greatly sensitize NB4 cells to all-trans retinoic acid-induced differentiation. Our findings indicate that KDM5A contributed to the differentiation blockage in the APL cell line NB4, and inhibition of KDM5A could greatly potentiate NB4 differentiation.]]> Wed, 31 Dec 1969 19:00:00 EST Visualizing and Annotating Hi-C Data. Pal K, Ferrari F
Methods Mol Biol (2022)

Epigenomics studies require the combined analysis and integration of multiple types of data and annotations to extract biologically relevant information. In this context, sophisticated data visualization techniques are fundamental to identify meaningful patterns in the data in relation to the genomic coordinates. Data visualization for Hi-C contact matrices is even more complex as each data point represents the interaction between two distant genomic loci and their three-dimensional positioning must be considered. In this chapter we illustrate how to obtain sophisticated plots showing Hi-C data along with annotations for other genomic features and epigenomics data. For the example code used in this chapter we rely on a Bioconductor package able to handle even high-resolution Hi-C datasets. The provided examples are explained in details and highly customizable, thus facilitating their extension and adoption by end users for other studies.]]> Wed, 31 Dec 1969 19:00:00 EST echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline. Schilder BM, Humphrey J, Raj T
Bioinformatics (Sep 2021)

echolocatoR integrates a diverse suite of statistical and functional fine-mapping tools in order to identify, test enrichment in, and visualize high-confidence causal consensus variants in any phenotype. It requires minimal input from users (a summary statistics file), can be run in a single R function, and provides extensive access to relevant datasets (e.g. reference linkage disequilibrium panels, quantitative trait loci, genome-wide annotations, cell-type-specific epigenomics), thereby enabling rapid, robust and scalable end-to-end fine-mapping investigations.]]> Wed, 31 Dec 1969 19:00:00 EST Ecotoxicological epigenetics in invertebrates: Emerging tool for the evaluation of present and past pollution burden. Å rut M
Chemosphere (Nov 2021)

The effect of environmental pollution on epigenetic changes and their heredity in affected organisms is of major concern as such changes can play a significant role in adaptation to changing environmental conditions. Changes of epigenetic marks including DNA methylation, histone modifications, and non-coding RNA's can induce changes in gene transcription leading to physiological long-term changes or even transgenerational inheritance. Such mechanisms have until recently been scarcely studied in invertebrate organisms, mainly focusing on model species including Caenorhabditis elegans and Daphnia magna. However, more data are becoming available, particularly focused on DNA methylation changes caused by anthropogenic pollutants in a wide range of invertebrates. This review examines the literature from field and laboratory studies utilising invertebrate species exposed to environmental pollutants and their effect on DNA methylation. Possible mechanisms of epigenetic modifications and their role on physiology and adaptation as well as the incidence of intergenerational and transgenerational inheritance are discussed. Furthermore, critical research challenges are defined and the way forward is proposed. Future studies should focus on the use of next generation sequencing tools to define invertebrate methylomes under environmental stress in higher resolution, those data should further be linked to gene expression patterns and phenotypes and detailed studies focusing on transgenerational effects are encouraged. Moreover, studies of other epigenetic mechanisms in various invertebrate species, apart from DNA methylation would provide better understanding of interconnected cross-talk between epigenetic marks. Taken together incorporating epigenetic studies in ecotoxicology context presents a promising tool for development of sensitive biomarkers for environmental stress assessment.]]> Wed, 31 Dec 1969 19:00:00 EST Effects of noninherited ancestral genotypes on offspring phenotypes†. Cullen SM, Hassan N, Smith-Raska M
Biol Reprod (Sep 2021)

It is well established that environmental exposures can modify the profile of heritable factors in an individual's germ cells, ultimately affecting the inheritance of phenotypes in descendants. Similar to exposures, an ancestor's genotype can also affect the inheritance of phenotypes across generations, sometimes in offspring who do not inherit the genetic aberration. This can occur via a variety of prenatal, in utero, or postnatal mechanisms. In this review, we discuss the evidence for this process in mammals, with a focus on examples that are potentially mediated through the germline, while also considering alternate routes of inheritance. Noninherited ancestral genotypes may influence descendant's disease risk to a much greater extent than currently appreciated, and focused evaluation of this phenomenon may reveal novel mechanisms of inheritance.]]> Wed, 31 Dec 1969 19:00:00 EST Triploid pregnancy-Clinical implications. Massalska D, Bijok J, Kucińska-Chahwan A, Zimowski JG, Ozdarska K, Panek G, Roszkowski T
Clin Genet (Oct 2021)

Triploidy is a life-limiting genetic aberration resulting from an extra haploid set of chromosomes of paternal (diandric triploidy) or maternal origin (digynic triploidy). Triploidy affects around 1%-2% of all conceptions. The majority of cases is miscarried at early developmental stages. In consequence of genomic imprinting, parental origin affects the phenotype of triploid pregnancies as well as the prevalence and spectrum of related maternal complications. Distinctive ultrasound features of both triploid phenotypes as well as characteristic patterns of biochemical markers may be useful in diagnosis. Molecular confirmation of the parental origin allows to predict the risk of complications, such as gestational trophoblastic neoplasia, hyperthyroidism, hypertension, or preeclampsia associated with the paternal origin of triploidy. Diagnosis of partial hydatidiform mole associated with diandric triploidy is challenging especially in the first trimester pregnancy loss due to the limitations of both histopathology and ultrasound. We present important clinical aspects of triploid pregnancies and indicate unresolved issues demanding further studies.]]> Wed, 31 Dec 1969 19:00:00 EST Clinical Utility of Methylation-Specific Multiplex Ligation-Dependent Probe Amplification for the Diagnosis of Prader-Willi Syndrome and Angelman Syndrome. Kim B, Park Y, Cho SI, Kim MJ, Chae JH, Kim JY, Seong MW, Park SS
Ann Lab Med (Jan 2022)

Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are genomic imprinting disorders that are mainly caused by a deletion on 15q11-q13, the uniparental disomy of chromosome 15, or an imprinting defect. We evaluated the utility of methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as a diagnostic tool and for demonstrating the relationship between molecular mechanisms and clinical presentation.]]> Wed, 31 Dec 1969 19:00:00 EST The DNA cytosine-5-methyltransferase 3 (DNMT3) involved in regulation of CgIL-17 expression in the immune response of oyster Crassostrea gigas. Zhao Q, Wang W, Li JX, Yuan P, Liu Y, Li Y, Wang L, Song L
Dev Comp Immunol (Oct 2021)

DNA methyltransferase, a key enzyme mediating DNA methylation, is involved in numerous processes including genomic imprinting, X chromosome inactivation, transposable element suppression, and immune defense in vertebrates. In the present study, a DNA cytosine-5-methyltransferase 3 was identified from oyster Crassostrea gigas (designed as CgDNMT3). There were a PWWP domain, a PHD domain and a DNA-methylase domain in the deduced amino acid sequences of CgDNMT3, and the conserved motifs I, IV, VI, Ⅷ, IX and X were identified in its C-terminal catalytic DNA-methylase domain. The mRNA transcripts of CgDNMT3 were detected in haemocytes, mantle, gill, adductor muscle, digestive gland and labial palp, with higher expression level in haemocytes (6.54 folds of those in gill, p < 0.01). The expression level of CgDNMT3 mRNA in haemocytes increased significantly after LPS primed (2.87 folds of that in control group, p < 0.05) in vitro or Vibrio splendidus challenging (1.94 folds of that in control group, p < 0.05) in vivo. Immunocytochemical analysis revealed that CgDNMT3 protein was distributed mainly in cytoplasm and partial in nucleus of oyster haemocytes. After CgDNMT3 was transfected and expressed in HEK293T cells, the DNA 5-methylcytosine (5-mc) level in the transfected group was significantly increased, which was 1.22 folds (p < 0.05) of the pcDNA-3.1 group. The expressions of oyster CgIL17-1, CgIL17-2 and CgIL17-5 in haemocytes increased (13.05 folds, 4.78 folds and 9.41 folds of that in control group, respectively) at 12 h after V. splendidus challenging, but the increase were significantly inhibited when the oysters were pre-treated with DNA methyltransferase inhibitor 5-Azacytidine, which were 9 folds, 1.93 folds and 3.22 folds of that in control group, respectively. These results collectively suggested that CgDNMT3 was a conserved member of DNA methyltransferase 3 family in oyster, and participated in regulating the expression of cytokines during immune response.]]> Wed, 31 Dec 1969 19:00:00 EST New Findings in Immune Epigenomics Are a Return on Investment. Dettmer AM
Brain Behav Immun (Sep 2021)

]]> Wed, 31 Dec 1969 19:00:00 EST Optimal sample size for calibrating DNA methylation age estimators. Mayne B, Berry O, Jarman S
Mol Ecol Resour (Oct 2021)

Age is a fundamental parameter in wildlife management as it is used to determine the risk of extinction, manage invasive species, and regulate sustainable harvest. In a broad variety of vertebrates species, age can be determined by measuring DNA methylation. Animals with known ages are initially required during development, calibration, and validation of these epigenetic clocks. However, wild animals with known ages are frequently difficult to obtain. Here, we perform Monte-Carlo simulations to determine the optimal sample size required to create an accurate calibration model for age estimation by elastic net regression modelling of cytosine-phosphate-guanine methylation data. Our results suggest a minimum calibration population size of 70, but ideally 134 individuals or more for accurate and precise models. We also provide estimates to the extent a model can be extrapolated beyond a distribution of ages that was used during calibration. The findings can assist researchers to better design age estimation models and decide if their model is adequate for determining key population attributes.]]> Wed, 31 Dec 1969 19:00:00 EST De novo genome assembly and in natura epigenomics reveal salinity-induced DNA methylation in the mangrove tree Bruguiera gymnorhiza. Miryeganeh M, Marlétaz F, Gavriouchkina D, Saze H
New Phytol (Sep 2021)

Mangroves are adapted to harsh environments, such as high UV light, low nutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources. We performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant mangrove species. We also performed the first genome-guided transcriptome assembly for mangrove species. The 309 Mb of the genome is predicted to encode 34,403 genes and has a repeat content of 48%. Depending on its growing environment, the natural B. gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. Moreover, high-salinity environments induced genome-wide DNA hypermethylation of transposable elements (TEs) in the B. gymnorhiza. DNA hypermethylation was concurrent with the transcriptional regulation of chromatin modifier genes, suggesting robust epigenome regulation of TEs in the B. gymnorhiza genome under high-salinity environments. The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating, harsh natural environments.]]> Wed, 31 Dec 1969 19:00:00 EST LncRNAs as putative biomarkers and therapeutic targets for Parkinson's disease. Taghizadeh E, Gheibihayat SM, Taheri F, Afshani SM, Farahani N, Saberi A
Neurol Sci (Oct 2021)

Parkinson's disease (PD) is known as one of the most common degenerative disorders related to the damage of the central nervous system (CNS). This brain disorder is also characterized by the formation of Lewy bodies in the cytoplasm of the dopaminergic neurons in the substantia nigra pars compacta (SNc), which consequently leads to motor and non-motor symptoms. With regard to the growing trend in the number of cases with PD and its effects on individuals, families, and communities, immediate treatments together with diagnostic methods are required. In this respect, long non-coding ribonucleic acids (lncRNAs) represent a large class of ncRNAs with more than 200 nucleotides in length, playing key roles in some important processes including gene expression, cell differentiation, genomic imprinting, apoptosis, and cell cycle. They are highly expressed in the CNS and previous studies have further reported that the expression profile of lncRNAs is disrupted in human diseases such as neurodegenerative disorders. Since the levels of some lncRNAs change over time in the brains of patients with PD, a number of previous studies have examined their potentials as biomarkers for this brain disorder. Therefore, the main purpose of this study was to review the advances in the related literature on lncRNAs as diagnostic, therapeutic, and prognostic biomarkers for PD.]]> Wed, 31 Dec 1969 19:00:00 EST Germ cells: ENCODE's forgotten cell type†. McCarrey JR, Cheng K
Biol Reprod (Sep 2021)

More than a decade ago, the ENCODE and NIH Epigenomics Roadmap consortia organized large multilaboratory efforts to profile the epigenomes of >110 different mammalian somatic cell types. This generated valuable publicly accessible datasets that are being mined to reveal genome-wide patterns of a variety of different epigenetic parameters. This consortia approach facilitated the powerful and comprehensive multiparametric integrative analysis of the epigenomes in each cell type. However, no germ cell types were included among the cell types characterized by either of these consortia. Thus, comprehensive epigenetic profiling data are not generally available for the most evolutionarily important cells, male and female germ cells. We discuss the need for reproductive biologists to generate similar multiparametric epigenomic profiling datasets for both male and female germ cells at different developmental stages and summarize our recent effort to derive such data for mammalian spermatogonial stem cells and progenitor spermatogonia.]]> Wed, 31 Dec 1969 19:00:00 EST Maternal immune activation in rodent models: A systematic review of neurodevelopmental changes in gene expression and epigenetic modulation in the offspring brain. Woods RM, Lorusso JM, Potter HG, Neill JC, Glazier JD, Hager R
Neurosci Biobehav Rev (10 2021)

Maternal immune activation (mIA) during pregnancy is hypothesised to disrupt offspring neurodevelopment and predispose offspring to neurodevelopmental disorders such as schizophrenia. Rodent models of mIA have explored possible mechanisms underlying this paradigm and provide a vital tool for preclinical research. However, a comprehensive analysis of the molecular changes that occur in mIA-models is lacking, hindering identification of robust clinical targets. This systematic review assesses mIA-driven transcriptomic and epigenomic alterations in specific offspring brain regions. Across 118 studies, we focus on 88 candidate genes and show replicated changes in expression in critical functional areas, including elevated inflammatory markers, and reduced myelin and GABAergic signalling proteins. Further, disturbed epigenetic markers at nine of these genes support mIA-driven epigenetic modulation of transcription. Overall, our results demonstrate that current outcome measures have direct relevance for the hypothesised pathology of schizophrenia and emphasise the importance of mIA-models in contributing to the understanding of biological pathways impacted by mIA and the discovery of new drug targets.]]> Wed, 31 Dec 1969 19:00:00 EST How family histories can inform research about germ cell exposures: the example of autism. Escher J
Biol Reprod (Sep 2021)

Throughout the scientific literature, heritable traits are routinely presumed to be genetic in origin. However, as emerging evidence from the realms of genetic toxicology and epigenomics demonstrate, heritability may be better understood as encompassing not only DNA sequence passed down through generations, but also disruptions to the parental germ cells causing de novo mutations or epigenetic alterations, with subsequent shifts in gene expression and functions in offspring. The Beyond Genes conference highlighted advances in understanding these aspects at molecular, experimental, and epidemiological levels. In this commentary I suggest that future research on this topic could be inspired by collecting parents' germ cell exposure histories, with particular attention to cases of families with multiple children suffering idiopathic disorders. In so doing I focus on the endpoint of autism spectrum disorders (ASDs). Rates of this serious neurodevelopment disability have climbed around the world, a growing crisis that cannot be explained by diagnostic shifts. ASD's strong heritability has prompted a research program largely focused on DNA sequencing to locate rare and common variants, but decades of this gene-focused research have revealed surprisingly little about the molecular origins of the disorder. Based on my experience as the mother of two children with idiopathic autism, and as a research philanthropist and autism advocate, I suggest ways researchers might probe parental germ cell exposure histories to develop new hypotheses that may ultimately reveal sources of nongenetic heritability in a subset of idiopathic heritable pathologies.]]> Wed, 31 Dec 1969 19:00:00 EST Multi-locus imprinting disturbances of Beckwith-Wiedemann and Large offspring syndrome/Abnormal offspring syndrome: A brief review. Mangiavacchi PM, Caldas-Bussiere MC, Mendonça MDS, Dias AJB, Rios ÃFL
Theriogenology (Oct 2021)

In vitro fertilization and somatic cell nuclear transfer are assisted reproduction technologies commonly used in humans and cattle, respectively. Despite advances in these technologies, molecular failures can occur, increasing the chance of the onset of imprinting disorders in the offspring. Large offspring syndrome/abnormal offspring syndrome (LOS/AOS) has been described in cattle and has features such as hypergrowth, malformation of organs, and skeletal and placental defects. In humans, Beckwith-Wiedemann syndrome (BWS) has phenotypic characteristics similar to those found in LOS/AOS. In both syndromes, disruption of genomic imprinting associated with loss of parental-specific expression and parental-specific epigenetic marks is involved in the molecular etiology. Changes in the imprinting pattern of these genes lead to loss of imprinting (LOI) due to gain or loss of methylation, inducing the emergence of these syndromes. Several studies have reported locus-specific alterations in these syndromes, such as hypomethylation in imprinting control region 2 (KvDMR1) in BWS and LOS/AOS. These LOI events can occur at multiple imprinted loci in the same affected individual, which are called multi-locus methylation defect (MLMD) events. Although the bovine species has been proposed as a developmental model for human imprinting disorders, there is little information on bovine imprinted genes in the literature, even the correlation of epimutation data with clinical characteristics. In this study, we performed a systematic review of all the multi-locus LOI events described in human BWS and LOS/AOS, in order to determine in which imprinted genes the largest changes in the pattern of DNA methylation and expression occur, helping to fill gaps for a better understanding of the etiology of both syndromes.]]> Wed, 31 Dec 1969 19:00:00 EST Beckwith-Wiedemann syndrome: Clinical, histopathological and molecular study of two Tunisian patients and review of literature. Sassi H, Elaribi Y, Jilani H, Rejeb I, Hizem S, Sebai M, Kasdallah N, Bouthour H, Hannachi S, Beygo J, Saad A, Buiting K, H'mida Ben-Brahim D, BenJemaa L
Mol Genet Genomic Med (Sep 2021)

Beckwith-Wiedemann syndrome (BWS) is a rare overgrowth syndrome characterized by congenital malformations and predisposition to embryonic tumors. Loss of methylation of imprinting center 2 (IC2) is the most frequent alteration and rarely associated with tumors compared to paternal uniparental disomy of chromosome 11 (UPD(11)pat) and gain of methylation of imprinting center 1.]]> Wed, 31 Dec 1969 19:00:00 EST