'; ?> 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 Wed, 21 Mar 2018 05:18:49 EDT Wed, 21 Mar 2018 05:18:49 EDT jirtle@radonc.duke.edu james001@jirtle.com Intergenerational response to the endocrine disruptor vinclozolin is influenced by maternal genotype and crossing scheme. Pietryk EW, Clement K, Elnagheeb M, Kuster R, Kilpatrick K, Love MI, Ideraabdullah FY
Reprod Toxicol (Mar 2018)

In utero exposure to vinclozolin (VIN), an antiandrogenic fungicide, is linked to multigenerational phenotypic and epigenetic effects. Mechanisms remain unclear. We assessed the role of antiandrogenic activity and DNA sequence context by comparing effects of VIN vs. M2 (metabolite with greater antiandrogenic activity) and wild-type C57BL/6 (B6) mice vs. mice carrying mutations at the previously reported VIN-responsive H19/Igf2 locus. First generation offspring from VIN-treated 8nrCG mutant dams exhibited increased body weight and decreased sperm ICR methylation. Second generation pups sired by affected males exhibited decreased neonatal body weight but only when dam was unexposed. Offspring from M2 treatments, B6 dams, 8nrCG sires or additional mutant lines were not similarly affected. Therefore, pup response to VIN over two generations detected here was an 8nrCG-specific maternal effect, independent of antiandrogenic activity. These findings demonstrate that maternal effects and crossing scheme play a major role in multigenerational response to in utero exposures.]]>
Wed, 31 Dec 1969 19:00:00 EST
Obituary: Denise Barlow (1950-2017). Ferguson-Smith AC, Bartolomei MS
Development (Mar 2018)

Anne Ferguson-Smith and Marisa Bartolomei look back at the life and science of Denise Barlow, a pioneer in genomic imprinting and epigenetics.]]>
Wed, 31 Dec 1969 19:00:00 EST
Classification of heterogeneous genetic variations of microRNA regulome in cancer. Hrovatin K, Kunej T
Cancer Lett (Apr 2018)

Genetic variations and differential expression of miRNA regulome components are associated with cancer. Thus miRNA based diagnosis and treatments have been proposed. However, to better explore these options, the molecular changes in miRNA regulome must be understood. MicroRNAs can be involved in regulation of oncogenes and tumour suppressors. As each miRNA targets broad range of genes, minor changes in miRNAs can have great effects, contributing to cell transformation. Many genetic variants of miRNA regulome have been reported to be associated with cancer, but this information needs to be systematized. Therefore, we here classify different types of genetic variations of miRNA regulome in cancer. Genetic variations are comprised of structural and short polymorphisms and changes in epigenetic landscape. Additionally, unexplained differential expression is often reported. These alterations affect miRNA genes and their regulatory elements, processing machinery, degradation machinery, and targets, leading to changes in miRNA silencing. However, miRNA regulome components are not equally explored. A systematic overview over miRNA regulome can contribute to more targeted study design and understanding of miRNA function. We also present treatments and diagnosis based on miRNA regulome genetic variability and expression.]]>
Wed, 31 Dec 1969 19:00:00 EST
The NIEHS TaRGET II Consortium and environmental epigenomics. Wang T, Pehrsson EC, Purushotham D, Li D, Zhuo X, Zhang B, Lawson HA, Province MA, Krapp C, Lan Y, Coarfa C, Katz TA, Tang WY, Wang Z, Biswal S, Rajagopalan S, Colacino JA, Tsai ZT, Sartor MA, Neier K, Dolinoy DC, Pinto J, Hamanaka RB, Mutlu GM, Patisaul HB, Aylor DL, Crawford GE, Wiltshire T, Chadwick LH, Duncan CG, Garton AE, McAllister KA,  , Bartolomei MS, Walker CL, Tyson FL
Nat Biotechnol (Mar 2018)

Wed, 31 Dec 1969 19:00:00 EST
Epigenome dysregulation in cholangiocarcinoma. O'Rourke CJ, Munoz-Garrido P, Aguayo EL, Andersen JB
Biochim Biophys Acta (Apr 2018)

Epigenomics is a fast-evolving field of research that has lately attracted considerable interest, mainly due to the reversibility of epigenetic marks. Clinically, among solid tumors, the field is still limited. In cholangiocarcinoma (CCA) it is well known that the epigenetic landscape is deregulated both during carcinogenesis and disease progression as a consequence of aberrant mechanisms leading to genome instability. In this article, we will briefly review the molecular alterations that have been described in the transformation of normal cholangiocytes into malignant derivatives, focusing on the role of non-coding RNA (ncRNA) interactions, DNA methylation, post-translational modifications (PTMs) of histones and chromatin remodeling complexes.]]>
Wed, 31 Dec 1969 19:00:00 EST
Imprinted gene dysregulation in anull mouse model is stochastic and variable in the germline and offspring. SanMiguel JM, Abramowitz LK, Bartolomei MS
Development (Mar 2018)

Imprinted genes are expressed from one parental allele and regulated by differential DNA methylation at imprinting control regions (ICR). ICRs are reprogrammed in the germline through erasure and reestablishment of DNA methylation. Although much is known about DNA methylation establishment, DNA demethylation is less well understood. Recently, the Ten-Eleven Translocation proteins (TET1-3) have been shown to initiate DNA demethylation, withmice exhibiting aberrant levels of imprinted gene expression and ICR methylation. Nevertheless, TET1's role in demethylating ICRs in the female germline and controlling allele-specific expression remains to be determined. Here, we examined ICR-specific DNA methylation ingerm cells and ascertained whether abnormal ICR methylation impacted imprinted gene expression in F1 hybrid somatic tissues derived fromeggs or sperm. We show thatdeficiency is associated with hypermethylation of a subset of ICRs in germ cells. Moreover, ICRs with defective germline reprogramming exhibit aberrant DNA methylation and biallelic expression of linked imprinted genes in somatic tissues. Thus, we define a discrete set of genomic regions that require TET1 for germline reprogramming and discuss mechanisms for stochastic imprinting defects.]]>
Wed, 31 Dec 1969 19:00:00 EST
Evidence establishing a link between prenatal and early-life stress and asthma development. Rosa MJ, Lee AG, Wright RJ
Curr Opin Allergy Clin Immunol (Apr 2018)

The objective of this review is to provide an update on our evolving understanding of the effects of stress in pregnancy and during early development on the onset of asthma-related phenotypes across childhood, adolescence, and into early adulthood.]]>
Wed, 31 Dec 1969 19:00:00 EST
Genomic imprinting, growth and maternal-fetal interactions. Cassidy FC, Charalambous M
J Exp Biol (Mar 2018)

In the 1980s, mouse nuclear transplantation experiments revealed that both male and female parental genomes are required for successful development to term ( McGrath and Solter, 1983; Surani and Barton, 1983). This non-equivalence of parental genomes is because imprinted genes are predominantly expressed from only one parental chromosome. Uniparental inheritance of these genomic regions causes paediatric growth disorders such as Beckwith-Wiedemann and Silver-Russell syndromes (reviewed in Peters, 2014). More than 100 imprinted genes have now been discovered and the functions of many of these genes have been assessed in murine models. The first such genes described were the fetal growth factor() and its inhibitor() ( DeChiara et al., 1991; Lau et al., 1994; Wang et al., 1994). Since then, it has emerged that most imprinted genes modulate fetal growth and resource acquisition in a variety of ways. First, imprinted genes are required for the development of a functional placenta, the organ that mediates the exchange of nutrients between mother and fetus. Second, these genes act in an embryo-autonomous manner to affect the growth rate and organogenesis. Finally, imprinted genes can signal the nutritional status between mother and fetus, and can modulate levels of maternal care. Importantly, many imprinted genes have been shown to affect postnatal growth and energy homeostasis. Given that abnormal birthweight correlates with adverse adult metabolic health, including obesity and cardiovascular disease, it is crucial to understand how the modulation of this dosage-sensitive, epigenetically regulated class of genes can contribute to fetal and postnatal growth, with implications for lifelong health and disease.]]>
Wed, 31 Dec 1969 19:00:00 EST
Health, wealth and behavioural change: an exploration of role responsibilities in the wake of epigenetics. Vears DF, D'Abramo F
J Community Genet (Apr 2018)

The field of epigenetics is leading to new conceptualizations of the role of environmental factors in health and genetic disease. Although more evidence is required, epigenetic mechanisms are being implicated in the link between low socioeconomic status and poor health status. Epigenetic phenomena work in a number of ways: they can be established early in development, transmitted from previous generations and/or responsive to environmental factors. Knowledge about these types of epigenetic traits might therefore allow us to move away from a genetic deterministic perspective, and provide individuals with the opportunity to change their health status. Although this could be equated with patient empowerment, it could also lead to stigmatization and discrimination where individuals are deemed responsible for their health, even if they are not in social situations where they are able to enact change that would alter their health status. In this paper, we will explore the responsibilities of different actors in the healthcare sphere in relation to epigenetics across four different contexts: (1) genetic research, (2) clinical practice, (3) prenatal care and (4) the workplace. Within this exploration of role responsibilities, we will also discuss the potential constraints that might prevent the patient, mother-to-be, research participant or employee, from enacting any necessary steps in order to increase their health status in response to epigenetic information.]]>
Wed, 31 Dec 1969 19:00:00 EST
The effects of DNA methylation on human psychology. Kader F, Ghai M, Maharaj L
Behav Brain Res (Jul 2018)

DNA methylation is a fundamental epigenetic modification in the human genome; pivotal in development, genomic imprinting, X inactivation, chromosome stability, gene expression and methylation aberrations are involved in an array of human diseases. Methylation at promoters is associated with transcriptional repression, whereas gene body methylation is generally associated with gene expression. Extrinsic factors such as age, diets and lifestyle affect DNA methylation which consequently alters gene expression. Stress, anxiety, depression, life satisfaction, emotion among numerous other psychological factors also modify DNA methylation patterns. This correlation is frequently investigated in four candidate genes; NR3C1, SLC6A4, BDNF and OXTR, since regulation of these genes directly impact responses to social situations, stress, threats, behaviour and neural functions. Such studies underpin the hypothesis that DNA methylation is involved in deviant human behaviour, psychological and psychiatric conditions. These candidate genes may be targeted in future to assess the correlation between methylation, social experiences and long-term behavioural phenotypes in humans; and may potentially serve as biomarkers for therapeutic intervention.]]>
Wed, 31 Dec 1969 19:00:00 EST
Dad's Snoring May Have Left Molecular Scars in Your DNA: the Emerging Role of Epigenetics in Sleep Disorders. Morales-Lara D, De-la-Peña C, Murillo-Rodríguez E
Mol Neurobiol (Apr 2018)

The sleep-wake cycle is a biological phenomena under the orchestration of neurophysiological, neurochemical, neuroanatomical, and genetical mechanisms. Moreover, homeostatic and circadian processes participate in the regulation of sleep across the light-dark period. Further complexity of the understanding of the genesis of sleep engages disturbances which have been characterized and classified in a variety of sleep-wake cycle disorders. The most prominent sleep alterations include insomnia as well as excessive daytime sleepiness. On the other side, several human diseases have been linked with direct changes in DNA, such as chromatin configuration, genomic imprinting, DNA methylation, histone modifications (acetylation, methylation, ubiquitylation or sumoylation, etc.), and activating RNA molecules that are transcribed from DNA but not translated into proteins. Epigenetic theories primarily emphasize the interaction between the environment and gene expression. According to these approaches, the environment to which mammals are exposed has a significant role in determining the epigenetic modifications occurring in chromosomes that ultimately would influence not only development but also the descendants' physiology and behavior. Thus, what makes epigenetics intriguing is that, unlike genetic variation, modifications in DNA are altered directly by the environment and, in some cases, these epigenetic changes may be inherited by future generations. Thus, it is likely that epigenetic phenomena might contribute to the homeostatic and/or circadian control of sleep and, possibly, have an undescribed link with sleep disorders. An exciting new horizon of research is arising between sleep and epigenetics since it represents the relevance of the study of how the genome learns from its experiences and modulates behavior, including sleep.]]>
Wed, 31 Dec 1969 19:00:00 EST
iDREM: Interactive visualization of dynamic regulatory networks. Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z
PLoS Comput Biol (Mar 2018)

The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Combining all available time series and static datasets in a unified model remains an important challenge and goal. To address this challenge we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and combines them with existing interaction data to reconstruct networks that can lead to novel hypotheses on the function and timing of regulators. Users can interactively visualize and query the resulting model. We showcase the functionality of the new tool by applying it to microglia developmental data from multiple labs.]]>
Wed, 31 Dec 1969 19:00:00 EST
Expert consensus document: Clinical and molecular diagnosis, screening and management of Beckwith-Wiedemann syndrome: an international consensus statement. Brioude F, Kalish JM, Mussa A, Foster AC, Bliek J, Ferrero GB, Boonen SE, Cole T, Baker R, Bertoletti M, Cocchi G, Coze C, De Pellegrin M, Hussain K, Ibrahim A, Kilby MD, Krajewska-Walasek M, Kratz CP, Ladusans EJ, Lapunzina P, Le Bouc Y, Maas SM, Macdonald F, Õunap K, Peruzzi L, Rossignol S, Russo S, Shipster C, Skórka A, Tatton-Brown K, Tenorio J, Tortora C, Grønskov K, Netchine I, Hennekam RC, Prawitt D, Tümer Z, Eggermann T, Mackay DJG, Riccio A, Maher ER
Nat Rev Endocrinol (Apr 2018)

Beckwith-Wiedemann syndrome (BWS), a human genomic imprinting disorder, is characterized by phenotypic variability that might include overgrowth, macroglossia, abdominal wall defects, neonatal hypoglycaemia, lateralized overgrowth and predisposition to embryonal tumours. Delineation of the molecular defects within the imprinted 11p15.5 region can predict familial recurrence risks and the risk (and type) of embryonal tumour. Despite recent advances in knowledge, there is marked heterogeneity in clinical diagnostic criteria and care. As detailed in this Consensus Statement, an international consensus group agreed upon 72 recommendations for the clinical and molecular diagnosis and management of BWS, including comprehensive protocols for the molecular investigation, care and treatment of patients from the prenatal period to adulthood. The consensus recommendations apply to patients with Beckwith-Wiedemann spectrum (BWSp), covering classical BWS without a molecular diagnosis and BWS-related phenotypes with an 11p15.5 molecular anomaly. Although the consensus group recommends a tumour surveillance programme targeted by molecular subgroups, surveillance might differ according to the local health-care system (for example, in the United States), and the results of targeted and universal surveillance should be evaluated prospectively. International collaboration, including a prospective audit of the results of implementing these consensus recommendations, is required to expand the evidence base for the design of optimum care pathways.]]>
Wed, 31 Dec 1969 19:00:00 EST
Functional analyses of PtRDM1 gene overexpression in poplars and evaluation of its effect on DNA methylation and response to salt stress. Movahedi A, Zhang J, Sun W, Mohammadi K, Almasi Zadeh Yaghuti A, Wei H, Wu X, Yin T, Zhuge Q
Plant Physiol Biochem (Mar 2018)

Epigenetic modification by DNA methylation is necessary for all cellular processes, including genetic expression events, DNA repair, genomic imprinting and regulation of tissue development. It occurs almost exclusively at the C5 position of symmetric CpG and asymmetric CpHpG and CpHpH sites in genomic DNA. The RNA-directed DNA methylation (RDM1) gene is crucial for heterochromatin and DNA methylation. We overexpressed PtRDM1 gene from Populus trichocarpa to amplify transcripts of orthologous RDM1 in 'Nanlin895' (P. deltoides × P. euramericana 'Nanlin895'). This overexpression resulted in increasing RDM1 transcript levels: by ∼150% at 0 mM NaCl treatment and by ∼300% at 60 mM NaCl treatment compared to WT (control) poplars. Genomic cytosine methylation was monitored within 5.8S rDNA and histone H3 loci by bisulfite sequencing. In total, transgenic poplars revealed more DNA methylation than WT plants. In our results, roots revealed more methylated CG contexts than stems and leaves whereas, histone H3 presented more DNA methylation than 5.8S rDNA in both WT and transgenic poplars. The NaCl stresses enhanced more DNA methylation in transgenic poplars than WT plants through histone H3 and 5.8 rDNA loci. Also, the overexpression of PtRDM1 resulted in hyper-methylation, which affected plant phenotype. Transgenic poplars revealed significantly more regeneration of roots than WT poplars via NaCl treatments. Our results proved that RDM1 protein enhanced the DNA methylation by chromatin remodeling (e.g. histone H3) more than repetitive DNA sequences (e.g. 5.8S rDNA).]]>
Wed, 31 Dec 1969 19:00:00 EST
Human disease glycomics: technology advances enabling protein glycosylation analysis - part 2. Everest-Dass AV, Moh ESX, Ashwood C, Shathili AMM, Packer NH
Expert Rev Proteomics (Mar 2018)

The changes in glycan structures have been attributed to disease states for several decades. The surface glycosylation pattern is a signature of physiological state of a cell. In this review we provide a link between observed substructural glycan changes and a range of diseases. Areas covered: We highlight biologically relevant glycan substructure expression in cancer, inflammation, neuronal diseases and diabetes. Furthermore, the alterations in antibody glycosylation in a disease context are described. Expert commentary: Advances in technologies, as described in Part 1 of this review have now enabled the characterization of specific glycan structural markers of a range of disease states. The requirement of including glycomics in cross-disciplinary omics studies, such as genomics, proteomics, epigenomics, transcriptomics and metabolomics towards a systems glycobiology approach to understanding disease mechanisms and management are highlighted.]]>
Wed, 31 Dec 1969 19:00:00 EST
Transgenerational epigenetic influences of paternal environmental exposures on brain function and predisposition to psychiatric disorders. Yeshurun S, Hannan AJ
Mol Psychiatry (Mar 2018)

In recent years, striking new evidence has demonstrated non-genetic inheritance of acquired traits associated with parental environmental exposures. In particular, this transgenerational modulation of phenotypic traits is of direct relevance to psychiatric disorders, including depression, post-traumatic stress disorder, and other anxiety disorders. Here we review the recent progress in this field, with an emphasis on acquired traits of psychiatric illnesses transmitted epigenetically via the male lineage. We discuss the transgenerational effects of paternal exposure to stress vs. positive stimuli, such as exercise, and discuss their impact on the behavioral, affective and cognitive characteristics of their progeny. Furthermore, we review the recent evidence suggesting that these transgenerational effects are mediated by epigenetic mechanisms, including changes in DNA methylation and small non-coding RNAs in the sperm. We discuss the urgent need for more research exploring transgenerational epigenetic effects in animal models and human populations. These future studies may identify epigenetic mechanisms as potential contributors to the 'missing heritability' observed in genome-wide association studies of psychiatric illnesses and other human disorders. This exciting new field of transgenerational epigenomics will facilitate the development of novel strategies to predict, prevent and treat negative epigenetic consequences on offspring health, and psychiatric disorders in particular.]]>
Wed, 31 Dec 1969 19:00:00 EST
Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics. Hsu CL, Chou CH, Huang SC, Lin CY, Lin MY, Tung CC, Lin CY, Lai IP, Zou YF, Youngson NA, Lin SP, Yang CH, Chen SK, Gau SS, Huang HS
Hum Mol Genet (Mar 2018)

Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism through which monoallelic gene expression occurs in a parent-of-origin-specific manner. It is unknown if genomic imprinting contributes to visual system development. We profiled the transcriptome and imprintome during critical periods of mouse visual system development under normal- and dark-rearing conditions using B6/CAST F1 hybrid mice. We identified experience-regulated, isoform-specific and brain-region-specific imprinted genes. We also found imprinted microRNAs were predominantly clustered into the Dlk1-Dio3 imprinted locus with light experience affecting some imprinted miRNA expression. Our findings provide the first comprehensive analysis of light-experience regulation of the transcriptome and imprintome during critical periods of visual system development. Our results may contribute to therapeutic strategies for visual impairments and circadian rhythm disorders resulting from a dysfunctional imprintome.]]>
Wed, 31 Dec 1969 19:00:00 EST
CORRECTION: Genomic Imprinting Was Evolutionarily Conserved during Wheat Polyploidization. Yang G, Liu Z, Gao L, Yu K, Feng M, Yao Y, Peng H, Hu Z, Sun Q, Ni Z, Xin M
Plant Cell (Mar 2018)

Wed, 31 Dec 1969 19:00:00 EST
Delay in maternal transcript degradation in ovine embryos derived from low competence oocytes. Masala L, Ariu F, Bogliolo L, Bellu E, Ledda S, Bebbere D
Mol Reprod Dev (Mar 2018)

Oocytes from prepubertal animals have a reduced ability to undergo embryo development and produce viable offspring. The present work used an ovine model consisting of oocytes derived from adult and prepubertal donors to assess the molecular status of oocytes and preimplantation embryos with different developmental competence. The lower potential of oocytes of young donors was confirmed in terms of in vitro developmental capabilities and kinetics. A panel of genes including maternal effect (DPPA3, GDF9, NMP2, ZAR1) and housekeeping genes (ACTB, RPL19, SDHA, YWHAZ, ATP1A1), genes involved in DNA methylation (DNMT1, DNMT3A, DNMT3B), genomic imprinting (IGF2R), pluripotency (NANOG, POU5F1) and cell cycle regulation (CCNB1, CDK1, MELK) was relatively quantified. Temporal analysis during oocyte maturation and preimplantation embryo development evidenced patterns associated with donor age. With a few gene-specific exceptions, the differential model showed a reduced transcript abundance in immature prepubertal oocytes that completely reversed trend after fertilization, when higher mRNA levels were consistently observed in early embryos, indicating a delay in maternal transcript degradation. We propose that the molecular shortage in the prepubertal oocyte may affect its developmental potential and impair the early pathways of maternal mRNA clearance in the embryo. While confirming the different potential of oocytes derived from adult and prepubertal donors, our work showed for the first time a consistent delay in maternal transcript degradation in embryos derived from low competence oocytes that interestingly recalls the delayed developmental kinetics. Such abnormal transcript persistence may hinder further development and represents a novel perspective on the complexity of developmental competence. This article is protected by copyright. All rights reserved.]]>
Wed, 31 Dec 1969 19:00:00 EST
Distinct chromatin signatures of DNA hypomethylation in aging and cancer. Pérez RF, Tejedor JR, Bayón GF, Fernández AF, Fraga MF
Aging Cell (Mar 2018)

Cancer is an aging-associated disease, but the underlying molecular links between these processes are still largely unknown. Gene promoters that become hypermethylated in aging and cancer share a common chromatin signature in ES cells. In addition, there is also global DNA hypomethylation in both processes. However, the similarity of the regions where this loss of DNA methylation occurs is currently not well characterized, and it is unknown if such regions also share a common chromatin signature in aging and cancer. To address this issue, we analyzed TCGA DNA methylation data from a total of 2,311 samples, including control and cancer cases from patients with breast, kidney, thyroid, skin, brain, and lung tumors and healthy blood, and integrated the results with histone, chromatin state, and transcription factor binding site data from the NIH Roadmap Epigenomics and ENCODE projects. We identified 98,857 CpG sites differentially methylated in aging and 286,746 in cancer. Hyper- and hypomethylated changes in both processes each had a similar genomic distribution across tissues and displayed tissue-independent alterations. The identified hypermethylated regions in aging and cancer shared a similar bivalent chromatin signature. In contrast, hypomethylated DNA sequences occurred in very different chromatin contexts. DNA hypomethylated sequences were enriched at genomic regions marked with the activating histone posttranslational modification H3K4me1 in aging, while in cancer, loss of DNA methylation was primarily associated with the repressive H3K9me3 mark. Our results suggest that the role of DNA methylation as a molecular link between aging and cancer is more complex than previously thought.]]>
Wed, 31 Dec 1969 19:00:00 EST