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Epigenetic modification

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https://www.readbyqxmd.com/read/28918065/the-role-of-epigenetics-in-lysosomal-storage-disorders-uncharted-territory
#1
REVIEW
Shahzeb Hassan, Ellen Sidransky, Nahid Tayebi
The study of the contribution of epigenetic mechanisms, including DNA methylation, histone modifications, and microRNAs, to human disease has enhanced our understanding of different cellular processes and diseased states, as well as the effect of environmental factors on phenotypic outcomes. Epigenetic studies may be particularly relevant in evaluating the clinical heterogeneity observed in monogenic disorders. The lysosomal storage disorders are Mendelian disorders characterized by a wide spectrum of associated phenotypes, ranging from neonatal presentations to symptoms that develop in late adulthood...
August 1, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28917501/personalized-translational-epilepsy-research-novel-approaches-and-future-perspectives-part-i-clinical-and-network-analysis-approaches
#2
REVIEW
Felix Rosenow, Natascha van Alphen, Albert Becker, Andreas Chiocchetti, Ralf Deichmann, Thomas Deller, Thomas Freiman, Christine M Freitag, Johannes Gehrig, Anke M Hermsen, Peter Jedlicka, Christian Kell, Karl Martin Klein, Susanne Knake, Dimitri M Kullmann, Stefan Liebner, Braxton A Norwood, Diana Omigie, Karlheinz Plate, Andreas Reif, Philipp S Reif, Yvonne Reiss, Jochen Roeper, Michael W Ronellenfitsch, Stephanie Schorge, Gerhard Schratt, Stephan W Schwarzacher, Joachim P Steinbach, Adam Strzelczyk, Jochen Triesch, Marlies Wagner, Matthew C Walker, Frederic von Wegner, Sebastian Bauer
Despite the availability of more than 15 new "antiepileptic drugs", the proportion of patients with pharmacoresistant epilepsy has remained constant at about 20-30%. Furthermore, no disease-modifying treatments shown to prevent the development of epilepsy following an initial precipitating brain injury or to reverse established epilepsy have been identified to date. This is likely in part due to the polyetiologic nature of epilepsy, which in turn requires personalized medicine approaches. Recent advances in imaging, pathology, genetics and epigenetics have led to new pathophysiological concepts and the identification of monogenic causes of epilepsy...
September 13, 2017: Epilepsy & Behavior: E&B
https://www.readbyqxmd.com/read/28917498/personalized-translational-epilepsy-research-novel-approaches-and-future-perspectives-part-ii-experimental-and-translational-approaches
#3
REVIEW
Sebastian Bauer, Natascha van Alphen, Albert Becker, Andreas Chiocchetti, Ralf Deichmann, Thomas Deller, Thomas Freiman, Christine M Freitag, Johannes Gehrig, Anke M Hermsen, Peter Jedlicka, Christian Kell, Karl Martin Klein, Susanne Knake, Dimitri M Kullmann, Stefan Liebner, Braxton A Norwood, Diana Omigie, Karlheinz Plate, Andreas Reif, Philipp S Reif, Yvonne Reiss, Jochen Roeper, Michael W Ronellenfitsch, Stephanie Schorge, Gerhard Schratt, Stephan W Schwarzacher, Joachim P Steinbach, Adam Strzelczyk, Jochen Triesch, Marlies Wagner, Matthew C Walker, Frederic von Wegner, Felix Rosenow
Despite the availability of more than 15 new "antiepileptic drugs", the proportion of patients with pharmacoresistant epilepsy has remained constant at about 20-30%. Furthermore, no disease-modifying treatments shown to prevent the development of epilepsy following an initial precipitating brain injury or to reverse established epilepsy have been identified to date. This is likely in part due to the polyetiologic nature of epilepsy, which in turn requires personalized medicine approaches. Recent advances in imaging, pathology, genetics, and epigenetics have led to new pathophysiological concepts and the identification of monogenic causes of epilepsy...
September 13, 2017: Epilepsy & Behavior: E&B
https://www.readbyqxmd.com/read/28916632/tissue-sex-and-age-specific-dna-methylation-of-rat-glucocorticoid-receptor-gene-promoter-and-insulin-like-growth-factor-2-imprinting-control-region
#4
Ogechukwu Brenda Agba, Ludwig Lausser, Klaus Huse, Christoph Bergmeier, Niels Jahn, Marco Groth, Martin Bens, Arne Sahm, Maria Gall, Otto W Witte, Hans A Kestler, Matthias Schwab, Matthias Platzer
Tissue-, sex- and age-specific epigenetic modifications such as DNA methylation are largely unknown. Changes in DNA methylation of the glucocorticoid receptor gene (NR3C1) and imprinting control region (ICR) of IGF2 and H19 genes during the lifespan are particularly interesting since these genes are susceptible to epigenetic modifications by prenatal stress or malnutrition. They are important regulators of development and aging. Methylation changes of NR3C1 affect glucocorticoid receptor expression, which is associated with stress sensitivity and stress-related diseases predominantly occurring during aging...
September 15, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28915715/epigenetic-regulation-during-the-differentiation-of-stem-cells-to-germ-cells
#5
REVIEW
Yuan-Chao Sun, Yong-Yong Wang, Wei Ge, Shun-Feng Cheng, Paul W Dyce, Wei Shen
Gametogenesis is an essential process to ensure the transfer of genetic information from one generation to the next. It also provides a mechanism by which genetic evolution can take place. Although the genome of primordial germ cells (PGCs) is exactly the same with somatic cells within an organism, there are significant differences between their developments. For example, PGCs eventually undergo meiosis to become functional haploid gametes, and prior to that they undergo epigenetic imprinting which greatly alter their genetic regulation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915705/promising-landscape-for-regulating-macrophage-polarization-epigenetic-viewpoint
#6
REVIEW
Dexi Zhou, Kui Yang, Lu Chen, Wen Zhang, Zhenyu Xu, Jian Zuo, Hui Jiang, Jiajie Luan
Macrophages are critical myeloid cells with the hallmark of phenotypic heterogeneity and functional plasticity. Macrophages phenotypes are commonly described as classically-activated M1 and alternatively-activated M2 macrophages which play an essential role in the tissues homeostasis and diseases pathogenesis. Alternations of macrophage polarization and function states require precise regulation of target-gene expression. Emerging data demonstrate that epigenetic mechanisms and transcriptional factors are becoming increasingly appreciated in the orchestration of macrophage polarization in response to local environmental signals...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915699/biological-effects-and-epidemiological-consequences-of-arsenic-exposure-and-reagents-that-can-ameliorate-arsenic-damage-in-vivo
#7
REVIEW
Chinthalapally V Rao, Sanya Pal, Altaf Mohammed, Mudassir Farooqui, Mark P Doescher, Adam S Asch, Hiroshi Y Yamada
Through contaminated diet, water, and other forms of environmental exposure, arsenic affects human health. There are many U.S. and worldwide "hot spots" where the arsenic level in public water exceeds the maximum exposure limit. The biological effects of chronic arsenic exposure include generation of reactive oxygen species (ROS), leading to oxidative stress and DNA damage, epigenetic DNA modification, induction of genomic instability, and inflammation and immunomodulation, all of which can initiate carcinogenesis...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915632/decitabine-inhibits-t-cell-proliferation-via-a-novel-tet2-dependent-mechanism-and-exerts-potent-protective-effect-in-mouse-auto-and-allo-immunity-models
#8
Xue Wang, Jun Wang, Yong Yu, Tonghui Ma, Ping Chen, Bing Zhou, Ran Tao
Multiple sclerosis (MS) is an autoimmune disease characterized by the dysregulated immune response including innate and adaptive immune responses. Increasing evidence has proven the importance of epigenetic modification in the progression of MS. Recent studies revealed that low-dose decitabine (Dec, 5-Aza-2'-deoxycytidine), which incorporates into replicating DNA and inhibits DNA methylation, could prevent experimental autoimmune encephalomyelitis (EAE) development by increasing the number of regulatory T cells (Tregs)...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28912274/structure-mechanism-and-regulation-of-polycomb-repressive-complex-2
#9
Lindsay E Moritz, Raymond C Trievel
Polycomb Repressive Complex 2 (PRC2) methylates lysine 27 in histone H3, a modification associated with epigenetic gene silencing. This complex plays a fundamental role in regulating cellular differentiation and development, and PRC2 overexpression and mutations have been implicated in numerous cancers. In this review, we examine recent studies elucidating the first crystal structures of the PRC2 core complex, yielding seminal insights into its catalytic mechanism, substrate specificity, allosteric regulation, and inhibition by a class of small molecules that are currently undergoing cancer clinical trials...
September 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28912063/differential-expression-by-chromatin-modifications-of-alcohol-dehydrogenase-1-of-chorispora-bungeana-in-cold-stress
#10
Lijun Liu, Yuan Song, Jun Xu, Dongming Li, Gaopeng Li, Lizhe An
Epigenetic modifications regulate plant genes to cope with a variety of environmental stresses. Chorispora bungeana is an alpine subnival plant with strong tolerance to multiple abiotic stresses, especially cold stress. In this study, we characterized the alcohol dehydrogenase 1 gene from Chorispora bungeana, CbADH1, that is up-regulated in cold conditions. Overexpression of CbADH1 in Arabidopsis thaliana improved cold tolerance, as indicated by a decreased lethal temperature (LT50). Chromatin immunoprecipitation assays showed that histone H3 is removed from the promoter region and the middle-coding region of the gene...
September 11, 2017: Gene
https://www.readbyqxmd.com/read/28911528/macrophages-in-oxidative-stress-and-models-to-evaluate-the-antioxidant-function-of-dietary-natural-compounds
#11
REVIEW
Omir Adrian Castaneda, Sheng-Chi Lee, Chi-Tang Ho, Tzou-Chi Huang
Antioxidant testing of natural products has attracted increasing interest in recent years, mainly due to the fact that an antioxidant-rich diet might provide health benefits. Activated macrophages are a major source of reactive oxygen species, reactive nitrogen species, and peroxynitrite generated through the so-called respiratory burst. Constitutively released proinflammatory cytokine, especially tumor necrosis factor-α, triggers nuclear factor-κB, and activator protein-1 translocation leading to the over production of reactive oxygen species and reactive nitrogen species in macrophages...
January 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28910789/end-stage-renal-disease-inflammation-and-cardiovascular-outcomes
#12
Lu Dai, Edyta Golembiewska, Bengt Lindholm, Peter Stenvinkel
Despite marked improvements in renal replacement therapy during the last 30 years, the age-adjusted mortality rate in end-stage renal disease (ESRD) patients is still unacceptably high and comparable to that of many malignancies. Cardiovascular disease (CVD) remains the major cause of morbidity and mortality in ESRD patients. However, traditional risk factors can only partially explain the high premature cardiovascular burden in this population. Nontraditional risk factors, including persistent low-grade inflammation, are critical in the pathogenesis of atherosclerosis, vascular calcification, and other causes of CVD and may also contribute to protein-energy wasting and other complications in chronic kidney disease (CKD) patients...
2017: Contributions to Nephrology
https://www.readbyqxmd.com/read/28910574/o-glcnacylation-of-boundary-element-associated-factor-beaf-32-in-drosophila-melanogaster-correlates-with-active-histone-marks-at-the-promoters-of-its-target-genes
#13
Debaditya De, Satish Kallappagoudar, Jae-Min Lim, Rashmi U Pathak, Rakesh K Mishra
Boundary Element-Associated Factor 32 (BEAF 32) is a sequence specific DNA binding protein involved in functioning of chromatin domain boundaries in Drosophila. Several studies also show it to be involved in transcriptional regulation of a large number of genes, many of which are annotated to have cell cycle, development and differentiation related function. Since post-translational modifications (PTMs) of proteins add to their functional capacity, we investigated the PTMs on BEAF 32. The protein is known to be phosphorylated and O-GlcNAcylated...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28910569/hierarchical-recruitment-of-polycomb-complexes-revisited
#14
Eshagh Dorafshan, Tatyana G Kahn, Yuri B Schwartz
Polycomb Group (PcG) proteins epigenetically repress key developmental genes and thereby control alternative cell fates. PcG proteins act as complexes that can modify histones and these histone modifications play a role in transmitting the "memory" of the repressed state as cells divide. Here we consider mainstream models that link histone modifications to hierarchical recruitment of PcG complexes and compare them to results of a direct test of interdependence between PcG complexes for recruitment to Drosophila genes...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28906048/synthesis-of-rna-containing-5-hydroxymethyl-5-formyl-and-5-carboxycytidine
#15
Iacovos N Michaelides, Nobuhiro Tago, Bastien Viverge, Thomas Carell
5-Hydroxymethyl-, 5-formyl-, and 5-carboxycytidine are new epigenetic bases (hmdC, fdC, cadC) that were recently discovered in the DNA of higher eukaryotes. The same bases (hmC, fC and caC) have now also been detected in mammalian RNA with a high abundance in mRNA. While for the DNA bases phosphoramidites (PAs) are available that allow the synthesis of xdC-containing oligonucleotides for deeper biological studies, the corresponding RNA PAs for fC and caC have not yet been disclosed. Here we report novel RNA PAs for hmC, fC and caC that can be used in routine RNA synthesis...
September 14, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28905855/new-insights-into-the-epigenetics-of-inflammatory-rheumatic-diseases
#16
REVIEW
Esteban Ballestar, Tianlu Li
Over the past decade, awareness of the importance of epigenetic alterations in the pathogenesis of rheumatic diseases has grown in parallel with a general recognition of the fundamental role of epigenetics in the regulation of gene expression. Large-scale efforts to generate genome-wide maps of epigenetic modifications in different cell types, as well as in physiological and pathological contexts, illustrate the increasing recognition of the relevance of epigenetics. To date, although several reports have demonstrated the occurrence of epigenetic alterations in a wide range of inflammatory rheumatic conditions, epigenomic information is rarely used in a clinical setting...
September 14, 2017: Nature Reviews. Rheumatology
https://www.readbyqxmd.com/read/28904641/histone-code-and-long-non-coding-rnas-lncrnas-aberrations-in-lung-cancer-implications-in-the-therapy-response
#17
REVIEW
Abril Marcela Herrera-Solorio, Leonel Armas-López, Oscar Arrieta, Joaquín Zúñiga, Patricia Piña-Sánchez, Federico Ávila-Moreno
Respiratory diseases hold several genome, epigenome, and transcriptional aberrations as a cause of the accumulated damage promoted by, among others, environmental risk factors. Such aberrations can also come about as an adaptive response when faced with therapeutic oncological drugs. In epigenetic terms, aberrations in DNA methylation patterns, histone code marks balance, and/or chromatin-remodeling complexes recruitment, among Polycomb Repressive Complex-2 (PRC2) versus Trithorax (TRX) Activator Complex, have been proposed to be affected by several previously characterized functional long non-coding RNAs (lncRNAs)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28903900/genetics-association-study-and-functional-analysis-on-osteoporosis-susceptibility-gene-bdnf
#18
Man Yang, Bing-Jie Lu, Yuan-Yuan Duan, Xiao-Feng Chen, Jian-Gang Ma, Yan Guo
To explore the relationship between brain-derived neurotrophic factor (BDNF) gene and bone mineral density (BMD) in Chinese Han population, we performed association analysis of 14 tag SNPs on BDNF gene with hip/spine BMD in 1300 Han Chinese samples from Shaanxi Province. We found that 8 of the 14 SNPs were significantly associated with hip or spine BMD (P < 0.05). Moreover, the SNP rs16917237 was significantly associated with both hip and spine BMD, with significant Bonferroni correlation (P value 0.05/14 = 0...
August 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28903624/repair-of-calvarial-bone-defect-using-jarid1a-knockdown-bone-mesenchymal-stem-cells-in-rats
#19
Yuan Deng, Tao Guo, Jipeng Li, Li Guo, Ping Gu, Xianqun Fan
Histone methylation is regarded as an important epigenetic event during stem cell differentiation. Jumonji AT-rich interactive domain 1A (Jarid1a) is a histone demethylase that specifically catalyzes demethylation of dimethyl or trimethyl histone H3K4me3, which is normally associated with transcriptionally active genes. Runt-related transcription factor 2 (Runx2) has been identified as a key transcription factor in the early stage of osteogenesis. A better understanding of this epigenetic mechanism that governs osteogenic differentiation of bone mesenchymal stem cells (BMSCs) can provide new insights into BMSCs based bone tissue engineering...
September 13, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28903418/histone-modification-alteration-coordinated-with-acquisition-of-promoter-dna-methylation-during-epstein-barr-virus-infection
#20
Sayaka Funata, Keisuke Matsusaka, Ryota Yamanaka, Shogo Yamamoto, Atsushi Okabe, Masaki Fukuyo, Hiroyuki Aburatani, Masashi Fukayama, Atsushi Kaneda
Aberrant DNA hypermethylation is a major epigenetic mechanism to inactivate tumor suppressor genes in cancer. Epstein-Barr virus positive gastric cancer is the most frequently hypermethylated tumor among human malignancies. Herein, we performed comprehensive analysis of epigenomic alteration during EBV infection, by Infinium HumanMethylation 450K BeadChip for DNA methylation and ChIP-sequencing for histone modification alteration during EBV infection into gastric cancer cell line MKN7. Among 7,775 genes with increased DNA methylation in promoter regions, roughly half were "DNA methylation-sensitive" genes, which acquired DNA methylation in the whole promoter regions and thus were repressed...
August 15, 2017: Oncotarget
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