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https://www.readbyqxmd.com/read/28651214/dna-methylation-and-the-preservation-of-cell-identity
#1
REVIEW
Ozren Bogdanović, Ryan Lister
DNA methylation is a major epigenetic modification of vertebrate genomes that is mostly associated with transcriptional repression. During embryogenesis, DNA methylation together with other epigenetic factors plays an essential role in selecting and maintaining cell identity. Recent technological advances are now allowing for the exploration of this mark at unprecedented resolution. This has resulted in a wealth of studies describing the developmental roles of DNA methylation in various vertebrate model systems...
June 23, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28651171/the-relevance-of-inter-and-intrastrain-differences-in-mice-and-rats-and-their-implications-for-models-of-seizures-and-epilepsy
#2
REVIEW
Wolfgang Löscher, Russell J Ferland, Thomas N Ferraro
It is becoming increasingly clear that the genetic background of mice and rats, even in inbred strains, can have a profound influence on measures of seizure susceptibility and epilepsy. These differences can be capitalized upon through genetic mapping studies to reveal genes important for seizures and epilepsy. However, strain background and particularly mixed genetic backgrounds of transgenic animals need careful consideration in both the selection of strains and in the interpretation of results and conclusions...
June 23, 2017: Epilepsy & Behavior: E&B
https://www.readbyqxmd.com/read/28651105/heterogeneous-epigenetic-regulation-of-hace1-in-burkitt-lymphoma-derived-cells
#3
Abdelilah Bouzelfen, Hafid Kora, Marion Alcantara, Philippe Bertrand, Jean-Baptiste Latouche, Fabrice Jardin
We examined the consequences of 3-deazaneplanocin A (DZNep) on HACE1 expression in human Burkitt- Lymphoma-derived cells to investigate fundamental molecular mechanisms that control its expression. We treated the human Burkitt- Lymphoma-derived cells lines Ramos and Raji with DZNep and examined HACE1 mRNA expression by RT-PCR. We also studied the effect of DZNep on the methylation of lysine 9 and 27 of histone 3 (H3K27me3 and H3K9me2) associated with the CpG88 and CpG177 islands of the HACE1 promoters by chromatin immunoprecipitation and quantitative PCR...
June 16, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28651088/genetic-and-epigenetic-alterations-in-normal-and-sensitive-copd-diseased-human-bronchial-epithelial-cells-repeatedly-exposed-to-air-pollution-derived-pm2-5
#4
B Leclercq, A Platel, S Antherieu, L Y Alleman, E M Hardy, E Perdrix, N Grova, V Riffault, B M Appenzeller, M Happillon, F Nesslany, P Coddeville, J-M Lo-Guidice, G Garçon
Even though clinical, epidemiological and toxicological studies have progressively provided a better knowledge of the underlying mechanisms by which air pollution-derived particulate matter (PM) exerts its harmful health effects, further in vitro studies on relevant cell systems are still needed. Hence, aiming of getting closer to the human in vivo conditions, primary human bronchial epithelial cells derived from normal subjects (NHBE) or sensitive chronic obstructive pulmonary disease (COPD)-diseased patients (DHBE) were differentiated at the air-liquid interface...
June 23, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28650965/epigenetic-adaptation-of-the-placental-serotonin-transporter-gene-slc6a4-to-gestational-diabetes-mellitus
#5
Sofia Blazevic, Marina Horvaticek, Maja Kesic, Peter Zill, Dubravka Hranilovic, Marina Ivanisevic, Gernot Desoye, Jasminka Stefulj
We tested the hypothesis that gestational diabetes mellitus (GDM) alters the DNA methylation pattern of the fetal serotonin transporter gene (SLC6A4), and examined the functional relevance of DNA methylation for regulation of the SLC6A4 expression in the human placenta. The study included 50 mother-infant pairs. Eighteen mothers were diagnosed with GDM and 32 had normal glucose tolerance (NGT). All neonates were of normal birth weight and born at term by planned Cesarean section. DNA and RNA were isolated from samples of tissue collected from the fetal side of the placenta immediately after delivery...
2017: PloS One
https://www.readbyqxmd.com/read/28650731/combination-treatments-with-luteolin-and-fisetin-enhance-anti-inflammatory-effects-in-high-glucose-treated-thp-1-cells-through-histone-acetyltransferase-histone-deacetylase-regulation
#6
Arang Kim, Jung-Mi Yun
Hyperglycemia leads to diabetes and its diabetic complications. In this study, we investigated the synergistic effects of luteolin and fisetin on proinflammatory cytokine secretion and its underlying epigenetic regulation in human monocytes exposed to hyperglycemic (HG) concentrations. Human monocytic cells (THP-1) were cultured under controlled (14.5 mM mannitol), normoglycemic (5.5 mM glucose), or HG (20 mM glucose) conditions in the absence or presence of the two phytochemicals for 48 h. Whereas HG conditions significantly induced histone acetylation, nuclear factor-kappa B (NF-κB) activation, interleukin 6, and tumor necrosis factor-α release from THP-1 cells; combination treatments with the two phytochemicals (500 nM fisetin, and l μM and 500 nM luteolin) suppressed NF-κB activity and inflammatory cytokine release...
June 26, 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28650485/neuroblastoma-is-composed-of-two-super-enhancer-associated-differentiation-states
#7
Tim van Groningen, Jan Koster, Linda J Valentijn, Danny A Zwijnenburg, Nurdan Akogul, Nancy E Hasselt, Marloes Broekmans, Franciska Haneveld, Natalia E Nowakowska, Johannes Bras, Carel J M van Noesel, Aldo Jongejan, Antoine H van Kampen, Linda Koster, Frank Baas, Lianne van Dijk-Kerkhoven, Margriet Huizer-Smit, Maria C Lecca, Alvin Chan, Arjan Lakeman, Piet Molenaar, Richard Volckmann, Ellen M Westerhout, Mohamed Hamdi, Peter G van Sluis, Marli E Ebus, Jan J Molenaar, Godelieve A Tytgat, Bart A Westerman, Johan van Nes, Rogier Versteeg
Neuroblastoma and other pediatric tumors show a paucity of gene mutations, which has sparked an interest in their epigenetic regulation. Several tumor types include phenotypically divergent cells, resembling cells from different lineage development stages. It has been proposed that super-enhancer-associated transcription factor (TF) networks underlie lineage identity, but the role of these enhancers in intratumoral heterogeneity is unknown. Here we show that most neuroblastomas include two types of tumor cells with divergent gene expression profiles...
June 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28650470/signaling-coupled-epigenomic-regulation-of-gene-expression
#8
REVIEW
R Kumar, S Deivendran, T R Santhoshkumar, M R Pillai
Inheritance of genomic information independent of the DNA sequence, the epigenetics, as well as gene transcription are profoundly shaped by serine/threonine and tyrosine signaling kinases and components of the chromatin remodeling complexes. To precisely respond to a changing external milieu, human cells efficiently translate upstream signals into post-translational modifications (PTMs) on histones and coregulators such as corepressors, coactivators, DNA-binding factors and PTM modifying enzymes. Because a protein with multiple residues for putative PTMs is expected to undergo more than one PTM in cells stimulated with growth factors, the outcome of combinational PTM codes on histones and coregulators is profoundly shaped by regulatory interplays between PTMs...
June 26, 2017: Oncogene
https://www.readbyqxmd.com/read/28650429/acetate-mediated-novel-survival-strategy-against-drought-in-plants
#9
Jong-Myong Kim, Taiko Kim To, Akihiro Matsui, Keitaro Tanoi, Natsuko I Kobayashi, Fumio Matsuda, Yoshiki Habu, Daisuke Ogawa, Takuya Sakamoto, Sachihiro Matsunaga, Khurram Bashir, Sultana Rasheed, Marina Ando, Hiroko Takeda, Kanako Kawaura, Miyako Kusano, Atsushi Fukushima, Takaho A Endo, Takashi Kuromori, Junko Ishida, Taeko Morosawa, Maho Tanaka, Chieko Torii, Yumiko Takebayashi, Hitoshi Sakakibara, Yasunari Ogihara, Kazuki Saito, Kazuo Shinozaki, Alessandra Devoto, Motoaki Seki
Water deficit caused by global climate changes seriously endangers the survival of organisms and crop productivity, and increases environmental deterioration(1,2). Plants' resistance to drought involves global reprogramming of transcription, cellular metabolism, hormone signalling and chromatin modification(3-8). However, how these regulatory responses are coordinated via the various pathways, and the underlying mechanisms, are largely unknown. Herein, we report an essential drought-responsive network in which plants trigger a dynamic metabolic flux conversion from glycolysis into acetate synthesis to stimulate the jasmonate (JA) signalling pathway to confer drought tolerance...
June 26, 2017: Nature Plants
https://www.readbyqxmd.com/read/28649883/middle-down-proteomics-a-still-unexploited-resource-for-chromatin-biology
#10
Simone Sidoli, Benjamin A Garcia
Introduction Analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has become a fundamental tool for the characterization of chromatin composition and dynamics. Histone PTMs benchmark several biological states of chromatin, including regions of active enhancers, active/repressed gene promoters and damaged DNA. These complex regulatory mechanisms are often defined by combinatorial histone PTMs; for instance, active enhancers are commonly occupied by both marks H3K4me1 and H3K27ac...
June 26, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28649671/early-life-stress-mood-and-anxiety-disorders
#11
Shariful A Syed, Charles B Nemeroff
Early life stress has been shown to exert profound short- and long-term effects on human physiology both in the central nervous system and peripherally. Early life stress has demonstrated clear association with many psychiatric disorders including major depression, posttraumatic stress disorder, and bipolar disorder. The Diagnostic and Statistics Manuel of Mental Disorders (DSM) diagnostic categorical system has served as a necessary framework for clinical service, delivery, and research, however has not been completely matching the neurobiological research perspective...
February 2017: Chronic stress
https://www.readbyqxmd.com/read/28649654/cell-state-plasticity-stem-cells-emt-and-the-generation-of-intra-tumoral-heterogeneity
#12
Geoffrey M Wahl, Benjamin T Spike
Cellular heterogeneity in cancer represents a significant challenge. In order to develop effective and lasting therapies, it is essential to understand the source of this heterogeneity, and its role in tumor progression and therapy resistance. Here, we consider not only genetic and epigenetic mechanisms, but also inflammation and cell state reprogramming in creating tumor heterogeneity. We discuss similarities between normal mammary epithelial developmental states and various breast cancer molecular sub-types, and the cells that are thought to propagate them...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28649606/elevated-5hmc-levels-characterize-dna-of-the-cerebellum-in-parkinson-s-disease
#13
Reinhard Stöger, Paula J Scaife, Freya Shephard, Lisa Chakrabarti
5-methylcytosine and the oxidation product 5-hydroxymethylcytosine are two prominent epigenetic variants of the cytosine base in nuclear DNA of mammalian brains. We measured levels of 5-methylcytosine and 5-hydroxymethylcytosine by enzyme-linked immunosorbent assay in DNA from post-mortem cerebella of individuals with Parkinson's disease and age-matched controls. 5-methylcytosine levels showed no significant differences between Parkinson's disease and control DNA sample sets. In contrast, median 5-hydroxymethylcytosine levels were almost twice as high (p < 0...
2017: NPJ Parkinson's Disease
https://www.readbyqxmd.com/read/28649363/genetic-and-epigenetic-control-of-gene-expression-by-crispr-cas-systems
#14
REVIEW
Albert Lo, Lei Qi
The discovery and adaption of bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems has revolutionized the way researchers edit genomes. Engineering of catalytically inactivated Cas variants (nuclease-deficient or nuclease-deactivated [dCas]) combined with transcriptional repressors, activators, or epigenetic modifiers enable sequence-specific regulation of gene expression and chromatin state. These CRISPR-Cas-based technologies have contributed to the rapid development of disease models and functional genomics screening approaches, which can facilitate genetic target identification and drug discovery...
2017: F1000Research
https://www.readbyqxmd.com/read/28649287/regulating-role-of-fetal-thyroid-hormones-on-placental-mitochondrial-dna-methylation-epidemiological-evidence-from-the-environage-birth-cohort-study
#15
Bram G Janssen, Hyang-Min Byun, Harry A Roels, Wilfried Gyselaers, Joris Penders, Andrea A Baccarelli, Tim S Nawrot
BACKGROUND: Fetal development largely depends on thyroid hormone availability and proper placental function with an important role played by placental mitochondria. The biological mechanisms by which thyroid hormones exert their effects on mitochondrial function are not well understood. We investigated the role of fetal thyroid hormones on placental mitochondrial DNA (mtDNA) content and mtDNA methylation. We collected placental tissue and cord blood from 305 mother-child pairs that were enrolled between February 2010 and June 2014 in the ENVIRONAGE (ENVIRonmental influence ON early AGEing) birth cohort (province of Limburg, Belgium)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28649192/deleterious-effects-of-chronic-folate-deficiency-in-the-ts65dn-mouse-model-of-down-syndrome
#16
Susan Helm, Morgan Blayney, Taylor Whited, Mahjabin Noroozi, Sen Lin, Semira Kern, David Green, Ahmad Salehi
Folate is an important B vitamin naturally found in the human diet and plays a critical role in methylation of nucleic acids. Indeed, abnormalities in this major epigenetic mechanism play a pivotal role in the pathogenesis of cognitive deficit and intellectual disability in humans. The most common cause of cognitive dysfunction in children is Down syndrome (DS). Since folate deficiency is very common among the pediatric population, we questioned whether chronic folate deficiency (CFD) exacerbates cognitive dysfunction in a mouse model of DS...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28649134/cancer-epigenetics-therapy-induced-transcription-is-cryptically-widespread
#17
Darren J Burgess
No abstract text is available yet for this article.
June 26, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28648961/uterine-fluid-in-pregnancy-a-biological-and-clinical-outlook
#18
REVIEW
Ying Zhang, Qiang Wang, Hongmei Wang, Enkui Duan
Once considered a simple medium for sperm and embryo transport, the functional spectrum of uterine fluid is now expanding. Novel molecular players, such as extracellular vesicles and mobile RNAs, have been detected in the uterine fluid of livestock, rodents, and humans. These novel molecules, together with previously known ions and proteins, ensure uterine fluid homeostasis and facilitate embryo-maternal interactions. Here, we propose that these molecules may also carry information that mirrors maternal environmental exposure and possibly relay such information to the embryo via uterine fluid, generating long-term epigenetic effects on the offspring via embryonic and placental programming...
May 25, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28648900/tet-catalyzed-5-hydroxymethylation-precedes-hnf4a-promoter-choice-during-differentiation-of-bipotent-liver-progenitors
#19
Pierre-Benoit Ancey, Szilvia Ecsedi, Marie-Pierre Lambert, Fazlur Rahman Talukdar, Marie-Pierre Cros, Denise Glaise, Diana Maria Narvaez, Veronique Chauvet, Zdenko Herceg, Anne Corlu, Hector Hernandez-Vargas
Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity...
June 19, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28648898/genome-wide-single-cell-dna-methylomics-reveals-increased-non-cpg-methylation-during-human-oocyte-maturation
#20
Bo Yu, Xiao Dong, Silvia Gravina, Önder Kartal, Timothy Schimmel, Jacques Cohen, Drew Tortoriello, Raifa Zody, R David Hawkins, Jan Vijg
The establishment of DNA methylation patterns in oocytes is a highly dynamic process marking gene-regulatory events during fertilization, embryonic development, and adulthood. However, after epigenetic reprogramming in primordial germ cells, how and when DNA methylation is re-established in developing human oocytes remains to be characterized. Here, using single-cell whole-genome bisulfite sequencing, we describe DNA methylation patterns in three different maturation stages of human oocytes. We found that while broad-scale patterns of CpG methylation have been largely established by the immature germinal vesicle stage, localized changes continue into later development...
June 19, 2017: Stem Cell Reports
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