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Epigenetic modification

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https://www.readbyqxmd.com/read/29792685/vertical-ultrafiltration-facilitated-dna-digestion-for-rapid-and-sensitive-uhplc-ms-ms-detection-of-dna-modifications
#1
Weiyi Lai, Cong Lyu, Hailin Wang
LC-MS/MS technologies provide important and powerful analytical tools for chemical structure-dependent identification and quantification of epigenetically crucial DNA modifications. To perform LC-MS/MS analysis, it is better to convert DNA to 2'-deoxynucleosides through enzymatic digestion. Here, we observed that inorganic cations Na+ and K+ and phosphate buffers, which were often found in various DNA solutions, significantly inhibited DNA digestion as catalyzed by typical set of DNase I, snake venom phosphodiesterase, and calf intestine alkaline phosphatase, leading to poor or varying performance on UHPLC-MS/MS analysis...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29792271/dna-methylation-yields-epigenetic-clues-into-the-diabetic-nephropathy-of-pima-indians
#2
Karol Bomsztyk, Oleg Denisenko, Yuliang Wang
Environmental factors drive epigenetic programming. DNA methylation is the best studied modification transmitting epigenetic information. A study by Qiu et al. examined potential epigenetic roots for the decline of renal function in Pima Indians. A genomewide survey of blood leukocytes uncovered differentially methylated DNA sites in regulatory regions of genes associated with chronic kidney disease. This longitudinal study provides the first clues on epigenetic links between environmental factors and a high prevalence of diabetic kidney disease in Pima Indians...
June 2018: Kidney International
https://www.readbyqxmd.com/read/29792221/sex-differences-in-cardiovascular-epigenetics-a-systematic-review
#3
REVIEW
Robin J G Hartman, Sarah E Huisman, Hester M den Ruijter
BACKGROUND: Differences in cardiovascular diseases are evident in men and women throughout life and are mainly attributed to the presence of sex hormones and chromosomes. Epigenetic mechanisms drive the regulation of the biological processes that may lead to CVD and are possibly influenced by sex. In order to gain an overview of the status quo on sex differences in cardiovascular epigenetics, we performed a systematic review. MATERIALS AND METHODS: A systematic search was performed on PubMed and Embase for studies mentioning cardiovascular disease, epigenetics, and anything related to sex differences...
May 23, 2018: Biology of Sex Differences
https://www.readbyqxmd.com/read/29792069/maternal-nutrition-and-the-developmental-origins-of-osteoporosis-in-offspring-potential-mechanisms-and-clinical-implications
#4
Jia Zheng, Qianyun Feng, Sheng Zheng, Xinhua Xiao
Osteoporosis, the most frequent metabolic disorder of bone, is a complex disease with a multifactorial origin that is influenced by genes and environments. However, the pathogenesis of osteoporosis has not been fully elucidated. The theory of "Developmental Origins of Health and Disease" indicates that early life environment exposure determines the risks of cardiometabolic diseases in adulthood. However, investigations into the effects of maternal nutrition and nutrition exposure during early life on the development of osteoporosis are limited...
January 1, 2018: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/29791073/elevated-histone-h3-acetylation-is-associated-with-genes-involving-in-t-lymphocyte-activation-and-gada-production-in-patients-with-type-1-diabetes
#5
Yanfei Wang, Can Hou, Jonathan Wisler, Kanhaiya Singh, Chao Wu, Zhiguo Xie, Qianjin Lu, Zhiguang Zhou
AIM: Genetic and epigenetic mechanisms have been implicated in the pathogenesis of type 1 diabetes (T1D), and histone acetylation is an epigenetic modification pattern that activates gene transcription. However, the genome-wide histone H3 acetylation in newly onset T1D patients has been less described. Accordingly, we aimed to unveil the genome-wide promoter acetylation profile in CD4+ T lymphocytes from T1D patients, especially for those with glutamate decarboxylase antibody (GADA) positive...
May 23, 2018: Journal of Diabetes Investigation
https://www.readbyqxmd.com/read/29790754/epiprofile-2-0-a-computational-platform-for-processing-epi-proteomics-mass-spectrometry-data
#6
Zuo-Fei Yuan, Simone Sidoli, Dylan M Marchione, Johayra Simithy, Kevin A Janssen, Mary R Szurgot, Benjamin A Garcia
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here, we present EpiProfile 2.0, an extended version of our 2015 software (v1.0) for accurate quantification of histone peptides based on liquid chromatography - tandem mass spectrometry (LC-MS/MS) analysis...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29790249/the-mechanisms-of-epigenetic-inheritance-how-diverse-are-they
#7
Oleg N Tikhodeyev
Although epigenetic inheritance (EI) is a rapidly growing field of modern biology, it still has no clear place in fundamental genetic concepts which are traditionally based on the hereditary role of DNA. Moreover, not all mechanisms of EI attract the same attention, with most studies focused on DNA methylation, histone modification, RNA interference and amyloid prionization, but relatively few considering other mechanisms such as stable inhibition of plastid translation. Herein, we discuss all known and some hypothetical mechanisms that can underlie the stable inheritance of phenotypically distinct hereditary factors that lack differences in DNA sequence...
May 22, 2018: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29789810/rna-from-trained-aplysia-can-induce-an-epigenetic-engram-for-long-term-sensitization-in-untrained-aplysia
#8
Alexis Bédécarrats, Shanping Chen, Kaycey Pearce, Diancai Cai, David L Glanzman
The precise nature of the engram, the physical substrate of memory, remains uncertain. Here, it is reported that RNA extracted from the central nervous system of Aplysia given long-term sensitization (LTS) training induced sensitization when injected into untrained animals; furthermore, the RNA-induced sensitization, like training-induced sensitization, required DNA methylation. In cellular experiments, treatment with RNA extracted from trained animals was found to increase excitability in sensory neurons, but not in motor neurons, dissociated from naïve animals...
May 2018: ENeuro
https://www.readbyqxmd.com/read/29788225/lnchrom-a-resource-of-experimentally-validated-lncrna-chromatin-interactions-in-human-and-mouse
#9
Fulong Yu, Guanxiong Zhang, Aiai Shi, Jing Hu, Feng Li, Xinxin Zhang, Yan Zhang, Jian Huang, Yun Xiao, Xia Li, Shujun Cheng
Long non-coding RNAs (lncRNAs) constitute an important layer of chromatin regulation that contributes to various biological processes and diseases. By interacting with chromatin, many lncRNAs can regulate that state of chromatin by recruiting chromatin-modifying complexes and thus control large-scale gene expression programs. However, the available information on interactions between lncRNAs and chromatin is hidden in a large amount of dispersed literature and has not been extensively collected. We established the LnChrom database, a manually curated resource of experimentally validated lncRNA-chromatin interactions...
January 1, 2018: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29788048/robustness-of-transposable-element-regulation-but-no-genomic-shock-observed-in-interspecific-arabidopsis-hybrids
#10
Ulrike Göbel, Agustin Arce, Fei He, Alain Rico, Gregor Schmitz, Juliette de Meaux
The merging of two divergent genomes in a hybrid is believed to trigger a "genomic shock", disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species...
May 18, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29787577/analysis-of-micrornas-in-familial-mediterranean-fever
#11
Gil Amarilyo, Nir Pillar, Ilan Ben-Zvi, Daphna Weissglas-Volkov, Jonatan Zalcman, Liora Harel, Avi Livneh, Noam Shomron
OBJECTIVES: Although Familial Mediterranean fever (FMF) is categorized as autosomal recessive, frequent exceptions to this model exist and therefore we aimed to search epigenetic modifications in this disease. METHODS: Ten M694V homozygous FMF patients (the most severe phenotype) were recruited for this study. Patients with inflammatory flare were excluded. Total RNA was extracted from peripheral blood, and microRNA expression profiled using NanoString nCounter technology...
2018: PloS One
https://www.readbyqxmd.com/read/29786745/histone-modifications-in-fatty-acid-synthase-modulated-by-carbohydrate-responsive-element-binding-protein-are-associated-with-non%C3%A2-alcoholic-fatty-liver-disease
#12
Can Cai, Huihong Yu, Guangming Huang, Xuan Du, Xiaoqing Yu, Youping Zhou, Wei Shen
Non‑alcoholic fatty liver disease (NAFLD) is a manifestation of metabolic syndrome in the liver and is closely associated with diabetes; however, its pathogenesis remains to be elucidated. Carbohydrate responsive element binding protein (ChREBP), the hub of glucolipid metabolism, regulates the induction of fatty acid synthase (FASN), the key enzyme of de novo lipogenesis, by directly binding to carbohydrate response element (ChoRE) in its promoter. Investigations of histone modifications on NAFLD remain in their infancy...
May 22, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29786685/regulation-of-chromatin-states-and-gene-expression-during-hsn-neuronal-maturation-is-mediated-by-eor-1-plzf-mau-2-cohesin-loader-and-swi-snf-complex
#13
Yoichi Shinkai, Masahiro Kuramochi, Motomichi Doi
Newborn neurons mature by distinct and sequential steps through the timely induction of specific gene expression programs in concert with epigenetic changes. However, it has been difficult to investigate the relationship between gene expression and epigenetic changes at a single-cell resolution during neuronal maturation. In this study, we investigated the maturation of hermaphrodite-specific neurons (HSNs) in C. elegans, which provided the link between chromatin dynamics, gene expression, and the degree of neuronal maturation at a single-cell resolution...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784956/dynamics-and-function-of-dna-methylation-in-plants
#14
REVIEW
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu
DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so-called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions...
May 21, 2018: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29784800/epigenetic-switch-from-repressive-to-permissive-chromatin-in-response-to-cold-stress
#15
Junghoon Park, Chae Jin Lim, Mingzhe Shen, Hee Jin Park, Joon-Yung Cha, Elisa Iniesto, Vicente Rubio, Tesfaye Mengiste, Jian-Kang Zhu, Ray A Bressan, Sang Yeol Lee, Byeong-Ha Lee, Jing Bo Jin, Jose M Pardo, Woe-Yeon Kim, Dae-Jin Yun
Switching from repressed to active status in chromatin regulation is part of the critical responses that plants deploy to survive in an ever-changing environment. We previously reported that HOS15, a WD40-repeat protein, is involved in histone deacetylation and cold tolerance in Arabidopsis However, it remained unknown how HOS15 regulates cold responsive genes to affect cold tolerance. Here, we show that HOS15 interacts with histone deacetylase 2C (HD2C) and both proteins together associate with the promoters of cold-responsive COR genes, COR15A and COR47 Cold induced HD2C degradation is mediated by the CULLIN4 (CUL4)-based E3 ubiquitin ligase complex in which HOS15 acts as a substrate receptor...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784784/uncovering-universal-rules-governing-the-selectivity-of-the-archetypal-dna-glycosylase-tdg
#16
Thomas Dodd, Chunli Yan, Bradley R Kossmann, Kurt Martin, Ivaylo Ivanov
Thymine DNA glycosylase (TDG) is a pivotal enzyme with dual roles in both genome maintenance and epigenetic regulation. TDG is involved in cytosine demethylation at CpG sites in DNA. Here we have used molecular modeling to delineate the lesion search and DNA base interrogation mechanisms of TDG. First, we examined the capacity of TDG to interrogate not only DNA substrates with 5-carboxyl cytosine modifications but also G:T mismatches and nonmismatched (A:T) base pairs using classical and accelerated molecular dynamics...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784032/metabolic-recoding-of-epigenetics-in-cancer
#17
REVIEW
Yi-Ping Wang, Qun-Ying Lei
Dysregulation of metabolism allows tumor cells to generate needed building blocks as well as to modulate epigenetic marks to support cancer initiation and progression. Cancer-induced metabolic changes alter the epigenetic landscape, especially modifications on histones and DNA, thereby promoting malignant transformation, adaptation to inadequate nutrition, and metastasis. Recent advances in cancer metabolism shed light on how aberrations in metabolites and metabolic enzymes modify epigenetic programs. The metabolism-induced recoding of epigenetics in cancer depends strongly on nutrient availability for tumor cells...
May 21, 2018: Cancer communications
https://www.readbyqxmd.com/read/29782530/histone-methylation-changes-are-required-for-life-cycle-progression-in-the-human-parasite-schistosoma-mansoni
#18
David Roquis, Aaron Taudt, Kathrin K Geyer, Gilda Padalino, Karl F Hoffmann, Nancy Holroyd, Matt Berriman, Benoît Aliaga, Cristian Chaparro, Christoph Grunau, Ronaldo de Carvalho Augusto
Epigenetic mechanisms and chromatin structure play an important role in development. Their impact is therefore expected to be strong in parasites with complex life cycles and multiple, strikingly different, developmental stages, i.e. developmental plasticity. Some studies have already described how the chromatin structure, through histone modifications, varies from a developmental stage to another in a few unicellular parasites. However, this, to our knowledge, has never been done before in multicellular metazoan parasites...
May 21, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29780815/endometriosis-malignant-transformation-epigenetics-as-a-probable-mechanism-in-ovarian-tumorigenesis
#19
REVIEW
Jiaxing He, Weiqin Chang, Chunyang Feng, Manhua Cui, Tianmin Xu
Endometriosis, defined as the presence of ectopic endometrial glands and stroma outside the uterine cavity, is a chronic, hormone-dependent gynecologic disease affecting millions of women across the world, with symptoms including chronic pelvic pain, dysmenorrhea, dyspareunia, dysuria, and subfertility. In addition, there is well-established evidence that, although endometriosis is considered benign, it is associated with an increased risk of malignant transformation, with the involvement of various mechanisms of development...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29779941/the-epigenetic-state-of-prdm16-regulated-enhancers-in-radial-glia-controls-cortical-neuron-position
#20
José-Manuel Baizabal, Meeta Mistry, Miguel Turrero García, Nicolás Gómez, Olubusola Olukoya, Diana Tran, Matthew B Johnson, Christopher A Walsh, Corey C Harwell
The epigenetic landscape is dynamically remodeled during neurogenesis. However, it is not understood how chromatin modifications in neural stem cells instruct the formation of complex structures in the brain. We report that the histone methyltransferase PRDM16 is required in radial glia to regulate lineage-autonomous and stage-specific gene expression programs that control number and position of upper layer cortical projection neurons. PRDM16 regulates the epigenetic state of transcriptional enhancers to activate genes involved in intermediate progenitor cell production and repress genes involved in cell migration...
May 15, 2018: Neuron
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