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https://www.readbyqxmd.com/read/29161537/association-of-h3k79-monomethylation-an-epigenetic-signature-with-arsenic-induced-skin-lesions
#1
Pritha Bhattacharjee, Somnath Paul, Sandip Bhattacharjee, Ashok K Giri, Pritha Bhattacharjee
Arsenic, a non mutagenic carcinogen, poses a profound health risk upon prolonged exposure. The objective of the study was to analyze the post-translational modifications of the major histone H3 and the associated molecular crosstalk to identify the epigenetic signature of arsenic susceptibility. Herein, we identified significant upregulation of H3K79me1, in individuals with arsenic-induced skin lesion (WSL), and H3K79me1 was found to be regulated by the upstream methyltransferase DOT1L. Moreover, the downstream target molecule 53BP1, a tumor suppressor protein that has a docking preference for H3K79me1 at a site of a double-strand break (DSB), was downregulated, indicating greater DNA damage in the WSL group...
November 14, 2017: Mutation Research
https://www.readbyqxmd.com/read/29161430/methbank-3-0-a-database-of-dna-methylomes-across-a-variety-of-species
#2
Rujiao Li, Fang Liang, Mengwei Li, Dong Zou, Shixiang Sun, Yongbing Zhao, Wenming Zhao, Yiming Bao, Jingfa Xiao, Zhang Zhang
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multiple species and equipping with more enhanced functionalities for data annotation and more friendly web interfaces for data presentation, search and visualization. MethBank 3.0 features large-scale integration of high-quality methylomes, involving 34 consensus reference methylomes derived from a large number of human samples, 336 single-base resolution methylomes from different developmental stages and/or tissues of five plants, and 18 single-base resolution methylomes from gametes and early embryos at multiple stages of two animals...
November 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29161428/arabidopsis-inositol-polyphosphate-multikinase-delays-flowering-time-through-mediating-transcriptional-activation-of-flowering-locus-c
#3
Sihong Sang, Yao Chen, Qiaofeng Yang, Peng Wang
Timely flowering is critical for successful reproduction and seed yield in plants. A diverse range of regulators have been found to control flowering time in response to environmental and endogenous signals. Among these regulators, FLOWERING LOCUS C (FLC) acts as a central repressor of floral transition by blocking the expression of flowering integrator genes. Here, we report that Arabidopsis inositol polyphosphate multikinase (AtIPK2β) functions in flowering time control by mediating transcriptional regulation of FLC at the chromatin level...
November 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29161414/structural-diversity-of-the-nucleosome
#4
Masako Koyama, Hitoshi Kurumizaka
In eukaryotes, genomic DNA is compacted in chromatin, which generally suppresses transcription, replication, repair, and recombination. The fundamental unit of chromatin is the nucleosome, whose structure was first determined at atomic resolution in 1997. However, recent findings have revealed that the nucleosome is not a structurally homogenous entity. Nucleosomes containing histone variants often have subtle but clear differences in their structural and functional characteristics, as compared to the canonical nucleosome...
November 17, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29161273/enrichment-of-colorectal-cancer-associations-in-functional-regions-insight-for-using-epigenomics-data-in-the-analysis-of-whole-genome-sequence-imputed-gwas-data
#5
Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stéphane Bézieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister, Christian Fuchsberger, Mark A Jenkins, Suzanne M Leal, Mathieu Lemire, Polly A Newcomb, Steven Gallinger, John D Potter, Robert E Schoen, Martha L Slattery, Joshua D Smith, Loic Le Marchand, Emily White, Brent W Zanke, Goncalo R Abeçasis, Christopher S Carlson, Ulrike Peters, Deborah A Nickerson, Anshul Kundaje, Li Hsu
BACKGROUND: The evaluation of less frequent genetic variants and their effect on complex disease pose new challenges for genomic research. To investigate whether epigenetic data can be used to inform aggregate rare-variant association methods (RVAM), we assessed whether variants more significantly associated with colorectal cancer (CRC) were preferentially located in non-coding regulatory regions, and whether enrichment was specific to colorectal tissues. METHODS: Active regulatory elements (ARE) were mapped using data from 127 tissues and cell-types from NIH Roadmap Epigenomics and Encyclopedia of DNA Elements (ENCODE) projects...
2017: PloS One
https://www.readbyqxmd.com/read/29161231/epigenetic-regulation-mechanisms-of-microrna-expression
#6
Sara Morales, Mariano Monzo, Alfons Navarro
MicroRNAs (miRNAs) are single-stranded RNAs of 18-25 nucleotides that regulate gene expression at the post-transcriptional level. They are involved in many physiological and pathological processes, including cell proliferation, apoptosis, development and carcinogenesis. Because of the central role of miRNAs in the regulation of gene expression, their expression needs to be tightly controlled. Here, we summarize the different mechanisms of epigenetic regulation of miRNAs, with a particular focus on DNA methylation and histone modification...
November 21, 2017: Biomolecular Concepts
https://www.readbyqxmd.com/read/29161229/sex-and-dose-specific-effects-of-maternal-bisphenol-a-exposure-on-pancreatic-islets-of-first-and-second-generation-adult-mice-offspring
#7
Amita Bansal, Cetewayo Rashid, Frances Xin, Changhong Li, Erzsebet Polyak, Anna Duemler, Tom van der Meer, Martha Stefaniak, Sana Wajid, Nicolai Doliba, Marisa S Bartolomei, Rebecca A Simmons
BACKGROUND: Exposure to the environmental endocrine disruptor bisphenol A (BPA) is ubiquitous and associated with the increased risk of diabetes and obesity. However, the underlying mechanisms remain unknown. We recently demonstrated that perinatal BPA exposure is associated with higher body fat, impaired glucose tolerance, and reduced insulin secretion in first- (F1) and second-generation (F2) C57BL/6J male mice offspring. OBJECTIVE: We sought to determine the multigenerational effects of maternal bisphenol A exposure on mouse pancreatic islets...
September 27, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/29161028/exploring-the-active-centre-of-lsd1-corest-complex-by-molecular-dynamics-simulation-utilizing-its-co-crystallized-cofactor-tetrahydrofolate-as-a-probe
#8
Waleed A A Zalloum, Hiba M Zalloum
Epigenetic targeting of cancer is a recent era to manipulate the gene without destroying the genetic material. Lysine-specific demethylase 1 (LSD1) is one of the enzymes associated with the chromatin for post-translational modifications, where it demethylates lysine amino acid in the chromatin H3 tail. Many studies showed that inhibiting LSD1 could potentially be used to treat cancer epigenetically. LSD1 is associated with its corepressor protein CoREST, and uses tetrahydrofolate as a cofactor to accept CH2 from the demethylation process...
November 21, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29160764/dna-methylation-profile-in-chronic-myelomonocytic-leukemia-associates-with-distinct-clinical-biological-and-genetic-features
#9
Laura Palomo, Roberto Malinverni, Marta Cabezón, Blanca Xicoy, Montserrat Arnan, Rosa Coll, Helena Pomares, Olga García, Francisco Fuster-Tormo, Javier Grau, Evarist Feliu, Francesc Solé, Marcus Buschbeck, Lurdes Zamora
Chromosomal abnormalities are detected in 20-30% of patients with chronic myelomonocytic leukemia (CMML) and correlate with prognosis. On the mutation level, disruptive alterations are particularly frequent in chromatin regulatory genes. However, little is known about the consequential alterations in the epigenetic marking of the genome. Here, we report the analysis of genomic DNA methylation patterns of 64 CMML patients and 10 healthy controls, using a DNA methylation microarray focused on promoter regions...
November 21, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29160738/h4k20me2-distinguishes-pre-replicative-from-post-replicative-chromatin-to-appropriately-direct-dna-repair-pathway-choice-by-53bp1-rif1-mad2l2
#10
Marco Simonetta, Inge de Krijger, Judit Serrat, Nathalie Moatti, Diogo Fortunato, Liesbeth Hoekman, Onno B Bleijerveld, A F Maarten Altelaar, Jacqueline J L Jacobs
The main pathways for the repair of DNA double strand breaks (DSBs) are non-homologous end-joining (NHEJ) and homologous recombination directed repair (HDR). These operate mutually exclusive and are activated by 53BP1 and BRCA1, respectively. As HDR can only succeed in the presence of an intact copy of replicated DNA, cells employ several mechanisms to inactivate HDR in the G1 phase of cell cycle. As cells enter S-phase, these inhibitory mechanisms are released and HDR becomes active. However, during DNA replication, NHEJ and HDR pathways are both functional and non-replicated and replicated DNA regions co-exist, with the risk of aberrant HDR activity at DSBs in non-replicated DNA...
November 21, 2017: Cell Cycle
https://www.readbyqxmd.com/read/29160620/dna-methylation-of-mb-comt-in-malaysian-schizophrenia-patients
#11
Abd Rahim Nour El Huda, Ku Zaifah Norsidah, Rahim Mohd Nabil Fikri, Mohd Noor Hanisah, Abdullah Kartini, A Talib Norlelawati
AIM: This study examined catechol-O-methyltransferase (COMT) DNA methylation in the peripheral blood of schizophrenia patients and also in healthy controls to investigate its potential use as a peripheral biomarker of schizophrenia and its relationships with the clinical variables of schizophrenia patients. METHODS: We examined the DNA methylation levels of COMT using genomic DNA from the peripheral blood of schizophrenia patients (n = 138) and healthy control participants (n = 132); all were Malaysian Malays...
November 21, 2017: Psychiatry and Clinical Neurosciences
https://www.readbyqxmd.com/read/29160179/the-miage-calculator-a-dna-methylation-based-mitotic-age-calculator-of-human-tissue-types
#12
Ahrim Youn, Shuang Wang
Cell division is important in human aging and cancer. To estimate the number of cell divisions (mitotic age) of a given tissue type between individuals is of great interest as that not only allows to study biological aging using a new molecular aging target but also allows the stratification of prospective cancer risk. Here we introduce the MiAge Calculator, a mitotic age calculator based on a novel statistical framework, the MiAge model. MiAge is designed to quantitatively estimate mitotic age (total number of lifetime cell divisions) of a tissue using the stochastic replication errors accumulated in the epigenetic inheritance process during cell divisions...
November 21, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29160132/active-h3k27me3-demethylation-by-kdm6b-is-required-for-normal-development-of-bovine-preimplantation-embryos
#13
Nhi Chung, Yanina S Bogliotti, Wei Ding, Marcela Vilarino, Kazuki Takahashi, James L Chitwood, Richard M Schultz, Pablo J Ross
The substantial epigenetic remodeling that occurs during early stages of mammalian embryonic development likely contributes to reprogramming the parental genomes from a differentiated to a totipotent state and activation of the embryonic genome. Trimethylation of lysine 27 of histone 3 (H3K27me3) is a repressive mark that undergoes global dynamic changes during preimplantation development of several species. To ascertain the role of H3K27me3 in bovine preimplantation development we perturbed the activity of KDM6B, which demethylates H3K27me3...
November 21, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29160110/peroxiredoxin6-a-multitask-antioxidant-enzyme-involved-in-the-pathophysiology-of-chronic-non-communicable-diseases
#14
Francesca Pacifici, David Della-Morte, Barbara Capuani, Donatella Pastore, Alfonso Bellia, Paolo Sbraccia, Nicola Di Daniele, Renato Lauro, Davide Lauro
SIGNIFICANCE: Chronic Non-Communicable Diseases (NCDs) are the leading causes of disability and death worldwide. NCDs mainly comprise diabetes mellitus, cardiovascular diseases, chronic obstructive pulmonary disease (COPD), cancer, and neurological degenerative diseases, which kill more than 80% of population, especially elderlies, worldwide. Recent Advances: Several recent theories established NCDs as multifactorial diseases, where a combination of genetic, epigenetic and environmental factors contributes to their pathogenesis...
November 21, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29159718/genetics-and-epigenetics-in-the-pathogenesis-of-primary-biliary-cholangitis
#15
REVIEW
Satoru Joshita, Takeji Umemura, Eiji Tanaka, Masao Ota
Primary biliary cholangitis (PBC) is a chronic, slowly progressive cholestatic autoimmune liver disease predominantly afflicting women. PBC is characterized by the presence of disease-specific antimitochondrial antibodies and the histological destruction of intrahepatic bile ducts, which eventually lead to cirrhosis and hepatic failure. Fortunately, ursodeoxycholic acid therapy has improved the outcome of the vast majority of PBC cases. Although the etiology of PBC has not yet been elucidated, human leukocyte antigen (HLA) class II alleles have been consistently associated with disease onset for decades...
November 20, 2017: Clinical Journal of Gastroenterology
https://www.readbyqxmd.com/read/29159566/editorial-epigenetic-regulation-of-plant-development-and-stress-responses
#16
EDITORIAL
Tarek Hewezi
No abstract text is available yet for this article.
November 20, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29159506/a-longitudinal-study-of-dna-methylation-as-a-potential-mediator-of-age-related-diabetes-risk
#17
Crystal D Grant, Nadereh Jafari, Lifang Hou, Yun Li, James D Stewart, Guosheng Zhang, Archana Lamichhane, JoAnn E Manson, Andrea A Baccarelli, Eric A Whitsel, Karen N Conneely
DNA methylation (DNAm) has been found to show robust and widespread age-related changes across the genome. DNAm profiles from whole blood can be used to predict human aging rates with great accuracy. We sought to test whether DNAm-based predictions of age are related to phenotypes associated with type 2 diabetes (T2D), with the goal of identifying risk factors potentially mediated by DNAm. Our participants were 43 women enrolled in the Women's Health Initiative. We obtained methylation data via the Illumina 450K Methylation array on whole blood samples from participants at three timepoints, covering on average 16 years per participant...
November 20, 2017: GeroScience
https://www.readbyqxmd.com/read/29159499/redistribution-of-cell-cycle-by-arsenic-trioxide-is-associated-with-demethylation-and-expression-changes-of-cell-cycle-related-genes-in-acute-promyelocytic-leukemia-cell-line-nb4
#18
Saeed Hassani, Ali Khaleghian, Shahin Ahmadian, Shaban Alizadeh, Kamran Alimoghaddam, Ardeshir Ghavamzadeh, Seyed H Ghaffari
PML-RARα perturbs the normal epigenetic setting, which is essential to oncogenic transformation in acute promyelocytic leukemia (APL). Transcription induction and recruitment of DNA methyltransferases (DNMTs) by PML-RARα and subsequent hypermethylation are components of this perturbation. Arsenic trioxide (ATO), an important drug in APL therapy, concurrent with degradation of PML-RARα induces cell cycle change and apoptosis. How ATO causes cell cycle alteration has remained largely unexplained. Here, we investigated DNA methylation patterns of cell cycle regulatory genes promoters, the effects of ATO on the methylated genes and cell cycle distribution in an APL cell line, NB4...
November 20, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/29159407/association-of-salivary-microrna-changes-with-prolonged-concussion-symptoms
#19
Jeremiah J Johnson, Andrea C Loeffert, Jennifer Stokes, Robert P Olympia, Harry Bramley, Steven D Hicks
Importance: Approximately one-third of children who experience a concussion develop prolonged concussion symptoms. To our knowledge, there are currently no objective or easily administered tests for predicting prolonged concussion symptoms. Several studies have identified alterations in epigenetic molecules known as microRNAs (miRNAs) following traumatic brain injury. No studies have examined whether miRNA expression can detect prolonged concussion symptoms. Objective: To evaluate the efficacy of salivary miRNAs for identifying children with concussion who are at risk for prolonged symptoms...
November 20, 2017: JAMA Pediatrics
https://www.readbyqxmd.com/read/29159284/measuring-quantitative-effects-of-methylation-on-transcription-factor-dna-binding-affinity
#20
Zheng Zuo, Basab Roy, Yiming Kenny Chang, David Granas, Gary D Stormo
Methylation of CpG (cytosine-phosphate-guanine) dinucleotides is a common epigenetic mark that influences gene expression. The effects of methylation on transcription factor (TF) binding are unknown for most TFs and, even when known, such knowledge is often only qualitative. In reality, methylation sensitivity is a quantitative effect, just as changes to the DNA sequence have quantitative effects on TF binding affinity. We describe Methyl-Spec-seq, an easy-to-use method that measures the effects of CpG methylation (mCPG) on binding affinity for hundreds to thousands of variants in parallel, allowing one to quantitatively assess the effects at every position in a binding site...
November 2017: Science Advances
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