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Epigenomics

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https://www.readbyqxmd.com/read/28548108/drugging-the-pain-epigenome
#1
REVIEW
Ellen Niederberger, Eduard Resch, Michael J Parnham, Gerd Geisslinger
More than 20% of adults worldwide experience different types of chronic pain, which are frequently associated with several comorbidities and a decrease in quality of life. Several approved painkillers are available, but current analgesics are often hampered by insufficient efficacy and/or severe adverse effects. Consequently, novel strategies for safe, highly efficacious treatments are highly desirable, particularly for chronic pain. Epigenetic mechanisms such as DNA methylation, histone modifications and microRNAs (miRNAs) strongly affect the regulation of gene expression, potentially for long periods over years or even generations, and have been associated with pathophysiological pain...
May 26, 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/28546580/remembrance-of-epigenomes-past
#2
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
May 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28546346/epigenomic-disruption-of-cardiovascular-care-what-it-will-take
#3
EDITORIAL
Emma Monte, Matthew A Fischer, Thomas M Vondriska
No abstract text is available yet for this article.
May 26, 2017: Circulation Research
https://www.readbyqxmd.com/read/28543738/crispr-editing-in-biological-and-biomedical-investigation
#4
Xing-Da Ju, Jing Xu, Zhong Sheng Sun
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR--associated protein) system, a prokaryotic RNA-based adaptive immune system against viral infection, is emerging as a powerful genome editing tool in broad research areas. To further improve and expand its functionality, various CRISPR delivery strategies have been tested and optimized, and key CRISPR system components such as Cas protein have been engineered with different purposes. Benefiting from more in-depth understanding and further development of CRISPR, versatile CRISPR-based platforms for genome editing have been rapidly developed to advance investigations in biology and biomedicine...
May 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28542388/targeted-dna-methylation-in-pericentromeres-with-genome-editing-based-artificial-dna-methyltransferase
#5
Taiga Yamazaki, Yu Hatano, Tetsuya Handa, Sakiko Kato, Kensuke Hoida, Rui Yamamura, Takashi Fukuyama, Takayuki Uematsu, Noritada Kobayashi, Hiroshi Kimura, Kazuo Yamagata
To study the impact of epigenetic changes on biological functions, the ability to manipulate the epigenetic status of certain genomic regions artificially could be an indispensable technology. "Epigenome editing" techniques have gradually emerged that apply TALE or CRISPR/Cas9 technologies with various effector domains isolated from epigenetic code writers or erasers such as DNA methyltransferase, 5-methylcytosine oxidase, and histone modification enzymes. Here we demonstrate that a TALE recognizing a major satellite, consisting of a repeated sequence in pericentromeres, could be fused with the bacterial CpG methyltransferase, SssI...
2017: PloS One
https://www.readbyqxmd.com/read/28541490/glanet-genomic-loci-annotation-and-enrichment-tool
#6
Burçak Otlu, Can Firtina, Sündüz Keles, Oznur Tastan
Motivation: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. Results: We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28541380/a-fully-bayesian-latent-variable-model-for-integrative-clustering-analysis-of-multi-type-omics-data
#7
Qianxing Mo, Ronglai Shen, Cui Guo, Marina Vannucci, Keith S Chan, Susan G Hilsenbeck
Identification of clinically relevant tumor subtypes and omics signatures is an important task in cancer translational research for precision medicine. Large-scale genomic profiling studies such as The Cancer Genome Atlas (TCGA) Research Network have generated vast amounts of genomic, transcriptomic, epigenomic, and proteomic data. While these studies have provided great resources for researchers to discover clinically relevant tumor subtypes and driver molecular alterations, there are few computationally efficient methods and tools for integrative clustering analysis of these multi-type omics data...
May 24, 2017: Biostatistics
https://www.readbyqxmd.com/read/28540928/anxiety-associated-increased-cpg-methylation-in-the-promoter-of-asb1-a-translational-approach-evidenced-by-epidemiological-and-clinical-studies-and-a-murine-model
#8
Rebecca T Emeny, Jens Baumert, Anthony S Zannas, Sonja Kunze, Simone Wahl, Stella Iurato, Janine Arloth, Angelika Erhardt, Georgia Balsevich, Mathias V Schmidt, Peter Weber, Anja Kretschmer, Liliane Pfeiffer, Johannes Kruse, Konstantin Strauch, Michael Roden, Christian Herder, Wolfgang Koenig, Christian Gieger, Melanie Waldenberger, Annette Peters, Elisabeth B Binder, Karl-Heinz Ladwig
Epigenetic regulation in anxiety is suggested, but evidence from large studies is needed. We conducted an epigenome-wide association study (EWAS) on anxiety in a population-based cohort and validated our finding in a clinical cohort as well as a murine model. In the KORA cohort, participants (n=1522, age 32-72 years) were administered the Generalized Anxiety Disorder (GAD-7) instrument, whole blood DNA methylation was measured (Illumina 450 K BeadChip) and circulating levels of hs-CRP and IL-18 were assessed in the association between anxiety and methylation...
May 25, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28540331/in-silico-deconvolution-and-purification-of-cancer-epigenomes
#9
EDITORIAL
Martí Duran-Ferrer, Renée Beekman, José I Martín-Subero
No abstract text is available yet for this article.
March 2017: Oncoscience
https://www.readbyqxmd.com/read/28539122/an-inference-method-from-multi-layered-structure-of-biomedical-data
#10
Myungjun Kim, Yonghyun Nam, Hyunjung Shin
BACKGROUND: Biological system is a multi-layered structure of omics with genome, epigenome, transcriptome, metabolome, proteome, etc., and can be further stretched to clinical/medical layers such as diseasome, drugs, and symptoms. One advantage of omics is that we can figure out an unknown component or its trait by inferring from known omics components. The component can be inferred by the ones in the same level of omics or the ones in different levels. METHODS: To implement the inference process, an algorithm that can be applied to the multi-layered complex system is required...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28537914/epigenomic-study-identifies-a-novel-mesenchyme-homeobox2-gli1-transcription-axis-involved-in-cancer-drug-resistance-overall-survival-and-therapy-prognosis-in-lung-cancer-patients
#11
Leonel Armas-López, Patricia Piña-Sánchez, Oscar Arrieta, Enrique Guzman de Alba, Blanca Ortiz-Quintero, Patricio Santillán-Doherty, David C Christiani, Joaquín Zúñiga, Federico Ávila-Moreno
Several homeobox-related gene (HOX) transcription factors such as mesenchyme HOX-2 (MEOX2) have previously been associated with cancer drug resistance, malignant progression and/or clinical prognostic responses in lung cancer patients; however, the mechanisms involved in these responses have yet to be elucidated. Here, an epigenomic strategy was implemented to identify novel MEOX2 gene promoter transcription targets and propose a new molecular mechanism underlying lung cancer drug resistance and poor clinical prognosis...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28537485/a-nad-parp1-sirt1-axis-in-aging
#12
Andrew R Mendelsohn, James Larrick
NAD+ levels decline with age in diverse animals from C. elegans to mice. Raising NAD+ levels by dietary supplementation with NAD+ precursors NR or NMN improves mitochondrial function and muscle, neural and melanocyte stem cell function in mice as well as increasing murine lifespan. Decreased NAD+ levels with age reduces SIRT1 function and reduces the mitochondrial unfolded protein response, which can be overcome by NR supplementation. Decreased NAD+ levels cause NAD+-binding protein DCB1 to form a complex with PARP1, inhibiting PARP catalytic activity...
May 24, 2017: Rejuvenation Research
https://www.readbyqxmd.com/read/28536537/-gestaltomics-systems-biology-schemes-for-the-study-of-neuropsychiatric-diseases
#13
REVIEW
Nora A Gutierrez Najera, Osbaldo Resendis-Antonio, Humberto Nicolini
The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the "psychiatric phenotype" is to provide an improved vision of the shape of the phenotype as it is visualized by "Gestalt" psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28535307/intergenerational-impact-of-paternal-lifetime-exposures-to-both-folic-acid-deficiency-and-supplementation-on-reproductive-outcomes-and-imprinted-gene-methylation
#14
Lundi Ly, Donovan Chan, Mahmoud Aarabi, Mylène Landry, Nathalie A Behan, Amanda J MacFarlane, Jacquetta Trasler
STUDY QUESTION: Do paternal exposures to folic acid deficient (FD), and/or folic acid supplemented (FS) diets, throughout germ cell development adversely affect male germ cells and consequently offspring health outcomes? SUMMARY ANSWER: Male mice exposed over their lifetimes to both FD and FS diets showed decreased sperm counts and altered imprinted gene methylation with evidence of transmission of adverse effects to the offspring, including increased postnatal-preweaning mortality and variability in imprinted gene methylation...
May 23, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28535256/epigenetic-and-genetic-contributions-to-adaptation-in-chlamydomonas
#15
Ilkka Kronholm, Andrew Bassett, David Baulcombe, Sinéad Collins
Epigenetic modifications, such as DNA methylation or histone modifications, can be transmitted between cellular or organismal generations. However, there are no experiments measuring their role in adaptation, so here we use experimental evolution to investigate how epigenetic variation can contribute to adaptation. We manipulated DNA methylation and histone acetylation in the unicellular green alga Chlamydomonas reinhardtii both genetically and chemically to change the amount of epigenetic variation generated or transmitted in adapting populations in three different environments (salt stress, phosphate starvation, and high CO2) for two hundred asexual generations...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535255/tea-and-coffee-consumption-in-relation-to-dna-methylation-in-four-european-cohorts
#16
Weronica E Ek, Elmar W Tobi, Muhammad Ahsan, Erik Lampa, Erica Ponzi, Soterios A Kyrtopoulos, Panagiotis Georgiadis, L H Lumey, Bastiaan T Heijmans, Maria Botsivali, Ingvar A Bergdahl, Torgny Karlsson, Mathias Rask-Andersen, Domenico Palli, Erik Ingelsson, Åsa K Hedman, Lena M Nilsson, Paolo Vineis, Lars Lind, James M Flanagan, Åsa Johansson
Lifestyle factors, such as food choices and exposure to chemicals, can alter DNA methylation and lead to changes in gene activity. Two such exposures with pharmacologically active components are coffee and tea consumption. Both coffee and tea has been suggested to play an important role in modulating disease-risk in humans by suppressing tumour progression, decreasing inflammation and influencing estrogen metabolism. These mechanisms may be mediated by changes in DNA methylation.To investigate if DNA methylation in blood is associated with coffee and tea consumption we performed a genome-wide DNA methylation study for coffee and tea consumption in four European cohorts (N = 3,096)...
May 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28534873/molecular-indicators-of-stress-induced-neuroinflammation-in-a-mouse-model-simulating-features-of-post-traumatic-stress-disorder
#17
S Muhie, A Gautam, N Chakraborty, A Hoke, J Meyerhoff, R Hammamieh, M Jett
A social-stress mouse model was used to simulate features of post-traumatic stress disorder (PTSD). The model involved exposure of an intruder (male C57BL/6) mouse to a resident aggressor (male SJL) mouse for 5 or 10 consecutive days. Transcriptome changes in brain regions (hippocampus, amygdala, medial prefrontal cortex and hemibrain), blood and spleen as well as epigenome changes in the hemibrain were assayed after 1- and 10-day intervals following the 5-day trauma or after 1- and 42-day intervals following the 10-day trauma...
May 23, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28534825/a-novel-combination-of-withaferin-a-and-sulforaphane-inhibits-epigenetic-machinery-cellular-viability-and-induces-apoptosis-of-breast-cancer-cells
#18
Kendra J Royston, Neha Udayakumar, Kayla Lewis, Trygve O Tollefsbol
With cancer often classified as a disease that has an important epigenetic component, natural compounds that have the ability to regulate the epigenome become ideal candidates for study. Humans have a complex diet, which illustrates the need to elucidate the mechanisms of interaction between these bioactive compounds in combination. The natural compounds withaferin A (WA), from the Indian winter cherry, and sulforaphane (SFN), from cruciferous vegetables, have numerous anti-cancer effects and some report their ability to regulate epigenetic processes...
May 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28533897/introduction-to-the-special-issue-tree-invasions-towards-a-better-understanding-of-their-complex-evolutionary-dynamics
#19
Heidi Hirsch, David M Richardson, Johannes J Le Roux
Many invasive plants show evidence of trait-based evolutionary change, but these remain largely unexplored for invasive trees. The increasing number of invasive trees and their tremendous impacts worldwide, however, illustrates the urgent need to bridge this knowledge gap to apply efficient management. Consequently, an interdisciplinary workshop, held in 2015 at Stellenbosch University in Stellenbosch, South Africa, brought together international researchers to discuss our understanding of evolutionary dynamics in invasive trees...
May 2017: AoB Plants
https://www.readbyqxmd.com/read/28529337/dynamic-chromatin-technologies-from-individual-molecules-to-epigenomic-regulation-in-cells
#20
REVIEW
Olivier Cuvier, Beat Fierz
The establishment and maintenance of chromatin states involves multiscale dynamic processes integrating transcription factor and multiprotein effector dynamics, cycles of chemical chromatin modifications, and chromatin structural organization. Recent developments in genomic technologies are emerging that are enabling a view beyond ensemble- and time-averaged properties and are revealing the importance of dynamic chromatin states for cell fate decisions, differentiation and reprogramming at the single-cell level...
May 22, 2017: Nature Reviews. Genetics
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