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https://www.readbyqxmd.com/read/29227115/fundamentals-of-precision-medicine
#1
Kimon Divaris
Precision medicine is no longer a distant vision; it is becoming part of the rapidly evolving present. Insights from studies of the human genome and microbiome, their associated transcriptomes, proteomes, and metabolomes, and epigenomics and exposomics have reached an unprecedented depth and scale. Much more needs to be done, however, particularly in dentistry.
September 2017: Compendium of Continuing Education in Dentistry
https://www.readbyqxmd.com/read/29225036/transcription-and-remodeling-produce-asymmetrically-unwrapped-nucleosomal-intermediates
#2
Srinivas Ramachandran, Kami Ahmad, Steven Henikoff
Nucleosomes are disrupted during transcription and other active processes, but the structural intermediates during nucleosome disruption in vivo are unknown. To identify intermediates, we mapped subnucleosomal protections in Drosophila cells using Micrococcal Nuclease followed by sequencing. At the first nucleosome position downstream of the transcription start site, we identified unwrapped intermediates, including hexasomes that lack either proximal or distal contacts. Inhibiting topoisomerases or depleting histone chaperones increased unwrapping, whereas inhibiting release of paused RNAPII or reducing RNAPII elongation decreased unwrapping...
December 6, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29224163/methylation-sensitive-high-resolution-melting-ms-hrm
#3
Dianna Hussmann, Lise Lotte Hansen
Methylation-Sensitive High Resolution Melting (MS-HRM) is an in-tube, PCR-based method to detect methylation levels at specific loci of interest. A unique primer design facilitates a high sensitivity of the assays enabling detection of down to 0.1-1% methylated alleles in an unmethylated background.Primers for MS-HRM assays are designed to be complementary to the methylated allele, and a specific annealing temperature enables these primers to anneal both to the methylated and the unmethylated alleles thereby increasing the sensitivity of the assays...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224161/quantitative-region-specific-dna-methylation-analysis-by-the-epityper%C3%A2-technology
#4
Sonja Kunze
DNA methylation plays a profound role in development and health as well as development and progression of disease. High-throughput quantitative DNA methylation analysis is therefore crucial for the study of the normal physiology of the epigenome and its dysregulation in disease. Many target areas are identified by a range of emerging genome-wide cytosine methylation techniques, but these whole genome scans usually only provide methylation data for a few individual CpG sites (CpGs) within a region. The EpiTYPER™ assay is a region-specific method for the detection and quantitative analysis of DNA methylation that allows performing a high-resolution scan of selected regions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224156/multiplexed-and-sensitive-dna-methylation-testing-using-methylation-sensitive-restriction-enzymes-msre-qpcr
#5
Gabriel Beikircher, Walter Pulverer, Manuela Hofner, Christa Noehammer, Andreas Weinhaeusel
DNA methylation is a chemically stable key-player in epigenetics. In the vertebrate genome the 5-methyl cytosine (5mC) has been found almost exclusively in the CpG dinucleotide context. CpG dinucleotides are enriched in CpG islands very frequently located within or close to gene promoters. Analyses of DNA methylation changes in human diagnostics have been conducted classically using methylation-sensitive restriction enzymes (MSRE). Since the discovery of bisulfite conversion-based sequencing and PCR assays, MSRE-based PCR assays have been less frequently used, although especially in the field of cancer epigenetics MSRE-based genome-wide discovery and targeted screening applications have been and are still performed successfully...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224150/bisulphite-sequencing-of-chromatin-immunoprecipitated-dna-bischip-seq
#6
Clare Stirzaker, Jenny Z Song, Aaron L Statham, Susan J Clark
Epigenetic regulation plays a critical role in gene expression, cellular differentiation, and disease. There is a complex interplay between the different layers of epigenetic information, including DNA methylation, nucleosome positions, histone modifications, histone variants, and other important epigenetic regulators. The different modifications do not act independently of each other and their relationship plays an important role in governing the regulation of the epigenome. Of these, DNA methylation is the best-studied epigenetic modification in mammals...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224140/whole-genome-bisulfite-sequencing-using-the-ovation%C3%A2-ultralow-methyl-seq-protocol
#7
Christian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, Jörg Tost
The analysis of genome-wide epigenomic alterations including DNA methylation has become a subject of intensive research for many complex diseases. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies can be considered the gold standard for a comprehensive and quantitative analysis of cytosine methylation throughout the genome. Several approaches including tagmentation- and post bisulfite adaptor tagging (PBAT)-based WGBS have been devised. Here, we provide a detailed protocol based on a commercial kit for the preparation of libraries for WGBS from limited amounts of input DNA (50-100 ng) using the classical approach of WGBS by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224136/a-summary-of-the-biological-processes-disease-associated-changes-and-clinical-applications-of-dna-methylation
#8
Gitte Brinch Andersen, Jörg Tost
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222187/mutant-idh1r132h-induces-transcriptional-and-epigenomic-reprogramming
#9
(no author information available yet)
A fraction of the chromatin state and DNA methylation changes induced by IDH1R132H are irreversible.
December 8, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/29221916/dna-methylation-signatures-at-endoplasmic-reticulum-stress-genes-are-associated-with-adiposity-and-insulin-resistance
#10
Omar Ramos-Lopez, Jose I Riezu-Boj, Fermin I Milagro, J Alfredo Martinez
A sustained activation of the unfolded protein response and the subsequent endoplasmic reticulum (ER) stress has been involved in the onset and severity of several metabolic diseases. The aim of this study was to analyze the association of DNA methylation signatures at ER stress genes with adiposity traits and related metabolic disorders. An epigenomic analysis within the Methyl Epigenome Network Association (MENA) project was conducted in an adult population (n=474). DNA methylation status in peripheral white blood cells was analyzed by a microarray approach...
November 28, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29221727/epigenetic-mechanisms-in-developmental-neurotoxicity
#11
REVIEW
M Raciti, S Ceccatelli
The constant interplay between environment (including both exogenous and endogenous factors) and epigenome (defined as the combination of chromatin, its covalent modifications and noncoding RNAs) triggers epigenetic events that, by modulating gene expression, capture information about changes in the environment. In this mini review, we will focus on the neurodevelopmental implications of exposure to adverse prenatal milieu with emphasis on mechanistic and functional aspects. Several neurotoxic insults have been shown to affect epigenetics with negative consequences on the development of the nervous system; among them are methylmercury, lead, arsenic and cadmium, as well as excess of glucocorticoids...
December 5, 2017: Neurotoxicology and Teratology
https://www.readbyqxmd.com/read/29220033/challenges-and-recommendations-for-epigenomics-in-precision-health
#12
Ava C Carter, Howard Y Chang, George Church, Ashley Dombkowski, Joseph R Ecker, Elad Gil, Paul G Giresi, Henry Greely, William J Greenleaf, Nir Hacohen, Chuan He, David Hill, Justin Ko, Isaac Kohane, Anshul Kundaje, Megan Palmer, Michael P Snyder, Joyce Tung, Alexander Urban, Marc Vidal, Wing Wong
No abstract text is available yet for this article.
December 8, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29218402/linking-inter-individual-variability-to-endocrine-disruptors-insights-for-epigenetic-inheritance
#13
Sarah E Latchney, Ashley M Fields, Martha Susiarjo
Endocrine disrupting chemicals (EDCs) can induce a myriad of adverse health effects. An area of active investigation is the multi- and transgenerational inheritance of EDC-induced adverse health effects referring to the transmission of phenotypes across multiple generations via the germline. The inheritance of EDC-induced adverse health effects across multiple generations can occur independent of genetics, spurring much research into the transmission of underlying epigenetic mechanisms. Epigenetic mechanisms play important roles in the development of an organism and are responsive to environmental exposures...
December 7, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29217127/epigenome-in-early-mammalian-development-inheritance-reprogramming-and-establishment
#14
REVIEW
Qianhua Xu, Wei Xie
Drastic epigenetic reprogramming takes place during preimplantation development, leading to the conversion of terminally differentiated gametes to a totipotent embryo. Deficiencies in remodeling of the epigenomes can cause severe developmental defects, including embryonic lethality. However, how chromatin modifications and chromatin organization are reprogrammed upon fertilization in mammals has long remained elusive. Here, we review recent progress in understanding how the epigenome is dynamically regulated during early mammalian development...
December 4, 2017: Trends in Cell Biology
https://www.readbyqxmd.com/read/29216191/transcription-factors-coregulators-and-epigenetic-marks-are-linearly-correlated-and-highly-redundant
#15
Tobias Ahsendorf, Franz-Josef Müller, Ved Topkar, Jeremy Gunawardena, Roland Eils
The DNA microstates that regulate transcription include sequence-specific transcription factors (TFs), coregulatory complexes, nucleosomes, histone modifications, DNA methylation, and parts of the three-dimensional architecture of genomes, which could create an enormous combinatorial complexity across the genome. However, many proteins and epigenetic marks are known to colocalize, suggesting that the information content encoded in these marks can be compressed. It has so far proved difficult to understand this compression in a systematic and quantitative manner...
2017: PloS One
https://www.readbyqxmd.com/read/29215091/cancer-induction-and-suppression-with-transcriptional-control-and-epigenome-editing-technologies
#16
REVIEW
Shota Nakade, Takashi Yamamoto, Tetsushi Sakuma
Cancer epigenetics is one of the most important research subjects in dissecting cancer mechanisms and therapeutic targets because the emergence and malignant transformation of various cancers are caused by unnatural expression of cancer-related genes attributed to their epigenetic errors. The original concept of cancer epigenetics basically stands on the analysis of the epigenetic status in naturally occurring cancer cells; however, the rapidly emerging technology called epigenome editing would change this situation drastically...
November 14, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29211860/changes-in-the-epigenome-and-transcriptome-of-the-poplar-shoot-apical-meristem-in-response-to-water-availability-affect-preferentially-hormone-pathways
#17
Clément Lafon-Placette, Anne-Laure Le Gac, Didier Chauveau, Vincent Segura, Alain Delaunay, Marie-Claude Lesage-Descauses, Irène Hummel, David Cohen, Béline Jesson, Didier Le Thiec, Marie-Béatrice Bogeat-Triboulot, Franck Brignolas, Stéphane Maury
The adaptive capacity of long-lived organisms such as trees to the predicted climate changes, including severe and successive drought episodes, will depend on the presence of genetic diversity and phenotypic plasticity. Here, the involvement of epigenetic mechanisms in phenotypic plasticity toward soil water availability was examined in Populus×euramericana. This work aimed at characterizing (i) the transcriptome plasticity, (ii) the genome-wide plasticity of DNA methylation, and (iii) the function of genes affected by a drought-rewatering cycle in the shoot apical meristem...
December 2, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29209557/line-1-in-response-to-exposure-to-ionizing-radiation
#18
COMMENT
Igor Koturbash
It is becoming increasingly recognized that Long Interspersed Nuclear Element, 1 (LINE-1), the most ubiquitous repetitive element in the mammalian genomes, plays an important role in the pathogenesis of disease and in the response to exposure to environmental stressors. Ionizing radiation is a known genotoxic stressor, but it is capable of targeting the cellular epigenome as well. Radiation-induced alterations in LINE-1 DNA methylation are the most frequently observed epigenetic effects of exposure. The extent of this aberrant DNA methylation, however, strongly depends on a number of factors, including the type and dose of radiation...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/29209433/novel-insights-into-epigenetic-drivers-of-oropharyngeal-squamous-cell-carcinoma-role-of-hpv-and-lifestyle-factors
#19
REVIEW
Paolo Boscolo-Rizzo, Carlo Furlan, Valentina Lupato, Jerry Polesel, Elisabetta Fratta
In the last years, the explosion of high throughput sequencing technologies has enabled epigenome-wide analyses, allowing a more comprehensive overview of the oropharyngeal squamous cell carcinoma (OPSCC) epigenetic landscape. In this setting, the cellular pathways contributing to the neoplastic phenotype, including cell cycle regulation, cell signaling, DNA repair, and apoptosis have been demonstrated to be potential targets of epigenetic alterations in OPSCC. Of note, it has becoming increasingly clear that HPV infection and OPSCC lifestyle risk factors differently drive the epigenetic machinery in cancer cells...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29209073/integrating-clinical-and-multiple-omics-data-for-prognostic-assessment-across-human-cancers
#20
Bin Zhu, Nan Song, Ronglai Shen, Arshi Arora, Mitchell J Machiela, Lei Song, Maria Teresa Landi, Debashis Ghosh, Nilanjan Chatterjee, Veera Baladandayuthapani, Hongyu Zhao
Multiple omic profiles have been generated for many cancer types; however, comprehensive assessment of their prognostic values across cancers is limited. We conducted a pan-cancer prognostic assessment and presented a multi-omic kernel machine learning method to systematically quantify the prognostic values of high-throughput genomic, epigenomic, and transcriptomic profiles individually, integratively, and in combination with clinical factors for 3,382 samples across 14 cancer types. We found that the prognostic performance varied substantially across cancer types...
December 5, 2017: Scientific Reports
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