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Epigenomics

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https://www.readbyqxmd.com/read/29233676/targeting-epigenome-with-dietary-nutrients-in-cancer-current-advances-and-future-challenges
#1
REVIEW
Mohammad Imran Khan, Suvasmita Rath, Vaqar Mustafa Adhami, Hasan Mukhtar
Tumorigenesis and epigenetic are closely linked with each other. Epigenetic changes are potential regulators of gene expression without involving any change in the DNA itself. More interestingly, epigenetic changes are reversible heritable changes which pass through generations. Many dietary bioactive ingredients regulate epigenetic control of cells and influence biochemical processes. Correlation between epigenetic regulation and cancer onset has been well established. Recent studies provide important information on the role of bioactive dietary components in cancer prevention and therapy...
December 9, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29232656/targeting-oral-cancer-epigenome-via-lsd1
#2
Manish V Bais
No abstract text is available yet for this article.
December 11, 2017: Aging
https://www.readbyqxmd.com/read/29230671/incorporating-dna-methyltransferase-inhibitors-dnmtis-in-the-treatment-of-genitourinary-malignancies-a-systematic-review
#3
Michal Chovanec, Fadi Taza, Maitri Kalra, Noah Hahn, Kenneth P Nephew, Michael J Spinella, Costantine Albany
Inhibition of DNA methyltransferases (DNMTs) has emerged as a novel treatment strategy in solid tumors. Aberrant hypermethylation in promoters of critical tumor suppressor genes is the basis for the idea that treatment with hypomethylating agents may lead to the restoration of a "normal" epigenome and produce clinically meaningful therapeutic outcomes. The aim of this review article is to summarize the current state of knowledge of DNMT inhibitors in the treatment of genitourinary malignancies. The efficacy of these agents in genitourinary malignancies was reported in a number of studies and suggests a role of induced DNA hypomethylation in overcoming resistance to conventional cytotoxic treatments...
December 11, 2017: Targeted Oncology
https://www.readbyqxmd.com/read/29230532/rna-mediated-transgenerational-inheritance-in-ciliates-and-plants
#4
REVIEW
Zachary T Neeb, Mariusz Nowacki
In the age of next-generation sequencing (NGS) and with the availability of whole sequenced genomes and epigenomes, some attention has shifted from purely sequence-based studies to those of heritable epigenetic modifications. Transgenerational inheritance can be defined as heritable changes to the state of DNA that may be passed on to subsequent generations without alterations to the underlying DNA sequence. Although this phenomenon has been extensively studied in many systems, studies of transgenerational inheritance in mammals and other higher-level eukaryotes may be complicated by the fact that many epigenetic marks are reprogrammed during sexual reproduction...
December 11, 2017: Chromosoma
https://www.readbyqxmd.com/read/29229600/genomic-and-epigenomic-signatures-in-ovarian-cancer-associated-with-re-sensitization-to-platinum-drugs
#5
Fang Fang, Horacio Cardenas, Hao Huang, Guanglong Jiang, Susan M Perkins, Chi Zhang, Harold N Keer, Yunlong Liu, Kenneth P Nephew, Daniela Matei
DNA methylation aberrations have been implicated in acquired resistance to platinum drugs in ovarian cancer (OC). In this study, we elucidated an epigenetic signature associated with platinum drug re-sensitization that may offer utility in predicting the outcomes of patients who are co-administered a DNA methyltransferase inhibitror. The OC specimens we analyzed were derived from a recent clinical trial that compared the responses of patients with recurrent platinum-resistant OC who received carboplatin plus the DNA methyltransferase inhibitor guadecitabine or a standard of care chemotherapy regimen selected by the treating physician...
December 11, 2017: Cancer Research
https://www.readbyqxmd.com/read/29228692/epigenetic-landscape-change-analysis-during-human-emt-sheds-light-on-a-key-emt-mediator-trim29
#6
Sung Kyung Choi, Kurinji Pandiyan, Jung Woo Eun, Xiaojing Yang, Seong Hwi Hong, Suk Woo Nam, Peter A Jones, Gangning Liang, Jueng Soo You
Epithelial to mesenchymal transition (EMT) is a key trans-differentiation process, which plays a critical role in physiology and pathology. Although gene expression changes in EMT have been scrutinized, study of epigenome is in its infancy. To understand epigenetic changes during TWIST-driven EMT, we used the AcceSssIble assay to study DNA methylation and chromatin accessibility in human mammary epithelial cells (HMECs). The DNA methylation changes were found to have functional significance in EMT - i.e. methylated genes were enriched for E-box motifs that can be recognized by TWIST, at the promoters suggesting a potential targeting phenomenon, whereas the demethylated regions were enriched for pro-metastatic genes, supporting the role of EMT in metastasis...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29227115/fundamentals-of-precision-medicine
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
(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
#16
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
#17
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
#18
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
#19
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
#20
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
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