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https://www.readbyqxmd.com/read/29683440/an-integrated-platform-for-genome-wide-mapping-of-chromatin-states-using-high-throughput-chip-sequencing-in-tumor-tissues
#1
Christopher Terranova, Ming Tang, Elias Orouji, Mayinuer Maitituoheti, Ayush Raman, Samirkumar Amin, Zhiyi Liu, Kunal Rai
Histone modifications constitute a major component of the epigenome and play important regulatory roles in determining the transcriptional status of associated loci. In addition, the presence of specific modifications has been used to determine the position and identity non-coding functional elements such as enhancers. In recent years, chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) has become a powerful tool in determining the genome-wide profiles of individual histone modifications...
April 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29682190/the-jmjn-domain-as-a-dimerization-interface-and-a-targeted-inhibitor-of-kdm4-demethylase-activity
#2
May Levin, Michal Stark, Yehuda G Assaraf
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity...
March 30, 2018: Oncotarget
https://www.readbyqxmd.com/read/29679371/fitting-the-epigenome-into-the-picture-methylation-classification-for-paediatric-brain-tumours
#3
EDITORIAL
J A Cotter, A R Judkins
Meaningful classification of paediatric brain tumours has been a topic of revived discussion in the current era of molecular analysis. In recent years, we have seen the practice of diagnostic neuropathology not only incorporate routine biomarker interpretation (e.g. INI1/SMARCB1 and BRAF V600E immunohistochemistry), but also extend its reach into the molecular pathology laboratory. Next-generation sequencing, fusion analysis, and copy number profiling are now commonly-employed diagnostic tools, particularly in histologically challenging or clinically difficult cases...
April 20, 2018: Neuropathology and Applied Neurobiology
https://www.readbyqxmd.com/read/29679055/towards-annotating-the-plant-epigenome-the-arabidopsis-thaliana-small-rna-locus-map
#4
Thomas J Hardcastle, Sebastian Y Müller, David C Baulcombe
Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29677564/-omic-technologies-as-a-helpful-tool-in-radioecological-research
#5
REVIEW
Polina Yu Volkova, Stanislav A Geras'kin
This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.
April 17, 2018: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/29676637/epigenomic-alterations-and-gene-expression-profiles-in-human-respiratory-epithelial-cells-mediated-by-hookah-and-cigarette-smoke
#6
Yin Xiong, Sichuan Xi, Jigui Shan, Elvin Hekimoglu, Shih-Hsin Hsiao, Mary Zhang, Julie A Hong, Chris Tao, Haobin Chen, R Taylor Ripley, Chuong D Hoang, David S Schrump
RATIONALE: The effects of hookah smoke on respiratory epithelia have not been well characterized. OBJECTIVES: To characterize and compare the effects of hookah tobacco smoke and conventional cigarette smoke on the epigenome and transcriptome of human respiratory epithelia. METHODS: Normal human small airway epithelial cells and cyclin-dependent kinase 4/human telomerase reverse transcriptase-immortalized human bronchial epithelial cells were cultured for 5 days in normal media in the presence or absence of water pipe condensates or cigarette smoke condensates under relevant exposure conditions...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29675472/low-input-and-multiplexed-microfluidic-assay-reveals-epigenomic-variation-across-cerebellum-and-prefrontal-cortex
#7
Sai Ma, Yuan-Pang Hsieh, Jian Ma, Chang Lu
Extensive effort is under way to survey the epigenomic landscape of primary ex vivo tissues to establish normal reference data and to discern variation associated with disease. The low abundance of some tissue types and the isolation procedure required to generate a homogenous cell population often yield a small quantity of cells for examination. This difficulty is further compounded by the need to profile a myriad of epigenetic marks. Thus, technologies that permit both ultralow input and high throughput are desired...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29673772/widespread-enhancer-activity-from-core-promoters
#8
REVIEW
Alejandra Medina-Rivera, David Santiago-Algarra, Denis Puthier, Salvatore Spicuglia
Gene expression in higher eukaryotes is precisely regulated in time and space through the interplay between promoters and gene-distal regulatory regions, known as enhancers. The original definition of enhancers implies the ability to activate gene expression remotely, while promoters entail the capability to locally induce gene expression. Despite the conventional distinction between them, promoters and enhancers share many genomic and epigenomic features. One intriguing finding in the gene regulation field comes from the observation that many core promoter regions display enhancer activity...
April 16, 2018: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/29672914/revisiting-the-nih-taskforce-on-the-research-needs-of-eosinophil-associated-diseases-re-tread
#9
REVIEW
Paneez Khoury, Praveen Akuthota, Steven J Ackerman, Joseph R Arron, Bruce S Bochner, Margaret H Collins, Jean-Emmanuel Kahn, Patricia C Fulkerson, Gerald J Gleich, Rashmi Gopal-Srivastava, Elizabeth A Jacobsen, Kristen M Leiferman, Levi-Schaffer Francesca, Sameer K Mathur, Michael Minnicozzi, Calman Prussin, Marc E Rothenberg, Florence Roufosse, Kathleen Sable, Dagmar Simon, Hans-Uwe Simon, Lisa A Spencer, Jonathan Steinfeld, Andrew J Wardlaw, Michael E Wechsler, Peter F Weller, Amy D Klion
BACKGROUND: Eosinophil-associated diseases (EADs) are rare, heterogeneous disorders characterized by the presence of eosinophils in tissues and/or peripheral blood resulting in immunopathology. The heterogeneity of tissue involvement, lack of sufficient animal models, technical challenges in working with eosinophils, and lack of standardized histopathologic approaches have hampered progress in basic research. Additionally, clinical trials and drug development for rare EADs are limited by the lack of primary and surrogate endpoints, biomarkers, and validated patient-reported outcomes...
April 19, 2018: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29671387/positioning-europe-for-the-epitranscriptomics-challenge
#10
Michael Jantsch, Alessandro Quattrone, Mary O'Connell, Mark Helm, Michaela Frye, Manuel Macias-Gonzales, Marie Ohman, Stefan Ameres, Luc Willems, Francois Fuks, Anastasis Oulas, Stepanka Vanacova, Henrik Nielsen, Cecile Bousquet-Antonelli, Yuri Motorin, Jean-Yves Roignant, Nikolaos Balatsos, Andras Dinnyes, Pavel Baranov, Vincent Kelly, Ayelet Lamm, Gideon Rechavi, Mattia Pelizzola, Janis Liepins, Irina Holodnuka Kholodnyuk, Vanessa Zammit, Duncan Ayers, Finn Drablos, John Arne Dahl, Janusz Bujnicki, Carmen Jeronimo, Raquel Almeida, Monica Neagu, Marieta Costache, Jasna Bankovic, Bojana Banovic, Jan Kyselovic, Luis Miguel Valor, Stefan Selbert, Pinar Pir, Turan Demircan, Victoria Cowling, Matthias Schäfer, Walter Rossmanith, Denis Lafontaine, Alexandre David, Clement Carre, Frank Lyko, Raffael Schaffrath, Schraga Schwartz, Andre Verdel, Arne Klungland, Elzbieta Purta, Gordana Timotijevic, Fernando Cardona, Alberto Davalos, Ester Ballana, Donal O Carroll, Jernej Ule, Rupert Fray
The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20 years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research...
April 19, 2018: RNA Biology
https://www.readbyqxmd.com/read/29669513/successful-application-of-human-based-methyl-capture-sequencing-for-methylome-analysis-in-non-human-primate-models
#11
Ja-Rang Lee, Dong-Sung Ryu, Sang-Je Park, Se-Hee Choe, Hyeon-Mu Cho, Sang-Rae Lee, Sun-Uk Kim, Young-Hyun Kim, Jae-Won Huh
BACKGROUND: The characterization of genomic or epigenomic variation in human and animal models could provide important insight into pathophysiological mechanisms of various diseases, and lead to new developments in disease diagnosis and clinical intervention. The African green monkey (AGM; Chlorocebus aethiops) and cynomolgus monkey (CM; Macaca fascicularis) have long been considered important animal models in biomedical research. However, non-human primate-specific methods applicable to epigenomic analyses in AGM and CM are lacking...
April 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29669403/epigenetic-applications-in-adverse-outcome-pathways-and-environmental-risk-evaluation
#12
Michelle M Angrish, Patrick Allard, Shaun D McCullough, Ingrid L Druwe, Lisa Helbling Chadwick, Erin Hines, Brian N Chorley
BACKGROUND: The epigenome may be an important interface between environmental chemical exposures and human health. However, the links between epigenetic modifications and health outcomes are often correlative and do not distinguish between cause and effect or common-cause relationships. The Adverse Outcome Pathway (AOP) framework has the potential to demonstrate, by way of an inference- and science-based analysis, the causal relationship between chemical exposures, epigenome, and adverse health outcomes...
April 12, 2018: Environmental Health Perspectives
https://www.readbyqxmd.com/read/29668744/data-quality-of-whole-genome-bisulfite-sequencing-on-illumina-platforms
#13
Amanda Raine, Ulrika Liljedahl, Jessica Nordlund
The powerful HiSeq X sequencers with their patterned flowcell technology and fast turnaround times are instrumental for many large-scale genomic and epigenomic studies. However, assessment of DNA methylation by sodium bisulfite treatment results in sequencing libraries of low diversity, which may impact data quality and yield. In this report we assess the quality of WGBS data generated on the HiSeq X system in comparison with data generated on the HiSeq 2500 system and the newly released NovaSeq system. We report a systematic issue with low basecall quality scores assigned to guanines in the second read of WGBS when using certain Real Time Analysis (RTA) software versions on the HiSeq X sequencer, reminiscent of an issue that was previously reported with certain HiSeq 2500 software versions...
2018: PloS One
https://www.readbyqxmd.com/read/29668600/chilean-gastric-cancer-task-force-a-study-protocol-to-obtain-a-clinical-and-molecular-classification-of-a-cohort-of-gastric-cancer-patients
#14
Gareth I Owen, Mauricio P Pinto, Ignacio N Retamal, María F Fernádez, Betzabe Cisternas, Sebastian Mondaca, Cesar Sanchez, Hector Galindo, Bruno Nervi, Carolina Ibañez, Francisco Acevedo, Jorge Madrid, José Peña, Maria Loreto Bravo, Maria Jose Maturana, Miguel Cordova-Delgado, Diego Romero, Nathaly de la Jara, Javiera Torres, Maria Rodriguez-Fernandez, Manuel Espinoza, Carlos Balmaceda, Matías Freire, Valentina Gárate-Calderón, Fernando Crovari, Paula Jimenez-Fonseca, Alberto Carmona-Bayonas, Ariel Zwenger, Ricardo Armisen, Alejandro H Corvalan, Marcelo Garrido
Gastric cancer (GC) is the world's second-leading cause of neoplastic mortality. Genetic alterations, response to treatments, and mortality rates are highly heterogeneous across different regions. Within Latin America, GC is the leading cause of cancer death in Chile, affecting 17.6 per 100,000 people and causing >3000 deaths/y. Clinical outcomes and response to "one size fits all" therapies are highly heterogeneous and thus a better stratification of patients may aid cancer treatment and response...
April 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29667349/asb1-differential-methylation-in-ischaemic-cardiomyopathy-relationship-with-left-ventricular-performance-in-end-stage-heart-failure-patients
#15
Ana Ortega, Estefanía Tarazón, Carolina Gil-Cayuela, Luis Martínez-Dolz, Francisca Lago, José Ramón González-Juanatey, Juan Sandoval, Manuel Portolés, Esther Roselló-Lletí, Miguel Rivera
AIMS: Ischaemic cardiomyopathy (ICM) leads to impaired contraction and ventricular dysfunction, causing high rates of morbidity and mortality. Epigenomics allows the identification of epigenetic signatures in human diseases. We analyse the differential epigenetic patterns of the ASB gene family in ICM patients and relate these alterations to their haemodynamic and functional status. METHODS AND RESULTS: Epigenomic analysis was carried out using 16 left ventricular (LV) tissue samples, eight from ICM patients undergoing heart transplantation and eight from control (CNT) subjects without cardiac disease...
April 17, 2018: ESC Heart Failure
https://www.readbyqxmd.com/read/29666783/development-of-neuroendocrine-prostate-cancers-by-the-ser-arg-repetitive-matrix-4-mediated-rna-splicing-network
#16
Ahn R Lee, Nicole Che, Jessica M Lovnicki, Xuesen Dong
While the use of next-generation androgen receptor pathway inhibition (ARPI) therapy has significantly increased the survival of patients with metastatic prostate adenocarcinoma (AdPC), several groups have reported a treatment-resistant mechanism, whereby cancer cells can become androgen receptor (AR) indifferent and gain a neuroendocrine (NE)-like phenotype. This subtype of castration-resistant prostate cancer has been termed "treatment-induced castration-resistant neuroendocrine prostate cancer" (CRPC-NE)...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29666451/exploring-the-extent-and-scope-of-epigenetic-inheritance
#17
REVIEW
Elizabeth J Radford
Environmental factors, particularly during early life, are important for the later metabolic health of the individual. In our obesogenic environment, it is of major socio-economic importance to investigate the mechanisms that contribute to the risk of metabolic ill health. Increasing evidence from a variety of model organisms suggests that non-genetically determined phenotypes, including metabolic effects such as glucose intolerance and obesity, can be passed between generations, which encourages us to revisit heredity...
April 17, 2018: Nature Reviews. Endocrinology
https://www.readbyqxmd.com/read/29666409/exposure-to-phthalate-an-endocrine-disrupting-chemical-alters-the-first-trimester-placental-methylome-and-transcriptome-in-women
#18
N M Grindler, L Vanderlinden, R Karthikraj, K Kannan, S Teal, A J Polotsky, T L Powell, I V Yang, T Jansson
Phthalates are known endocrine disruptors and associated with decreased fecundity, pregnancy loss, and adverse obstetrical outcomes, however the underlying mechanisms remain to be established. Environmental factors can influence gene expression and cell function by modifying epigenetic marks, impacting the developing embryo as well as future generations of offspring. The impact of phthalates on placental gene methylation and expression is largely unknown. We studied the effect of maternal phthalate exposure on the human placental DNA methylome and transcriptome...
April 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29666114/chronic-lymphocytic-leukemia-and-mantle-cell-lymphoma-crossroads-of-genetic-and-microenvironment-interactions
#19
Xose S Puente, Pedro Jares, Elias Campo
Chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) are two well defined entities that diverge in their basic pathogenic mechanisms and clinical evolution but they share epidemiological characteristics, cells of origin, molecular alterations, and clinical features that differ from other lymphoid neoplasms. CLL and MCL are classically considered indolent and aggressive neoplasms, respectively. However, the clinical evolution of both tumors is very heterogeneous, with subsets of patients having a stable disease for long time whereas others require immediate intervention...
April 17, 2018: Blood
https://www.readbyqxmd.com/read/29665409/epigenomic-biomarkers-for-prognostication-and-diagnosis-of-gastrointestinal-cancers
#20
REVIEW
Chi Chun Wong, Weilin Li, Bertina Chan, Jun Yu
Altered epigenetic regulation is central to many human diseases, including cancer. Over the past two decade, major advances have been made in our understanding of the role of epigenetic alterations in carcinogenesis, particularly for DNA methylation, histone modifications and non-coding RNAs. Aberrant hypermethylation of DNA at CpG islands is a well-established phenomenon that mediates transcriptional silencing of tumor suppressor genes, and it is an early event integral to gastrointestinal cancer development...
April 14, 2018: Seminars in Cancer Biology
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