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Epigenomics

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https://www.readbyqxmd.com/read/28432132/do-memory-cd4-t-cells-keep-their-cell-type-programming-plasticity-versus-fate-commitment-epigenome-a-dynamic-vehicle-for-transmitting-and-recording-cytokine-signaling
#1
John L Johnson, Golnaz Vahedi
CD4(+) T cells are critical for the elimination of an immense array of microbial pathogens. Although there are aspects of helper T-cell differentiation that can be modeled as a classic cell-fate commitment, CD4(+) T cells also maintain considerable flexibility in their transcriptional program. Here, we present an overview of chromatin biology during cellular reprogramming and, within this context, envision how the scope of cellular reprogramming may be expanded to further our understanding of the controversy surrounding CD4(+) T lymphocyte plasticity or determinism...
April 21, 2017: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28431857/modeling-human-infertility-with-pluripotent-stem-cells
#2
Di Chen, Joanna J Gell, Yu Tao, Enrique Sosa, Amander T Clark
Human fertility is dependent upon the correct establishment and differentiation of the germline. This is because no other cell type in the body is capable of passing a genome and epigenome from parent to child. Terminally differentiated germline cells in the adult testis and ovary are called gametes. However, the initial specification of germline cells occurs in the embryo around the time of gastrulation. Most of our knowledge regarding the cell and molecular events that govern human germline specification involves extrapolating scientific principles from model organisms, most notably the mouse...
April 13, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28431793/alcohol-effects-on-the-epigenome-in-the-germline-role-in-the-inheritance-of-alcohol-related-pathology
#3
REVIEW
Lucy G Chastain, Dipak K Sarkar
Excessive alcohol exposure has severe health consequences, and clinical and animal studies have demonstrated that disruptions in the epigenome of somatic cells, such as those in brain, are an important factor in the development of alcohol-related pathologies, such as alcohol-use disorders (AUDs) and fetal alcohol spectrum disorders (FASDs). It is also well known that alcohol-related health problems are passed down across generations in human populations, but the complete mechanisms for this phenomenon are currently unknown...
March 6, 2017: Alcohol
https://www.readbyqxmd.com/read/28431147/detection-of-epigenetic-mutagens-including-anthracene-derived-compounds-using-yeast-flo1-promoter-gfp-reporter-gene-assay
#4
Kei-Ichi Sugiyama, Hiroko Furusawa, Petr Grúz, Masamitsu Honma
Recently, we have reported that the FLO1-mediated flocculation levels of yeast are affected by an epigenetic mutagen, alizarin. Alizarin promoted flocculation and reduced the bulk levels of histone H3 in yeast cells. Since alizarin has been known to possess carcinogenesis-promoting properties, it is important to estimate the effect of alizarin-related compounds on epigenome as measured by the flocculation of yeast. In this study, we examined the effects of two anthracene-derived compounds other than alizarin on the flocculation level of yeast...
April 20, 2017: Mutagenesis
https://www.readbyqxmd.com/read/28428977/19th-workshop-of-the-international-stroke-genetics-consortium-april-28-29-2016-boston-massachusetts-usa-2016-001-mri-defined-cerebrovascular-genomics-the-charge-consortium
#5
S Debette, Y Saba, D Vojinovic, X Jian, H Adams, G Chauhan, M Sargurupremraj, S Kaffashian, J Ding, J C Bis, P Nyquist, K Mather, C Van Duijn, L J Launer, M A Ikram, H Schmidt, W T Longstreth, M Fornage, S Seshadri
The CHARGE consortium is an investigator-initiated collaboration to facilitate meta-analyses of genome-wide association studies (GWAS) and genomic analyses based on next generation sequencing (NGS), among multiple large and well-phenotyped population-based cohort studies around the world (http://www.chargeconsortium.com). Within the neuro-CHARGE working group, we are presenting an update of ongoing genomic studies on MRI-markers of cerebrovascular disease. Large population-based studies have shown that the burden of cerebrovascular disease extends far beyond that of clinical stroke...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28424740/essential-role-of-long-non-coding-rnas-in-de-novo-chromatin-modifications-the-genomic-address-code-hypothesis
#6
Ken Nishikawa, Akira R Kinjo
The epigenome, i.e., the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it has a different epigenome than its mother cell. Although de novo chromatin modification is an important event that comprises elementary processes of cell differentiation, its molecular mechanism remains poorly understood...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28424341/alterations-in-three-dimensional-organization-of-the-cancer-genome-and-epigenome
#7
Joanna Achinger-Kawecka, Phillippa C Taberlay, Susan J Clark
The structural and functional basis of the genome is provided by the three-dimensional (3D) chromatin state. To enable accurate gene regulation, enhancer elements and promoter regions are brought into close spatial proximity to ensure proper, cell type-specific gene expression. In cancer, genetic and epigenetic processes can deregulate the transcriptional program. To investigate whether the 3D chromatin state is also disrupted in cancer we performed Hi-C chromosome conformation sequencing in normal and prostate cancer cells and compared the chromatin interaction maps with changes to the genome and epigenome...
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28421636/leveraging-cell-type-specific-regulatory-regions-to-detect-snps-associated-with-tissue-factor-pathway-inhibitor-plasma-levels
#8
Jessica Dennis, Alejandra Medina-Rivera, Vinh Truong, Lina Antounians, Nora Zwingerman, Giovana Carrasco, Lisa Strug, Phil Wells, David-Alexandre Trégouët, Pierre-Emmanuel Morange, Michael D Wilson, France Gagnon
Tissue factor pathway inhibitor (TFPI) regulates the formation of intravascular blood clots, which manifest clinically as ischemic heart disease, ischemic stroke, and venous thromboembolism (VTE). TFPI plasma levels are heritable, but the genetics underlying TFPI plasma level variability are poorly understood. Herein we report the first genome-wide association scan (GWAS) of TFPI plasma levels, conducted in 251 individuals from five extended French-Canadian Families ascertained on VTE. To improve discovery, we also applied a hypothesis-driven (HD) GWAS approach that prioritized single nucleotide polymorphisms (SNPs) in (1) hemostasis pathway genes, and (2) vascular endothelial cell (EC) regulatory regions, which are among the highest expressers of TFPI...
April 18, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28421503/chapter-19-cryopreservation-effect-on-genetic-function-neonatal-outcomes
#9
Vanesa Robles, Marta F Riesco, David G Valcarce
Cryopreservation is a well-established technique commonly used in clinical practice. It is used widely for the conservation of gametes and embryos that will be used later for insemination or in vitro fertilization. However, several studies have shown that this technique can produce changes in messenger RNA levels, in the epigenome and induce DNA damage. Although the embryo has potent mechanisms for DNA repair, and molecular changes in spermatozoa are not necessarily reflected in the embryo, it is important to explore new molecular tests and diagnostic tools to design optimal cryopreservation protocols and avoid undesirable molecular alterations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28420141/coordinated-actions-of-micrornas-with-other-epigenetic-factors-regulate-skeletal-muscle-development-and-adaptation
#10
REVIEW
Marzia Bianchi, Alessandra Renzini, Sergio Adamo, Viviana Moresi
Epigenetics plays a pivotal role in regulating gene expression in development, in response to cellular stress or in disease states, in virtually all cell types. MicroRNAs (miRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate gene expression. miRNAs were discovered in 1993 and have been extensively studied ever since. They can be expressed in a tissue-specific manner and play a crucial role in tissue development and many biological processes. miRNAs are responsible for changes in the cell epigenome because of their ability to modulate gene expression post-transcriptionally...
April 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28418928/erk-signalling-modulates-epigenome-to-drive-epithelial-to-mesenchymal-transition
#11
Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay K Tiwari
The series of events that allow the conversion from adherent epithelial cells into migratory cells is collectively known as epithelial-mesenchymal transition (EMT). EMT is employed during embryonic development such as for gastrulation and neural crest migration and is misused in diseases, such as cancer metastasis. ERK signalling is known to be essential for EMT, however its influence on the epigenetic and transcriptional programme underlying EMT is poorly understood. Here, using a comprehensive genome-wide analysis of H3K27ac mark and gene expression in mammary epithelial cells undergoing EMT, we found that ERK signalling is essential for the epigenetic reprogramming underlying hallmark gene expression and phenotypic changes of EMT...
March 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418867/early-detection-of-gastric-cancer-using-global-genome-wide-and-irf4-elmo1-clip4-and-msc-dna-methylation-in-endoscopic-biopsies
#12
Francesca Pirini, Sassan Noazin, Martha H Jahuira-Arias, Sebastian Rodriguez-Torres, Leah Friess, Christina Michailidi, Jaime Cok, Juan Combe, Gloria Vargas, William Prado, Ethan Soudry, Jimena Pérez, Tikki Yudin, Andrea Mancinelli, Helen Unger, Carmen Ili-Gangas, Priscilla Brebi-Mieville, Douglas E Berg, Masamichi Hayashi, David Sidransky, Robert H Gilman, Rafael Guerrero-Preston
Clinically useful molecular tools to triage gastric cancer patients are not currently available. We aimed to develop a molecular tool to predict gastric cancer risk in endoscopy-driven biopsies obtained from high-risk gastric cancer clinics in low resource settings.We discovered and validated a DNA methylation biomarker panel in endoscopic samples obtained from 362 patients seen between 2004 and 2009 in three high-risk gastric cancer clinics in Lima, Perú, and validated it in 306 samples from the Cancer Genome Atlas project ("TCGA")...
March 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418097/genome-and-epigenome-of-a-novel-marine-thaumarchaeota-strain-suggest-viral-infection-phosphorothioation-dna-modification-and-multiple-restriction-systems
#13
Nathan A Ahlgren, Yangyang Chen, David M Needham, Alma E Parada, Rohan Sachdeva, Vicki Trinh, Ting Chen, Jed A Fuhrman
Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing features: putative phosphorothioation (PT) DNA modification genes; a region containing probable viral genes; and putative urea utilization genes...
April 18, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28418026/the-cac2-subunit-is-essential-for-productive-histone-binding-and-nucleosome-assembly-in-caf-1
#14
Francesca Mattiroli, Yajie Gu, Jeremy L Balsbaugh, Natalie G Ahn, Karolin Luger
Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28416947/dna-methylation-profiles-of-blood-cells-are-distinct-between-early-onset-obese-and-control-individuals
#15
Je-Keun Rhee, Jin-Hee Lee, Hae Kyung Yang, Tae-Min Kim, Kun-Ho Yoon
Obesity is a highly prevalent, chronic disorder that has been increasing in incidence in young patients. Both epigenetic and genetic aberrations may play a role in the pathogenesis of obesity. Therefore, in-depth epigenomic and genomic analyses will advance our understanding of the detailed molecular mechanisms underlying obesity and aid in the selection of potential biomarkers for obesity in youth. Here, we performed microarray-based DNA methylation and gene expression profiling of peripheral white blood cells obtained from six young, obese individuals and six healthy controls...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28415633/a-phase-2-study-of-vorinostat-in-locally-advanced-recurrent-or-metastatic-adenoid-cystic-carcinoma
#16
Priscila H Goncalves, Lance K Heilbrun, Michael T Barrett, Shivaani Kummar, Aaron R Hansen, Lillian L Siu, Richard L Piekarz, Ammar W Sukari, Joseph Chao, Mary Jo Pilat, Daryn W Smith, Lindsay Casetta, Scott A Boerner, Alice Chen, Elizabeth Lenkiewicz, Smriti Malasi, Patricia M LoRusso
PURPOSE: Vorinostat is a histone deacetylase inhibitor (HDACi). Based on a confirmed partial response (PR) in an adenoid cystic carcinoma (ACC) patient treated with vorinostat in a prior phase 1 trial, we initiated this phase 2 trial. METHODS: Vorinostat was administered orally 400 mg daily, 28 day cycles. The primary objective was to evaluate response rate (RR). Exploratory studies included whole exome sequencing (WES) of selected patients. RESULTS: Thirty patients were enrolled...
March 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414071/epigenetic-landscapes-underlining-global-patterns-of-gene-expression-in-the-human-malaria-parasite-plasmodium-falciparum
#17
REVIEW
Archana P Gupta, Zbynek Bozdech
The dynamic chromatin landscape displaying combinatorial complexity of the epigenome impacts gene expression that underlies many events of differentiation and cell cycle progression. In the past few years, epigenetic mechanisms have emerged as important processes involved in the tight gene regulation in malaria parasites, Plasmodium spp.. Focusing predominantly on Plasmodium falciparum, the species associated with the most severe form of the disease, many advances have been made in our understanding of the interaction between transcriptional regulation and epigenetic mechanisms as the pivotal processes in regulating life cycle progression, host parasite interactions and parasite adaptation to the host environment...
April 13, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28413450/fetal-testis-organ-culture-reproduces-the-dynamics-of-epigenetic-reprogramming-in-rat-gonocytes
#18
Arlette Rwigemera, Fabien Joao, Geraldine Delbes
BACKGROUND: Epigenetic reprogramming is a critical step in male germ cell development that occurs during perinatal life. It is characterized by the remodeling of different epigenetic marks such as DNA methylation (5mC) and methylation of histone H3. It has been suggested that endocrine disruptors can affect the male germline epigenome by altering epigenetic reprogramming, but the mechanisms involved are still unknown. We have previously used an organ culture system that maintains the development of the different fetal testis cell types, to evaluate the effects of various endocrine disruptors on gametogenesis and steroidogenesis in the rat...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28413449/links-between-dna-methylation-and-nucleosome-occupancy-in-the-human-genome
#19
Clayton K Collings, John N Anderson
BACKGROUND: DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28412585/the-promise-of-epigenetic-therapy-reprogramming-the-cancer-epigenome
#20
REVIEW
Andrew D Kelly, Jean-Pierre J Issa
Epigenetics refers to heritable molecular determinants of phenotype independent of DNA sequence. Epigenetic features include DNA methylation, histone modifications, non-coding RNAs, and chromatin structure. The epigenetic status of cells plays a crucial role in determining their differentiation state and proper function within multicellular organisms. Disruption of these processes is now understood to be a major contributor to cancer development and progression, and recent efforts have attempted to pharmacologically reverse such altered epigenetics...
April 13, 2017: Current Opinion in Genetics & Development
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