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https://www.readbyqxmd.com/read/28302790/complete-genome-and-methylome-analysis-of-psychrotrophic-bacterial-isolates-from-lake-untersee-in-antarctica
#1
Alexey Fomenkov, Vladimir N Akimov, Lina V Vasilyeva, Dale T Andersen, Tamas Vincze, Richard J Roberts
This paper describes the complete genome sequences and methylome analysis of six psychrotrophic strains isolated from perennially ice-covered Lake Untersee in Antarctica.
March 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28302778/complete-genome-and-methylome-sequences-of-salmonella-enterica-subsp-enterica-serovars-typhimurium-saintpaul-and-stanleyville-from-the-sara-sarb-collection
#2
Kuan Yao, Richard J Roberts, Marc W Allard, Maria Hoffmann
In this announcement, we report the complete genome and methylome sequences of three Salmonella enterica strains from the SARA and SARB collection: S. enterica subsp. enterica serovar Typhimurium (SARA13), S. enterica subsp. enterica serovar Saintpaul (SARA26), and S. enterica subsp. enterica serovar Stanleyville (SARB61).
March 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28298479/cyst-nematode-parasitism-induces-dynamic-changes-in-the-root-epigenome
#3
Tarek Hewezi, Thomas Lane, Sarbottam Piya, Aditi Rambani, J Hollis Rice, Meg Staton
A growing body of evidence indicates that epigenetic modifications can provide efficient, dynamic, and reversible cellular responses to a wide range of environmental stimuli. However, the significance of epigenetic modifications in plant-pathogen interactions remains largely unexplored. In this study, we provide a comprehensive analysis of epigenome changes during the compatible interaction between the beet cyst nematode Heterodera schachtii and Arabidopsis (Arabidopsis thaliana). Whole genome bisulfite sequencing was conducted to assess the dynamic changes in the methylome of Arabidopsis roots in response to H schachtii infection...
March 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28294656/the-nasal-methylome-a-key-to-understanding-allergic-asthma
#4
Ivana V Yang, Adam Richards, Elizabeth J Davidson, Allen D Stevens, Christena A Kolakowski, Richard J Martin, David A Schwartz
No abstract text is available yet for this article.
March 15, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28291257/integrated-transcriptome-and-methylome-analysis-in-youth-at-high-risk-for-bipolar-disorder-a-preliminary-analysis
#5
G R Fries, J Quevedo, C P Zeni, I F Kazimi, G Zunta-Soares, D E Spiker, C L Bowden, C Walss-Bass, J C Soares
First-degree relatives of patients with bipolar disorder (BD), particularly their offspring, have a higher risk of developing BD and other mental illnesses than the general population. However, the biological mechanisms underlying this increased risk are still unknown, particularly because most of the studies so far have been conducted in chronically ill adults and not in unaffected youth at high risk. In this preliminary study we analyzed genome-wide expression and methylation levels in peripheral blood mononuclear cells from children and adolescents from three matched groups: BD patients, unaffected offspring of bipolar parents (high risk) and controls (low risk)...
March 14, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28283040/functional-variation-in-allelic-methylomes-underscores-a-strong-genetic-contribution-and-reveals-novel-epigenetic-alterations-in-the-human-epigenome
#6
Warren A Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Marie-Michelle Simon, Elodie Boulier, Adriana Redensek, Stephen Watt, Avik Datta, Laura Clarke, Paul Flicek, Daniel Mead, Dirk S Paul, Stephan Beck, Guillaume Bourque, Mark Lathrop, André Tchernof, Marie-Claude Vohl, Florence Demenais, Isabelle Pin, Kate Downes, Hendrick G Stunnenberg, Nicole Soranzo, Tomi Pastinen, Elin Grundberg
BACKGROUND: The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have only been carried out in a limited set of samples. RESULTS: We describe a large-scale coordinated study of allelic and non-allelic effects on DNA methylation, histone mark deposition, and gene expression, detecting the interrelations between epigenetic and functional features at unprecedented resolution...
March 10, 2017: Genome Biology
https://www.readbyqxmd.com/read/28278225/identification-of-endometrial-cancer-methylation-features-using-combined-methylation-analysis-methods
#7
Michael P Trimarchi, Pearlly Yan, Joanna Groden, Ralf Bundschuh, Paul J Goodfellow
BACKGROUND: DNA methylation is a stable epigenetic mark that is frequently altered in tumors. DNA methylation features are attractive biomarkers for disease states given the stability of DNA methylation in living cells and in biologic specimens typically available for analysis. Widespread accumulation of methylation in regulatory elements in some cancers (specifically the CpG island methylator phenotype, CIMP) can play an important role in tumorigenesis. High resolution assessment of CIMP for the entire genome, however, remains cost prohibitive and requires quantities of DNA not available for many tissue samples of interest...
2017: PloS One
https://www.readbyqxmd.com/read/28276657/investigation-of-correlations-between-dna-methylation-suicidal-behavior-and-aging
#8
Richie Jeremian, Yi-An Chen, Vincenzo De Luca, John B Vincent, James L Kennedy, Clement C Zai, John Strauss
OBJECTIVES: Suicidal behavior (SB) is a major cause of mortality for patients diagnosed with bipolar disorder (BD). In this study, we investigated epigenetic differences in BD participants with and without a history of SB. METHODS: We used suicidality scores constructed from Schedule for Clinical Assessments in Neuropsychiatry (SCAN) interview questions about suicidal thought and behavior to identify individuals from a BD cohort of n=452; participants with the most extreme high (H-SB, n=18) and most extreme low (L-SB, n=22) scores were used as cases and controls, respectively...
March 9, 2017: Bipolar Disorders
https://www.readbyqxmd.com/read/28275209/concerted-flexibility-of-chromatin-structure-methylome-and-histone-modifications-along-with-plant-stress-responses
#9
REVIEW
Ana Paula Santos, Liliana J Ferreira, M Margarida Oliveira
The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype...
January 16, 2017: Biology
https://www.readbyqxmd.com/read/28271979/toward-a-taxonomy-for-multi-omics-science-terminology-development-for-whole-genome-study-approaches-by-omics-technology-and-hierarchy
#10
Nina Pirih, Tanja Kunej
Omics is a form of high-throughput systems science. However, taxonomies for omics studies are limited, inviting us to rethink new ways in which we classify, prioritize, and rank various omics systems science studies. In this overarching context, the genome-wide study approaches have proliferated in number and popularity over the past decade. However, their hierarchy is not well organized and the development of attendant terminology is not controlled. In the present study, we searched the literature in PubMed and the Web of Science databases published from March 1999 to September 2016 using the keywords, including genome-wide, association, whole genome, transcriptome-wide, metabolome, epigenome, and phenome...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28271161/dna-methylation-profiling-reveals-the-presence-of-population-specific-signatures-correlating-with-phenotypic-characteristics
#11
Anil K Giri, Soham Bharadwaj, Priyanka Banerjee, Shraddha Chakraborty, Vaisak Parekatt, Donaka Rajashekar, Abhishek Tomar, Aarthi Ravindran, Analabha Basu, Nikhil Tandon, Dwaipayan Bharadwaj
Phenotypic characteristics are known to vary substantially among different ethnicities around the globe. These variations are mediated by number of stochastic events and cannot be attributed to genetic architecture alone. DNA methylation is a well-established mechanism that sculpts our epigenome influencing phenotypic variation including disease manifestation. Since DNA methylation is an important determinant for health issues of a population, it demands a thorough investigation of the natural differences in genome wide DNA methylation patterns across different ethnic groups...
March 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28264723/developmental-pathways-to-adiposity-begin-before-birth-and-are-influenced-by-genotype-prenatal-environment-and-epigenome
#12
Xinyi Lin, Ives Yubin Lim, Yonghui Wu, Ai Ling Teh, Li Chen, Izzuddin M Aris, Shu E Soh, Mya Thway Tint, Julia L MacIsaac, Alexander M Morin, Fabian Yap, Kok Hian Tan, Seang Mei Saw, Michael S Kobor, Michael J Meaney, Keith M Godfrey, Yap Seng Chong, Joanna D Holbrook, Yung Seng Lee, Peter D Gluckman, Neerja Karnani
BACKGROUND: Obesity is an escalating health problem worldwide, and hence the causes underlying its development are of primary importance to public health. There is growing evidence that suboptimal intrauterine environment can perturb the metabolic programing of the growing fetus, thereby increasing the risk of developing obesity in later life. However, the link between early exposures in the womb, genetic susceptibility, and perturbed epigenome on metabolic health is not well understood...
March 7, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28259820/bclb-methylated-in-hepatocellular-carcinoma-is-a-starvation-stress%C3%A2-sensor-that-induces-apoptosis-and-autophagy-through-the%C3%A2-ampk-mtor-signaling-cascade
#13
Xiaolong Liu, Xiaotong Hu, Yeye Kuang, Peijian Yan, Lili Li, Chen Li, Qian Tao, Xiujun Cai
Epigenetic disruption of tumor suppressor genes (TSGs), particularly DNA methylation, plays a key role in hepatocellular carcinoma (HCC) pathogenesis. Through methylome study, we identified BCLB as a methylated gene in HCC. BCLB was methylated in all tumor cell lines with silenced or reduced expression. BCLB was further found to be silenced in 55.2% (58/105) of HCC samples, while 91.4% (96/105) of paired non-tumor tissues showed high BCLB expression. BCLB protein expression was significantly correlated with HBV status (p = 0...
March 2, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28259012/dna-methylome-analysis-identifies-accelerated-epigenetic-ageing-associated-with-postmenopausal-breast-cancer-susceptibility
#14
Srikant Ambatipudi, Steve Horvath, Flavie Perrier, Cyrille Cuenin, Hector Hernandez-Vargas, Florence Le Calvez-Kelm, Geoffroy Durand, Graham Byrnes, Pietro Ferrari, Liacine Bouaoun, Athena Sklias, Véronique Chajes, Kim Overvad, Gianluca Severi, Laura Baglietto, Françoise Clavel-Chapelon, Rudolf Kaaks, Myrto Barrdahl, Heiner Boeing, Antonia Trichopoulou, Pagona Lagiou, Androniki Naska, Giovanna Masala, Claudia Agnoli, Silvia Polidoro, Rosario Tumino, Salvatore Panico, Martijn Dollé, Petra H M Peeters, N Charlotte Onland-Moret, Torkjel M Sandanger, Therese H Nøst, Elisabete Weiderpass, J Ramón Quirós, Antonio Agudo, Miguel Rodriguez-Barranco, José María Huerta Castaño, Aurelio Barricarte, Ander Matheu Fernández, Ruth C Travis, Paolo Vineis, David C Muller, Elio Riboli, Marc Gunter, Isabelle Romieu, Zdenko Herceg
AIM OF THE STUDY: A vast majority of human malignancies are associated with ageing, and age is a strong predictor of cancer risk. Recently, DNA methylation-based marker of ageing, known as 'epigenetic clock', has been linked with cancer risk factors. This study aimed to evaluate whether the epigenetic clock is associated with breast cancer risk susceptibility and to identify potential epigenetics-based biomarkers for risk stratification. METHODS: Here, we profiled DNA methylation changes in a nested case-control study embedded in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (n = 960) using the Illumina HumanMethylation 450K BeadChip arrays and used the Horvath age estimation method to calculate epigenetic age for these samples...
February 28, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28255110/methylome-wide-association-study-of-whole-blood-dna-in-the-norfolk-island-isolate-identifies-robust-loci-associated-with-age
#15
Miles C Benton, Heidi G Sutherland, Donia Macartney-Coxson, Larisa M Haupt, Rodney A Lea, Lyn R Griffiths
Epigenetic regulation of various genomic functions, including gene expression, provide mechanisms whereby an organism can dynamically respond to changes in its environment and modify gene expression accordingly. One epigenetic mechanism implicated in human aging and age-related disorders is DNA methylation. Isolated populations such as Norfolk Island (NI) should be advantageous for the identification of epigenetic factors related to aging due to reduced genetic and environmental variation. Here we conducted a methylome-wide association study of age using whole blood DNA in 24 healthy female individuals from the NI genetic isolate (aged 24-47 years)...
February 28, 2017: Aging
https://www.readbyqxmd.com/read/28241876/erratum-to-methylome-evolution-in-plants
#16
Amaryllis Vidalis, Daniel Živković, René Wardenaar, David Roquis, Aurélien Tellier, Frank Johannes
No abstract text is available yet for this article.
February 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/28228259/sirt1-regulates-dna-methylation-and-differentiation-potential-of-embryonic-stem-cells-by-antagonizing-dnmt3l
#17
Jinbeom Heo, Jisun Lim, Seungun Lee, Jaeho Jeong, Hyunsook Kang, YongHwan Kim, Jeong Wook Kang, Hwan Yeul Yu, Eui Man Jeong, Kyunggon Kim, Magda Kucia, Sabine J Waigel, Wolfgang Zacharias, Yinlu Chen, In-Gyu Kim, Mariusz Z Ratajczak, Dong-Myung Shin
Embryonic stem cell (ESC) abnormalities in genome methylation hamper the utility of their therapeutic derivatives; however, the underlying mechanisms are unknown. Here, we show that the nicotinamide adenine dinucleotide (NAD)-dependent deacetylase, Sirt1, selectively prevents abnormal DNA methylation of some developmental genes in murine ESCs by antagonizing Dnmt3l. Transcriptome and DNA methylome analyses demonstrated that Sirt1-null (Sirt1(-/-)) ESCs repress expression of a subset of imprinted and germline genes concomitant with increased DNA methylation of regulatory elements...
February 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28226269/the-causes-and-consequences-of-dna-methylome-variation-in-plants
#18
REVIEW
Danelle K Seymour, Claude Becker
Epigenetic variation - polymorphisms at the level of DNA methylation or histone modifications - modulates chromatin accessibility, which can perturb transcriptional activity and spur phenotypic variation. Determining the origin, frequency spectrum, and consequences of epigenetic variants is key to understanding the role of this variation in generating stable phenotypic variation in plants. Here we review recent literature on DNA methylation variation in both model and crop plant species with a focus on the link between genotype, epigenotype, and transcription...
February 19, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28223400/distal-cpg-islands-can-serve-as-alternative-promoters-to-transcribe-genes-with-silenced-proximal-promoters
#19
Shrutii Sarda, Avinash Das, Charles Vinson, Sridhar Hannenhalli
DNA methylation at the promoter of a gene is presumed to render it silent, yet, a sizable fraction of genes with methylated proximal-promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a distal upstream CpG island (CGI) located several kilobases away that functions as an alternative promoter. Specifically, such genes are expressed precisely when the neighboring CGI remains unmethylated, but remain silenced otherwise...
February 21, 2017: Genome Research
https://www.readbyqxmd.com/read/28218898/detecting-dna-cytosine-methylation-using-nanopore-sequencing
#20
Jared T Simpson, Rachael E Workman, P C Zuzarte, Matei David, L J Dursi, Winston Timp
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.
February 20, 2017: Nature Methods
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