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https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#1
(no author information available yet)
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations)...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036466/insights-into-epigenome-evolution-from-animal-and-plant-methylomes
#2
Soojin V Yi
Evolutionary studies of DNA methylation begin to provide insights into the underlying forces governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the contents of repetitive sequences, while the underlying driver of this correlation is less clear in animal genomes...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29032243/dna-methylation-patterns-are-related-to-co-morbidity-status-and-circulating-c-reactive-protein-levels-in-the-nursing-home-elderly
#3
Chris P Verschoor, Lisa M McEwen, Michael S Kobor, Mark B Loeb, Dawn M E Bowdish
Elderly residents of long-term care commonly exhibit a number of age-related health deficits, including impaired physical and cognitive function, chronic illnesses, and chronic inflammation. Given our previous data relating the phenotype and function of innate and adaptive leukocytes from the nursing home elderly to chronic conditions and inflammatory biomarkers, we hypothesized that these factors would influence the regulatory programming of immune cells, thereby contributing to immune dysfunction. Since DNA methylation represents both an important regulatory mechanism of cells as well as a biomarker of health and disease, we sought to characterize the methylome of peripheral blood mononuclear cells (PBMCs) from the nursing home elderly (n=23; 82-98years old, 70% female), and compare these patterns to pathological factors such as dementia, co-morbidity score and frailty, and immune-related factors such as serum C-reactive protein (CRP) and cytokine levels and varicella-zoster virus (VZV) vaccine responsiveness...
October 12, 2017: Experimental Gerontology
https://www.readbyqxmd.com/read/29031162/dna-demethylation-activates-genes-in-seed-maternal-integument-development-in-rice-oryza-sativa-l
#4
Yifeng Wang, Haiyan Lin, Xiaohong Tong, Yuxuan Hou, Yuxiao Chang, Jian Zhang
DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development...
September 27, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29030974/dopamine-transporter-gene-methylation-is-associated-with-nucleus-accumbens-activation-during-reward-processing-in-healthy-but-not-alcohol-dependent-individuals
#5
Christine Muench, Corinde E Wiers, Carlos R Cortes, Reza Momenan, Falk W Lohoff
BACKGROUND: Alcohol's reinforcement is mediated by dopamine signaling in the ventral striatum, which is modulated by the dopamine transporter (DAT). We hypothesized that methylomic variation in the DAT gene (SLC6A3) affects DAT expression thus contributing to differences in brain reward circuitry in individuals with alcohol dependence (ALC). METHODS: Blood from 45 recently detoxified ALC and 45 healthy control (HC) individuals was used to assess DNA methylation across 5 functional regions of SLC6A3...
October 14, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/29029430/methylomics-of-nitroxidative-stress-on-precancerous-cells-reveals-dna-methylation-alteration-at-the-transition-from-in-situ-to-invasive-cervical-cancer
#6
Po-Hsuan Su, Yao-Wen Hsu, Rui-Lan Huang, Yu-Chun Weng, Hui-Chen Wang, Yu-Chih Chen, Yueh-Ju Tsai, Chiou-Chung Yuan, Hung-Cheng Lai
Epigenetic dysregulation is important in cervical cancer development, but the underlying mechanism is largely unknown. Increasing evidence indicates that DNA methylation is sensitive to changes in microenvironmental factors, such as nitric oxide (NO) in the chronic inflammatory cervix. However, the epigenomic effects of NO in cancer have not been investigated. In this study, we explored the methylomic effects of nitroxidative stress in HPV-immortalized precancerous cells. Chronic NO exposure promoted the acquisition of malignant phenotypes such as cell growth, migration, invasion, and anchorage-independent growth...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29026108/rifs-a-randomly-restarted-incremental-feature-selection-algorithm
#7
Yuting Ye, Ruochi Zhang, Weiwei Zheng, Shuai Liu, Fengfeng Zhou
The advent of big data era has imposed both running time and learning efficiency challenges for the machine learning researchers. Biomedical OMIC research is one of these big data areas and has changed the biomedical research drastically. But the high cost of data production and difficulty in participant recruitment introduce the paradigm of "large p small n" into the biomedical research. Feature selection is usually employed to reduce the high number of biomedical features, so that a stable data-independent classification or regression model may be achieved...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29025412/dynamic-transcriptome-and-dna-methylome-analyses-on-longissimus-dorsi-to-identify-genes-underlying-intramuscular-fat-content-in-pigs
#8
Yuding Wang, Cai Ma, Yi Sun, Yi Li, Li Kang, Yunliang Jiang
BACKGROUND: The intramuscular fat content (IMF) refers to the amount of fat within muscles, including the sum of phospholipids mainly found in cell membranes, triglycerides and cholesterol, and is determined both by hyperplasia and hypertrophy of adipocyte during the development of pigs. The IMF content is an important economic trait that is genetically controlled by multiple genes. The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by excessively higher level of IMF content (9%~12%), therefore, is suitable for the identification of genes controlling IMF variations...
October 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29020802/recent-advances-in-the-systems-biology-of-aging
#9
Daniel Edward Lee Promislow, Mark A McCormick
<b><i>Significance</i></b>: Reductionist studies have contributed greatly to our understanding of the basic biology of aging in recent years but we still do not understand fundamental mechanisms for many identified drugs and pathways. Use of systems approaches will help us move forward in our understanding of aging. <b><i>Recent Advances</i></b>: Recent work described here has illustrated the power of systems biology to inform our understanding of aging through the study of 1) diet restriction; 2) neurodegenerative disease; and 3) biomarkers of aging...
October 12, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/29019987/establishment-of-mouse-expanded-potential-stem-cells
#10
Jian Yang, David J Ryan, Wei Wang, Jason Cheuk-Ho Tsang, Guocheng Lan, Hideki Masaki, Xuefei Gao, Liliana Antunes, Yong Yu, Zhexin Zhu, Juexuan Wang, Aleksandra A Kolodziejczyk, Lia S Campos, Cui Wang, Fengtang Yang, Zhen Zhong, Beiyuan Fu, Melanie A Eckersley-Maslin, Michael Woods, Yosuke Tanaka, Xi Chen, Adam C Wilkinson, James Bussell, Jacqui White, Ramiro Ramirez-Solis, Wolf Reik, Berthold Göttgens, Sarah A Teichmann, Patrick P L Tam, Hiromitsu Nakauchi, Xiangang Zou, Liming Lu, Pentao Liu
Mouse embryonic stem cells derived from the epiblast contribute to the somatic lineages and the germline but are excluded from the extra-embryonic tissues that are derived from the trophectoderm and the primitive endoderm upon reintroduction to the blastocyst. Here we report that cultures of expanded potential stem cells can be established from individual eight-cell blastomeres, and by direct conversion of mouse embryonic stem cells and induced pluripotent stem cells. Remarkably, a single expanded potential stem cell can contribute both to the embryo proper and to the trophectoderm lineages in a chimaera assay...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29018624/genome-methylation-and-regulatory-functions-for-hypoxic-adaptation-in-tibetan-chicken-embryos
#11
Yawen Zhang, Wenyu Gou, Jun Ma, Hongliang Zhang, Ying Zhang, Hao Zhang
Tibetan chickens have unique adaptations to the extreme high-altitude environment that they inhabit. Epigenetic DNA methylation affects many biological processes, including hypoxic adaptation; however, the regulatory genes for DNA methylation in hypoxic adaptation remain unknown. In this study, methylated DNA immunoprecipitation with high-throughput sequencing (MeDIP-seq) was used to provide an atlas of the DNA methylomes of the heart tissue of hypoxic highland Tibetan and lowland Chahua chicken embryos. A total of 31...
2017: PeerJ
https://www.readbyqxmd.com/read/28994822/whole-genome-dna-methylation-sequencing-of-the-chicken-retina-cornea-and-brain
#12
Isac Lee, Bejan A Rasoul, Ashton S Holub, Alannah Lejeune, Raymond A Enke, Winston Timp
Whole genome bisulfite sequencing (WGBS) analysis of DNA methylation uses massively parallel next generation sequencing technology to characterize global epigenetic patterns and fluctuations throughout a range of tissue samples. Development of the vertebrate retina is thought to involve extensive epigenetic reprogramming during embryogenesis. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal methylome...
October 10, 2017: Scientific Data
https://www.readbyqxmd.com/read/28989734/detecting-rare-asymmetrically-methylated-cytosines-and-decoding-methylation-patterns-in-the-honeybee-genome
#13
Laura Welsh, Ryszard Maleszka, Sylvain Foret
Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that CpG hemimethylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome...
September 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28986422/the-arabidopsis-dna-methylome-is-stable-under-transgenerational-drought-stress
#14
Diep Ganguly, Peter Alexander Crisp, Steven R Eichten, Barry J Pogson
Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally-relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow onset water deprivation treatment in Arabidopsis we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations...
October 6, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28981577/-multi-omic-data-analysis-using-o-miner
#15
Ajanthah Sangaralingam, Abu Z Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, Ai Nagano, Helen Ross-Adams, Jun Wang, Nicholas R Lemoine, Claude Chelala
Innovations in -omics technologies have driven advances in biomedical research. However, integrating and analysing the large volumes of data generated from different high-throughput -omics technologies remain a significant challenge to basic and clinical scientists without bioinformatics skills or access to bioinformatics support. To address this demand, we have significantly updated our previous O-miner analytical suite, to incorporate several new features and data types to provide an efficient and easy-to-use Web tool for the automated analysis of data from '-omics' technologies...
August 4, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28978943/global-misregulation-of-genes-largely-uncoupled-to-dna-methylome-epimutations-characterizes-a-congenital-overgrowth-syndrome
#16
Zhiyuan Chen, Darren E Hagen, Tieming Ji, Christine G Elsik, Rocío M Rivera
Assisted reproductive therapies (ART) have become increasingly common worldwide and numerous retrospective studies have indicated that ART-conceived children are more likely to develop the overgrowth syndrome Beckwith-Wiedemann (BWS). In bovine, the use of ART can induce a similar overgrowth condition, which is referred to as large offspring syndrome (LOS). Both BWS and LOS involve misregulation of imprinted genes. However, it remains unknown whether molecular alterations at non-imprinted loci contribute to these syndromes...
October 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28978736/persistent-and-plastic-effects-of-temperature-on-dna-methylation-across-the-genome-of-threespine-stickleback-gasterosteus-aculeatus
#17
David C H Metzger, Patricia M Schulte
Epigenetic mechanisms such as changes in DNA methylation have the potential to affect the resilience of species to climate change, but little is known about the response of the methylome to changes in environmental temperature in animals. Using reduced representation bisulfite sequencing, we assessed the effects of development temperature and adult acclimation temperature on DNA methylation levels in threespine stickleback (Gasterosteus aculeatus). Across all treatments, we identified 2130 differentially methylated cytosines distributed across the genome...
October 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28978469/prostaglandin-e2-leads-to-the-acquisition-of-dnmt3a-dependent-tolerogenic-functions-in-human-myeloid-derived-suppressor-cells
#18
Javier Rodríguez-Ubreva, Francesc Català-Moll, Nataša Obermajer, Damiana Álvarez-Errico, Ricardo N Ramirez, Carlos Company, Roser Vento-Tormo, Gema Moreno-Bueno, Robert P Edwards, Ali Mortazavi, Pawel Kalinski, Esteban Ballestar
Myeloid-derived suppressor cells (MDSCs) and dendritic cells (DCs) arise from common progenitors. Tumor-derived factors redirect differentiation from immune-promoting DCs to tolerogenic MDSCs, an immunological hallmark of cancer. Indeed, in vitro differentiation of DCs from human primary monocytes results in the generation of MDSCs under tumor-associated conditions (PGE2 or tumor cell-conditioned media). Comparison of MDSC and DC DNA methylomes now reveals extensive demethylation with specific gains of DNA methylation and repression of immunogenic-associated genes occurring in MDSCs specifically, concomitant with increased DNA methyltransferase 3A (DNMT3A) levels...
October 3, 2017: Cell Reports
https://www.readbyqxmd.com/read/28977914/potential-link-between-fusobacterium-enrichment-and-dna-methylation-accumulation-in-the-inflammatory-colonic-mucosa-in-ulcerative-colitis
#19
Tomomitsu Tahara, Ichiro Hirata, Naoko Nakano, Sayumi Tahara, Noriyuki Horiguchi, Tomohiko Kawamura, Masaaki Okubo, Takamitsu Ishizuka, Hyuga Yamada, Dai Yoshida, Takafumi Ohmori, Kohei Maeda, Naruomi Komura, Hirokazu Ikuno, Yasutaka Jodai, Toshiaki Kamano, Mitsuo Nagasaka, Yoshihito Nakagawa, Tetsuya Tuskamoto, Makoto Urano, Tomoyuki Shibata, Makoto Kuroda, Naoki Ohmiya
BACKGROUND AND AIM: Fusobacterium enrichment has been associated with colorectal cancer development. Ulcerative colitis (UC) associated tumorigenesis is characterized as high degree of methylation accumulation through continuous colonic inflammation. The aim of this study was to investigate a potential link between Fusobacterium enrichment and DNA methylation accumulation in the inflammatory colonic mucosa in UC. METHODS: In the candidate analysis, inflamed colonic mucosa from 86 UC patients were characterized the methylation status of colorectal a panel of cancer related 24 genes...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28973837/ezh2-modulates-the-dna-methylome-and-controls-t-cell-adhesion-through-junctional-adhesion-molecule-a-in-lupus-patients
#20
Pei-Suen Tsou, Patrick Coit, Nathan C Kilian, Amr H Sawalha
OBJECTIVE: EZH2 is an epigenetic regulator that mediates H3K27 trimethylation and modulates DNA methylation. The aim of this study is to characterize the role of EZH2 in CD4+ T cells upon lupus pathogenesis. METHODS: EZH2 expression levels were determined in CD4+ T cells isolated from lupus patients and healthy controls. The epigenetic effects of EZH2 overexpression in CD4+ T cells were evaluated using a genome-wide DNA methylation approach. Gene expression and miRNAs were assessed by qPCR while protein expression was examined by Western blotting...
October 3, 2017: Arthritis & Rheumatology
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