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Methylomics

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https://www.readbyqxmd.com/read/27933100/genome-and-methylome-of-the-oleaginous-diatom-cyclotella-cryptica-reveal-genetic-flexibility-toward-a-high-lipid-phenotype
#1
Jesse C Traller, Shawn J Cokus, David A Lopez, Olga Gaidarenko, Sarah R Smith, John P McCrow, Sean D Gallaher, Sheila Podell, Michael Thompson, Orna Cook, Marco Morselli, Artur Jaroszewicz, Eric E Allen, Andrew E Allen, Sabeeha S Merchant, Matteo Pellegrini, Mark Hildebrand
BACKGROUND: Improvement in the performance of eukaryotic microalgae for biofuel and bioproduct production is largely dependent on characterization of metabolic mechanisms within the cell. The marine diatom Cyclotella cryptica, which was originally identified in the Aquatic Species Program, is a promising strain of microalgae for large-scale production of biofuel and bioproducts, such as omega-3 fatty acids. RESULTS: We sequenced the nuclear genome and methylome of this oleaginous diatom to identify the genetic traits that enable substantial accumulation of triacylglycerol...
2016: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/27924602/genome-wide-analysis-of-periodontal-and-peri-implant-cells-and-tissues
#2
Moritz Kebschull, Claudia Hülsmann, Per Hoffmann, Panos N Papapanou
Omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ or tissue sample, are powerful means of generating comprehensive genome-level data sets on complex diseases. We have systematically assessed the transcriptome, miRNome and methylome of gingival tissues from subjects with different diagnostic entities of periodontal disease, and studied the transcriptome of primary cells ex vivo, or in vitro after infection with periodontal pathogens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924600/generating-multiple-base-resolution-dna-methylomes-using-reduced-representation-bisulfite-sequencing
#3
Aniruddha Chatterjee, Euan J Rodger, Peter A Stockwell, Gwenn Le Mée, Ian M Morison
Reduced representation bisulfite sequencing (RRBS) is an effective technique for profiling genome-wide DNA methylation patterns in eukaryotes. RRBS couples size selection, bisulfite conversion, and second-generation sequencing to enrich for CpG-dense regions of the genome. The progressive improvement of second-generation sequencing technologies and reduction in cost provided an opportunity to examine the DNA methylation patterns of multiple genomes. Here, we describe a protocol for sequencing multiple RRBS libraries in a single sequencing reaction to generate base-resolution methylomes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924023/methsmrt-an-integrative-database-for-dna-n6-methyladenine-and-n4-methylcytosine-generated-by-single-molecular-real-time-sequencing
#4
Pohao Ye, Yizhao Luan, Kaining Chen, Yizhi Liu, Chuanle Xiao, Zhi Xie
DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923837/the-nci-60-methylome-and-its-integration-into-cellminer
#5
William C Reinhold, Sudhir Varma, Margot Sunshine, Vinodh Rajapakse, Augustin Luna, Kurt W Kohn, Holly Stevenson, Yonghong Wang, Holger Heyn, Vanesa Nogales, Sebastian Moran, David J Goldstein, James H Doroshow, Paul S Meltzer, Manel Esteller, Yves Pommier
A unique resource for systems pharmacology and genomic studies is the NCI-60 cancer cell line panel, which provides data for the largest publicly available library of compounds with cytotoxic activity (~21,000 compounds), including 108 FDA-approved and 70 clinical trial drugs as well as genomic data, including whole-exome sequencing, gene and microRNA transcripts, DNA copy number, and protein levels. Here we provide the first readily usable genome-wide DNA methylation database for the NCI-60, including 485,577 probes from the Infinium HumanMethylation450k BeadChip array, which yielded DNA methylation signatures for 17,559 genes integrated into our open access CellMiner version 2...
December 6, 2016: Cancer Research
https://www.readbyqxmd.com/read/27917918/distinct-epigenomes-in-cd4-t-cells-of-newborns-middle-ages-and-centenarians
#6
Ming Zhao, Jian Qin, Hanqi Yin, Yixin Tan, Wei Liao, Qian Liu, Shuangyan Luo, Min He, Gongping Liang, Yajing Shi, Qing Zhang, Wenjun Cai, Guangliang Yin, Yin Zhou, Jing Wang, Mengying Li, Yi Huang, Aiyun Liu, Haijing Wu, Zhiyong Zhang, Qianjin Lu
Age-related variations in genes and microRNAs expression and DNA methylation have been reported respectively; however, their interactions during aging are unclear. We therefore investigated alterations in the transcriptomes, miRNAomes and DNA methylomes in the same CD4(+)T cells from newborn (NB), middle-aged (MA) and long-lived (LL) individuals to elucidate the molecular changes and their interactions. A total 659 genes showed significantly expression changes across NB, MA and LL individuals, in which we identified four age-related co-expression modules with three hub networks of co-expressed genes and non-coding RNAs...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917903/global-dna-methylation-variations-after-short-term-heat-shock-treatment-in-cultured-microspores-of-brassica-napus-cv-topas
#7
Jun Li, Qian Huang, Mengxiang Sun, Tianyao Zhang, Hao Li, Biyun Chen, Kun Xu, Guizhen Gao, Feng Li, Guixin Yan, Jiangwei Qiao, Yongping Cai, Xiaoming Wu
Heat stress can induce the cultured microspores into embryogenesis. In this study, whole genome bisulphite sequencing was employed to study global DNA methylation variations after short-term heat shock (STHS) treatments in cultured microspores of Brassica napus cv. Topas. Our results indicated that treatment on cultured Topas microspores at 32 °C for 6 h triggered DNA hypomethylation, particularly in the CG and CHG contexts. And the total number of T32 (Topas 32 °C for 6 h) vs. T0 (Topas 0 h) differentially methylated region-related genes (DRGs) was approximately two-fold higher than that of T18 (Topas 18 °C for 6 h) vs...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27911846/dna-methylome-of-the-20-gigabase-norway-spruce-genome
#8
Israel Ausin, Suhua Feng, Chaowei Yu, Wanlu Liu, Hsuan Yu Kuo, Elise L Jacobsen, Jixian Zhai, Javier Gallego-Bartolome, Lin Wang, Ulrika Egertsdotter, Nathaniel R Street, Steven E Jacobsen, Haifeng Wang
DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27904456/methylome-analysis-of-two-xanthomonas-spp-using-single-molecule-real-time-sequencing
#9
Hoon Je Seong, Hye-Jee Park, Eunji Hong, Sung Chul Lee, Woo Jun Sul, Sang-Wook Han
Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv...
December 2016: Plant Pathology Journal
https://www.readbyqxmd.com/read/27899673/diseasemeth-version-2-0-a-major-expansion-and-update-of-the-human-disease-methylation-database
#10
Yichun Xiong, Yanjun Wei, Yue Gu, Shumei Zhang, Jie Lyu, Bin Zhang, Chuangeng Chen, Jiang Zhu, Yihan Wang, Hongbo Liu, Yan Zhang
The human disease methylation database (DiseaseMeth, http://bioinfo.hrbmu.edu.cn/diseasemeth/) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have promoted the production of methylome data that contain comprehensive knowledge of human diseases. In this DiseaseMeth update, we have increased the number of samples from 3610 to 32 701, the number of diseases from 72 to 88 and the disease-gene associations from 216 201 to 679 602...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899658/the-big-data-center-from-deposition-to-integration-to-translation
#11
(no author information available yet)
Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898055/increased-dna-methylation-variability-in-type-1-diabetes-across-three-immune-effector-cell-types
#12
Dirk S Paul, Andrew E Teschendorff, Mary A N Dang, Robert Lowe, Mohammed I Hawa, Simone Ecker, Huriya Beyan, Stephanie Cunningham, Alexandra R Fouts, Anita Ramelius, Frances Burden, Samantha Farrow, Sophia Rowlston, Karola Rehnstrom, Mattia Frontini, Kate Downes, Stephan Busche, Warren A Cheung, Bing Ge, Marie-Michelle Simon, David Bujold, Tony Kwan, Guillaume Bourque, Avik Datta, Ernesto Lowy, Laura Clarke, Paul Flicek, Emanuele Libertini, Simon Heath, Marta Gut, Ivo G Gut, Willem H Ouwehand, Tomi Pastinen, Nicole Soranzo, Sabine E Hofer, Beate Karges, Thomas Meissner, Bernhard O Boehm, Corrado Cilio, Helena Elding Larsson, Åke Lernmark, Andrea K Steck, Vardhman K Rakyan, Stephan Beck, R David Leslie
The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epigenome-wide association study across 406,365 CpGs in 52 monozygotic twin pairs discordant for T1D in three immune effector cell types. We observe a substantial enrichment of differentially variable CpG positions (DVPs) in T1D twins when compared with their healthy co-twins and when compared with healthy, unrelated individuals...
November 29, 2016: Nature Communications
https://www.readbyqxmd.com/read/27895318/whole-genome-dna-methylation-beyond-genes-silencing
#13
Roberto Tirado-Magallanes, Khadija Rebbani, Ricky Lim, Sriharsa Pradhan, Touati Benoukraf
The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution studies have revealed a role for very punctual DNA methylation in chromatin plasticity, gene regulation and splicing. Here, we aim to outline the major biological consequences of DNA methylation recently discovered...
November 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27886642/obesity-and-the-breast-cancer-methylome
#14
REVIEW
William B Coleman
Breast cancer is associated with risk factors such as advancing age and obesity. However, the linkages between these risk factors for breast cancer development and initiation of the disease are not yet clear. Obesity may drive breast cancer development through increases in circulating estrogens in postmenopausal women. Mammary cell susceptibility to neoplastic transformation requires both genetic and epigenetic alterations, including changes in DNA methylation. Obesity is also subject to epigenetic regulation...
November 22, 2016: Current Opinion in Pharmacology
https://www.readbyqxmd.com/read/27886132/the-future-is-the-past-methylation-qtls-in-schizophrenia
#15
REVIEW
Anke Hoffmann, Michael Ziller, Dietmar Spengler
Genome-wide association studies (GWAS) have remarkably advanced insight into the genetic basis of schizophrenia (SCZ). Still, most of the functional variance in disease risk remains unexplained. Hence, there is a growing need to map genetic variability-to-genes-to-functions for understanding the pathophysiology of SCZ and the development of better treatments. Genetic variation can regulate various cellular functions including DNA methylation, an epigenetic mark with important roles in transcription and the mediation of environmental influences...
November 24, 2016: Genes
https://www.readbyqxmd.com/read/27885609/methods-for-genome-wide-methylome-profiling-of-campylobacter-jejuni
#16
Kathy T Mou, Tyson A Clark, Usha K Muppirala, Andrew J Severin, Paul J Plummer
Methylation has a profound role in the regulation of numerous biological processes in bacteria including virulence. The study of methylation in bacteria has greatly advanced thanks to next-generation sequencing technologies. These technologies have expedited the process of uncovering unique features of many bacterial methylomes such as characterizing previously uncharacterized methyltransferases, cataloging genome-wide DNA methylations in bacteria, identifying the frequency of methylation at particular genomic loci, and revealing regulatory roles of methylation in the biology of various bacterial species...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27882781/age-related-epigenetic-drift-and-phenotypic-plasticity-loss-implications-in-prevention-of-age-related-human-diseases
#17
Yuanyuan Li, Trygve O Tollefsbol
Aging is considered as one of the most important developmental processes in organisms and is closely associated with global deteriorations of epigenetic markers such as aberrant methylomic patterns. This altered epigenomic state, referred to 'epigenetic drift', reflects deficient maintenance of epigenetic marks and contributes to impaired cellular and molecular functions in aged cells. Epigenetic drift-induced abnormal changes during aging are scantily repaired by epigenetic modulators. This inflexibility in the aged epigenome may lead to an age-related decline in phenotypic plasticity at the cellular and molecular levels due to epigenetic drift...
December 2016: Epigenomics
https://www.readbyqxmd.com/read/27877189/genome-wide-differences-in-dna-methylation-changes-in-two-contrasting-rice-genotypes-in-response-to-drought-conditions
#18
Wensheng Wang, Qiao Qin, Fan Sun, Yinxiao Wang, Dandan Xu, Zhikang Li, Binying Fu
Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27870873/herbivore-induced-dna-demethylation-changes-floral-signalling-and-attractiveness-to-pollinators-in-brassica-rapa
#19
Roman T Kellenberger, Philipp M Schlüter, Florian P Schiestl
Plants have to fine-tune their signals to optimise the trade-off between herbivore deterrence and pollinator attraction. An important mechanism in mediating plant-insect interactions is the regulation of gene expression via DNA methylation. However, the effect of herbivore-induced DNA methylation changes on pollinator-relevant plant signalling has not been systematically investigated. Here, we assessed the impact of foliar herbivory on DNA methylation and floral traits in the model crop plant Brassica rapa...
2016: PloS One
https://www.readbyqxmd.com/read/27867036/dna-methylation-dynamics-of-human-hematopoietic-stem-cell-differentiation
#20
Matthias Farlik, Florian Halbritter, Fabian Müller, Fizzah A Choudry, Peter Ebert, Johanna Klughammer, Samantha Farrow, Antonella Santoro, Valerio Ciaurro, Anthony Mathur, Rakesh Uppal, Hendrik G Stunnenberg, Willem H Ouwehand, Elisa Laurenti, Thomas Lengauer, Mattia Frontini, Christoph Bock
Hematopoietic stem cells give rise to all blood cells in a differentiation process that involves widespread epigenome remodeling. Here we present genome-wide reference maps of the associated DNA methylation dynamics. We used a meta-epigenomic approach that combines DNA methylation profiles across many small pools of cells and performed single-cell methylome sequencing to assess cell-to-cell heterogeneity. The resulting dataset identified characteristic differences between HSCs derived from fetal liver, cord blood, bone marrow, and peripheral blood...
December 1, 2016: Cell Stem Cell
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