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https://www.readbyqxmd.com/read/29668744/data-quality-of-whole-genome-bisulfite-sequencing-on-illumina-platforms
#1
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/29614954/bs-seeker3-ultrafast-pipeline-for-bisulfite-sequencing
#2
Kevin Yu Yuan Huang, Yan-Jiun Huang, Pao-Yang Chen
BACKGROUND: DNA methylation is an important epigenetic modification critical in regulation and transgenerational inheritance. The methylation level can be estimated at single-nucleotide resolution by whole-genome bisulfite sequencing (BS-seq; WGBS). Current bisulfite aligners provide pipelines for processing the reads by WGBS; however, few are able to analyze the BS-seqs in a reasonable timeframe that meets the needs of the rapid expansion of epigenome sequencing in biomedical research...
April 3, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29613827/experience-dependent-neuroplasticity-of-the-developing-hypothalamus-integrative-epigenomic-approaches
#3
Annie Vogel Ciernia, Benjamin I Laufer, Keith W Dunaway, Charles E Mordaunt, Rochelle L Coulson, Theresa S Totah, Danielle S Stolzenberg, Jaime Frahm, Akanksha Singh-Taylor, Tallie Z Baram, Janine M LaSalle, Dag H Yasui
Augmented maternal care during the first postnatal week promotes life-long stress resilience and improved memory compared with the outcome of routine rearing conditions. Recent evidence suggests that this programming commences with altered synaptic connectivity of stress sensitive hypothalamic neurons. However, the epigenomic basis of the long-lived consequences is not well understood. Here, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to examine the effects of augmented maternal care on DNA cytosine methylation, gene expression, and miRNA expression...
April 3, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29610480/dna-methylation-loss-in-late-replicating-domains-is-linked-to-mitotic-cell-division
#4
Wanding Zhou, Huy Q Dinh, Zachary Ramjan, Daniel J Weisenberger, Charles M Nicolet, Hui Shen, Peter W Laird, Benjamin P Berman
DNA methylation loss occurs frequently in cancer genomes, primarily within lamina-associated, late-replicating regions termed partially methylated domains (PMDs). We profiled 39 diverse primary tumors and 8 matched adjacent tissues using whole-genome bisulfite sequencing (WGBS) and analyzed them alongside 343 additional human and 206 mouse WGBS datasets. We identified a local CpG sequence context associated with preferential hypomethylation in PMDs. Analysis of CpGs in this context ('solo-WCGWs') identified previously undetected PMD hypomethylation in almost all healthy tissue types...
April 2, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29581568/author-correction-global-delay-in-nascent-strand-dna-methylation
#5
Jocelyn Charlton, Timothy L Downing, Zachary D Smith, Hongcang Gu, Kendell Clement, Ramona Pop, Veronika Akopian, Sven Klages, David P Santos, Alexander M Tsankov, Bernd Timmermann, Michael J Ziller, Evangelos Kiskinis, Andreas Gnirke, Alexander Meissner
Following online publication of this article, the Gene Expression Omnibus records corresponding to accession codes GSM2406773, MN-d6, and GSM2406772, MN-d14, listed in the data availability statement were deleted. The data are now available under accession codes GSM3039355, WGBS_hESC_WT_D6_R4 (MN day 6), and GSM3039351, WGBS_hESC_WT_D14_R4 (MN day 14), and the data availability statement has been updated with the new accession codes in the HTML and PDF versions of the article.
March 26, 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29550351/peripubertal-serum-dioxin-concentrations-and-subsequent-sperm-methylome-profiles-of-young-russian-adults
#6
J Richard Pilsner, Alex Shershebnev, Yulia A Medvedeva, Alexander Suvorov, Haotian Wu, Andrey Goltsov, Evgeny Loukianov, Tatiana Andreeva, Fedor Gusev, Andrey Manakhov, Luidmila Smigulina, Maria Logacheva, Victoria Shtratnikova, Irina Kuznetsova, Peter Speranskiy-Podobed, Jane S Burns, Paige L Williams, Susan Korrick, Mary M Lee, Evgeny Rogaev, Russ Hauser, Oleg Sergeyev
BACKGROUND: The association of exposure to endocrine disrupting chemicals in the peripubertal period with subsequent sperm DNA methylation is unknown. OBJECTIVE: We examined the association of peripubertal serum 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) concentrations with whole-genome bisulfite sequencing (WGBS) of sperm collected in young adulthood. METHODS: The Russian Children's Study is a prospective cohort of 516 boys who were enrolled at 8-9 years of age and provided semen samples at 18-19 years of age...
March 14, 2018: Reproductive Toxicology
https://www.readbyqxmd.com/read/29544553/comparison-of-whole-genome-bisulfite-sequencing-library-preparation-strategies-identifies-sources-of-biases-affecting-dna-methylation-data
#7
Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V Berrens, Miguel R Branco, Wolf Reik
BACKGROUND: Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. RESULTS: We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs...
March 15, 2018: Genome Biology
https://www.readbyqxmd.com/read/29524144/whole-genome-bisulfite-sequencing-for-the-analysis-of-genome-wide-dna-methylation-and-hydroxymethylation-patterns-at-single-nucleotide-resolution
#8
Magali Kernaleguen, Christian Daviaud, Yimin Shen, Eric Bonnet, Victor Renault, Jean-François Deleuze, Florence Mauger, Jörg Tost
The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29524143/approaches-for-the-analysis-and-interpretation-of-whole-genome-bisulfite-sequencing-data
#9
Tim Stuart, Sam Buckberry, Ryan Lister
DNA methylation is a covalent modification of DNA that plays important roles in processes such as the regulation of gene expression, transcription factor binding, and suppression of transposable elements. The use of whole genome bisulfite sequencing (WGBS) enables the genome-wide identification and quantification of DNA methylation patterns at single-base resolution and is the gold standard for analysis of DNA methylation. Computational analysis of WGBS data can be particularly challenging, as many computationally intensive steps are required...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29524142/generation-of-whole-genome-bisulfite-sequencing-libraries-for-comprehensive-dna-methylome-analysis
#10
Dulce B Vargas-Landin, Jahnvi Pflüger, Ryan Lister
Whole genome bisulfite sequencing (WGBS) enables the detection of DNA methylation at single base-pair resolution. The treatment of DNA with sodium bisulfite allows the discrimination of methylated and unmethylated cytosines, but the power of this technology can be limited by the input amounts of DNA and the length of DNA fragments due to DNA damage caused by the desulfonation process. Here, we describe a WGBS library preparation protocol that minimizes the loss and damage of DNA, generating high quality libraries amplified with fewer PCR cycles, and hence data with fewer PCR duplicates, from lower amounts of input material...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29514626/an-information-theoretic-approach-to-the-modeling-and-analysis-of-whole-genome-bisulfite-sequencing-data
#11
Garrett Jenkinson, Jordi Abante, Andrew P Feinberg, John Goutsias
BACKGROUND: DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA methylation by producing high resolution genome-wide methylation profiles. Statistical modeling and analysis is employed to computationally extract and quantify information from these profiles in an effort to identify regions of the genome that demonstrate crucial or aberrant epigenetic behavior...
March 7, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29402210/defiant-dmrs-easy-fast-identification-and-annotation-identifies-differentially-methylated-regions-from-iron-deficient-rat-hippocampus
#12
David E Condon, Phu V Tran, Yu-Chin Lien, Jonathan Schug, Michael K Georgieff, Rebecca A Simmons, Kyoung-Jae Won
BACKGROUND: Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. RESULTS: We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data...
February 5, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29361906/genome-wide-dna-methylation-analysis-in-response-to-salinity-in-the-model-plant-caliph-medic-medicago-truncatula
#13
Mahmoud W Yaish, Abbas Al-Lawati, Ibtisam Al-Harrasi, Himanshu Vishwas Patankar
BACKGROUND: DNA methylation has a potential role in controlling gene expression and may, therefore, contribute to salinity adaptation in plants. Caliph medic (Medicago truncatula) is a model legume of moderate salinity tolerance capacity; however, a base-resolution DNA methylome map is not yet available for this plant. RESULTS: In this report, a differential whole-genome bisulfite sequencing (WGBS) was carried out using DNA samples extracted from root tissues exposed to either control or saline conditions...
January 24, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29352281/differential-dna-methylation-and-transcription-profiles-in-date-palm-roots-exposed-to-salinity
#14
Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation...
2018: PloS One
https://www.readbyqxmd.com/read/29339507/large-scale-comparative-epigenomics-reveals-hierarchical-regulation-of-non-cg-methylation-in-arabidopsis
#15
Yu Zhang, C Jake Harris, Qikun Liu, Wanlu Liu, Israel Ausin, Yanping Long, Lidan Xiao, Li Feng, Xu Chen, Yubin Xie, Xinyuan Chen, Lingyu Zhan, Suhua Feng, Jingyi Jessica Li, Haifeng Wang, Jixian Zhai, Steven E Jacobsen
Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the landscape of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis, and a tremendous amount of WGBS data has been generated by the research community. However, the systematic comparison of DNA methylation profiles to identify regulatory mechanisms has yet to be fully explored. Here we reprocessed the raw data of over 500 publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments and also filtered them based on sequencing depth and efficiency of bisulfite conversion...
January 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29327208/analysis-of-dna-modifications-in-aging-research
#16
REVIEW
Dustin R Masser, Niran Hadad, Hunter Porter, Michael B Stout, Archana Unnikrishnan, David R Stanford, Willard M Freeman
As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through next-generation sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging...
February 2018: GeroScience
https://www.readbyqxmd.com/read/29288427/comparative-wgbs-identifies-genes-that-influence-non-ripe-phenotype-in-tomato-epimutant-colourless-non-ripening
#17
Weiwei Chen, Zhiming Yu, Junhua Kong, Hui Wang, Yichen Li, Mei Zhao, Xiaohong Wang, Qianqian Zheng, Nongnong Shi, Pengcheng Zhang, Silin Zhong, Paul Hunter, Mahmut Tör, Yiguo Hong
Whole-genome bisulfite sequencing (WGBS) allows single-base resolution and genome-wide profiling of DNA methylation in plants and animals. This technology provides a powerful tool to identify genes that are potentially controlled by dynamic changes of DNA methylation and demethylation. However, naturally occurring epimutants are rare and genes under epigenetic regulation as well as their biological relevances are often difficult to define. In tomato, fruit development and ripening are a complex process that involves epigenetic control...
February 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29224155/targeted-bisulfite-sequencing-using-the-seqcap-epi-enrichment-system
#18
Jennifer Wendt, Heidi Rosenbaum, Todd A Richmond, Jeffrey A Jeddeloh, Daniel L Burgess
Cytosine methylation has been shown to have a role in a host of biological processes. In mammalian biology these include stem cell differentiation, embryonic development, genomic imprinting, inflammation, and silencing of transposable elements. Given the central importance of these processes, it is not surprising to find aberrant cytosine methylation patterns associated with many disorders in humans, including cancer, cardiovascular disease, and neurological disease. While whole genome shotgun bisulfite sequencing (WGBS) has recently become feasible, generating high sequence coverage data for the entire genome is expensive, both in terms of money and analysis time, when generally only a small subset of the genome is of interest to most researchers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224147/comprehensive-whole-dna-methylome-analysis-by-integrating-medip-seq-and-mre-seq
#19
Xiaoyun Xing, Bo Zhang, Daofeng Li, Ting Wang
Understanding the role of DNA methylation often requires accurate assessment and comparison of these modifications in a genome-wide fashion. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA CpG methylomes. These include whole genome bisulfite sequencing (WGBS), Reduced-Representation Bisulfite-Sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. An investigator needs a method that is flexible with the quantity of input DNA, provides the appropriate balance among genomic CpG coverage, resolution, quantitative accuracy, and cost, and comes with robust bioinformatics software for analyzing the data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224142/post-bisulfite-adaptor-tagging-for-pcr-free-whole-genome-bisulfite-sequencing
#20
Fumihito Miura, Takashi Ito
Post-bisulfite adaptor tagging (PBAT) is a highly efficient procedure to construct libraries for whole-genome bisulfite sequencing (WGBS). PBAT attaches adaptors to bisulfite-converted genomic DNA to circumvent bisulfite-induced degradation of library DNA inherent to conventional WGBS protocols. Consequently, it enables PCR-free WGBS from nanogram quantities of mammalian DNA, thereby serving as an invaluable tool for methylomics.
2018: Methods in Molecular Biology
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