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https://www.readbyqxmd.com/read/28608346/computational-analysis-of-genome-wide-argonaute-dependent-dna-methylation-in-plants
#1
Kai Tang, Cheng-Guo Duan, Huiming Zhang, Jian-Kang Zhu
Whole-genome bisulfite sequencing (WGBS) has become a powerful tool to dissect genome-wide methylation profiles at single-base resolution. In this chapter we describe in detail the bioinformatics pipeline used for the analysis of ARGONAUTE-dependent DNA methylation in Arabidopsis thaliana. We provide tools and command lines used for mapping bisulfite sequencing reads, for estimating methylation levels at individual cytosine sites, for identifying differentially methylated regions (DMRs), and for calculating methylation levels of DMRs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28498935/the-association-of-changes-in-dna-methylation-with-temperature-dependent-sex-determination-in-cucumber
#2
Yun-Song Lai, Xiaohui Zhang, Wei Zhang, Di Shen, Haiping Wang, Yudong Xia, Yang Qiu, Jiangping Song, Chenchen Wang, Xixiang Li
Cucumber (Cucumis sativus L.) is characterized by its diverse and flexible sexual types. Here, we evaluated the effect of low temperature (LT) exposure on cucumber femaleness under short-day conditions. Shoot apices were subjected to whole-genome bisulfate sequencing (WGBS), mRNA-seq, and sRNA-seq. The results showed that temperature had a substantial and global impact on transposable element (TE)-related small RNA-directed DNA methylation (RdDM) mechanisms, resulting in large amounts of CHH-type cytosine demethylation...
May 12, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28439857/assessing-distribution-and-variation-of-genome-wide-dna-methylation-using-short-read-sequencing
#3
Jörg Hagmann, Claude Becker
DNA methylation is one of the most prominent epigenetic marks and is particularly complex in plant genomes. Whole-genome bisulfite sequencing (WGBS) using short reads has become the standard tool to study genome-wide patterns of DNA methylation. The goal of the present protocol is to enable readers to perform WGBS on both the wet lab and the computational side. We briefly outline important steps in bisulfite library preparation, then focus on the different aspects of DNA methylation analysis, from read mapping to identifying biologically relevant differential methylation between different samples...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28407801/single-base-resolution-methylomes-of-upland-cotton-gossypium-hirsutum-l-reveal-epigenome-modifications-in-response-to-drought-stress
#4
Xuke Lu, Xiaoge Wang, Xiugui Chen, Na Shu, Junjuan Wang, Delong Wang, Shuai Wang, Weili Fan, Lixue Guo, Xiaoning Guo, Wuwei Ye
BACKGROUND: DNA methylation, with a cryptic role in genome stability, gene transcription and expression, is involved in the drought response process in plants, but the complex regulatory mechanism is still largely unknown. RESULTS: Here, we performed whole-genome bisulfite sequencing (WGBS) and identified long non-coding RNAs on cotton leaves under drought stress and re-watering treatments. We obtained 31,223 and 30,997 differentially methylated regions (representing 2...
April 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28346445/potential-energy-landscapes-identify-the-information-theoretic-nature-of-the-epigenome
#5
Garrett Jenkinson, Elisabet Pujadas, John Goutsias, Andrew P Feinberg
Epigenetics is the study of biochemical modifications carrying information independent of DNA sequence, which are heritable through cell division. In 1940, Waddington coined the term "epigenetic landscape" as a metaphor for pluripotency and differentiation, but methylation landscapes have not yet been rigorously computed. Using principles from statistical physics and information theory, we derive epigenetic energy landscapes from whole-genome bisulfite sequencing (WGBS) data that enable us to quantify methylation stochasticity genome-wide using Shannon's entropy, associating it with chromatin structure...
May 2017: Nature Genetics
https://www.readbyqxmd.com/read/28248360/elimination-of-error-induced-by-a-beam-splitter-substrate-for-a-dispersion-compensated-polarization-sagnac-interferometer
#6
Jinyu Xing, Shiqun Jin, Penghao Hu, Guo Xia, Mingyong Hu
A wire grating beam splitter (WGBS) substrate in a dispersion-compensated polarization Sagnac interferometer (DCPSI) may introduce an additional shear distance in the shear distance generated by the DCPSI, thereby causing poor adaptability of the DCPSI to white light. This work applies a compensation scheme of an optical flat with the same material and thickness as the WGBS and parallel to the WGBS introduced in the other arm of the DCPSI. Theoretically, this method can decrease the additional shear distance approaching 0...
March 1, 2017: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/28213474/a-bayesian-approach-for-analysis-of-whole-genome-bisulfite-sequencing-data-identifies-disease-associated-changes-in-dna-methylation
#7
Owen J L Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto
DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome while taking into account the distance between CpG sites as a covariate...
April 2017: Genetics
https://www.readbyqxmd.com/read/28155665/tea-the-epigenome-platform-for-arabidopsis-methylome-study
#8
Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin Wang, Pao-Yang Chen, Chung-Yen Lin
BACKGROUND: Bisulfite sequencing (BS-seq) has become a standard technology to profile genome-wide DNA methylation at single-base resolution. It allows researchers to conduct genome-wise cytosine methylation analyses on issues about genomic imprinting, transcriptional regulation, cellular development and differentiation. One single data from a BS-Seq experiment is resolved into many features according to the sequence contexts, making methylome data analysis and data visualization a complex task...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28130229/genome-wide-analysis-of-dna-methylation-profiles-in-a-senescence-accelerated-mouse-prone-8-brain-using-whole-genome-bisulfite-sequencing
#9
Shuai Zhang, Chunxia Qin, Guoqiong Cao, Limin Guo, Chengqiang Feng, Wensheng Zhang
Motivation: The pathogenesis of AD is complex and contributed by both genetic and environmental factors. Recent work revealed a potential link between DNA methylation and AD. However, a genome-wide study to identify potential DNA methylation sites involved in AD is still at an early stage. WGBS, an up-to-date technology, was used in this study. We investigated mouse brain genome-wide DNA methylation profiles between seven-month-old SAMP8 and SAMR1 models through deep WGBS. Results: According to the results, the global ML slightly decreased in the SAMP8 mice than in the SAMR1 mice (4...
June 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28056787/software-updates-in-the-illumina-hiseq-platform-affect-whole-genome-bisulfite-sequencing
#10
Hidehiro Toh, Kenjiro Shirane, Fumihito Miura, Naoki Kubo, Kenji Ichiyanagi, Katsuhiko Hayashi, Mitinori Saitou, Mikita Suyama, Takashi Ito, Hiroyuki Sasaki
BACKGROUND: Methylation of cytosine in genomic DNA is a well-characterized epigenetic modification involved in many cellular processes and diseases. Whole-genome bisulfite sequencing (WGBS), such as MethylC-seq and post-bisulfite adaptor tagging sequencing (PBAT-seq), uses the power of high-throughput DNA sequencers and provides genome-wide DNA methylation profiles at single-base resolution. However, the accuracy and consistency of WGBS outputs in relation to the operating conditions of high-throughput sequencers have not been explored...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28055307/a-comparison-of-existing-global-dna-methylation-assays-to-low-coverage-whole-genome-bisulfite-sequencing-for-epidemiological-studies
#11
Florence K Crary-Dooley, Mitchell E Tam, Keith W Dunaway, Irva Hertz-Picciotto, Rebecca J Schmidt, Janine M LaSalle
DNA methylation is an epigenetic mark at the interface of genetic and environmental factors relevant to human disease. Quantitative assessments of global DNA methylation levels have therefore become important tools in epidemiology research, particularly for understanding effects of environmental exposures in complex diseases. Among the available methods of quantitative DNA methylation measurements, bisulfite sequencing is considered the gold standard, but whole-genome bisulfite sequencing (WGBS) has previously been considered too costly for epidemiology studies with high sample numbers...
March 4, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28032673/dental-pulp-stem-cells-model-early-life-and-imprinted-dna-methylation-patterns
#12
Keith Dunaway, Sarita Goorha, Lauren Matelski, Nora Urraca, Pamela J Lein, Ian Korf, Lawrence T Reiter, Janine M LaSalle
Early embryonic stages of pluripotency are modeled for epigenomic studies primarily with human embryonic stem cells (ESC) or induced pluripotent stem cells (iPSCs). For analysis of DNA methylation however, ESCs and iPSCs do not accurately reflect the DNA methylation levels found in preimplantation embryos. Whole genome bisulfite sequencing (WGBS) approaches have revealed the presence of large partially methylated domains (PMDs) covering 30%-40% of the genome in oocytes, preimplantation embryos, and placenta...
April 2017: Stem Cells
https://www.readbyqxmd.com/read/27899585/splinted-ligation-adapter-tagging-splat-a-novel-library-preparation-method-for-whole-genome-bisulphite-sequencing
#13
Amanda Raine, Erika Manlig, Per Wahlberg, Ann-Christine Syvänen, Jessica Nordlund
Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA...
April 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27794041/ngsmethdb-2017-enhanced-methylomes-and-differential-methylation
#14
Ricardo Lebrón, Cristina Gómez-Martín, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Michael Hackenberg, José L Oliver
The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high-quality methylomes, stringent quality controls were integrated with third-part software, adding also a two-step mapping process to exploit the advantages of the new genome assembly models. The samples were all profiled under constant parameter settings, thus enabling comparative downstream analyses. Besides a significant increase in the number of samples, NGSmethDB now includes two additional data-types, which are a valuable resource for the discovery of methylation epigenetic biomarkers: (i) differentially methylated single-cytosines; and (ii) methylation segments (i...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27782217/genome-wide-methylation-analysis-identified-sexually-dimorphic-methylated-regions-in-hybrid-tilapia
#15
Zi Yi Wan, Jun Hong Xia, Grace Lin, Le Wang, Valerie C L Lin, Gen Hua Yue
Sexual dimorphism is an interesting biological phenomenon. Previous studies showed that DNA methylation might play a role in sexual dimorphism. However, the overall picture of the genome-wide methylation landscape in sexually dimorphic species remains unclear. We analyzed the DNA methylation landscape and transcriptome in hybrid tilapia (Oreochromis spp.) using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found 4,757 sexually dimorphic differentially methylated regions (DMRs), with significant clusters of DMRs located on chromosomal regions associated with sex determination...
October 26, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27717381/critical-evaluation-of-the-illumina-methylationepic-beadchip-microarray-for-whole-genome-dna-methylation-profiling
#16
Ruth Pidsley, Elena Zotenko, Timothy J Peters, Mitchell G Lawrence, Gail P Risbridger, Peter Molloy, Susan Van Djik, Beverly Muhlhausler, Clare Stirzaker, Susan J Clark
BACKGROUND: In recent years the Illumina HumanMethylation450 (HM450) BeadChip has provided a user-friendly platform to profile DNA methylation in human samples. However, HM450 lacked coverage of distal regulatory elements. Illumina have now released the MethylationEPIC (EPIC) BeadChip, with new content specifically designed to target these regions. We have used HM450 and whole-genome bisulphite sequencing (WGBS) to perform a critical evaluation of the new EPIC array platform. RESULTS: EPIC covers over 850,000 CpG sites, including >90 % of the CpGs from the HM450 and an additional 413,743 CpGs...
October 7, 2016: Genome Biology
https://www.readbyqxmd.com/read/27662487/lmethyr-svm-predict-human-enhancers-using-low-methylated-regions-based-on-weighted-support-vector-machines
#17
Jingting Xu, Hong Hu, Yang Dai
BACKGROUND: The identification of enhancers is a challenging task. Various types of epigenetic information including histone modification have been utilized in the construction of enhancer prediction models based on a diverse panel of machine learning schemes. However, DNA methylation profiles generated from the whole genome bisulfite sequencing (WGBS) have not been fully explored for their potential in enhancer prediction despite the fact that low methylated regions (LMRs) have been implied to be distal active regulatory regions...
2016: PloS One
https://www.readbyqxmd.com/read/27552300/dna-methylome-analysis-of-acute-lymphoblastic-leukemia-cells-reveals-stochastic-de-novo-dna-methylation-in-cpg-islands
#18
Per Wahlberg, Anders Lundmark, Jessica Nordlund, Stephan Busche, Amanda Raine, Karolina Tandre, Lars Rönnblom, Daniel Sinnett, Erik Forestier, Tomi Pastinen, Gudmar Lönnerholm, Ann-Christine Syvänen
AIM: To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. MATERIALS & METHODS: Whole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. The findings were confirmed by 450k DNA methylation arrays in a large patient set. RESULTS: Compared with mature B or T cells WGBS detected on average 82,000 differentially methylated regions per patient...
October 2016: Epigenomics
https://www.readbyqxmd.com/read/27466624/walt-fast-and-accurate-read-mapping-for-bisulfite-sequencing
#19
Haifeng Chen, Andrew D Smith, Ting Chen
Whole-genome bisulfite sequencing (WGBS) has emerged as the gold-standard technique in genome-scale studies of DNA methylation. Mapping reads from WGBS requires unique considerations that make the process more time-consuming than in other sequencing applications. Typical WGBS data sets contain several hundred million reads, adding to this analysis challenge. We present the WALT tool for mapping WGBS reads. WALT uses a strategy of hashing periodic spaced seeds, which leads to significant speedup compared with the most efficient methods currently available...
November 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27349968/prenatal-maternal-stress-and-wheeze-in-children-novel-insights-into-epigenetic-regulation
#20
Saskia Trump, Matthias Bieg, Zuguang Gu, Loreen Thürmann, Tobias Bauer, Mario Bauer, Naveed Ishaque, Stefan Röder, Lei Gu, Gunda Herberth, Christian Lawerenz, Michael Borte, Matthias Schlesner, Christoph Plass, Nicolle Diessl, Markus Eszlinger, Oliver Mücke, Horst-Dietrich Elvers, Dirk K Wissenbach, Martin von Bergen, Carl Herrmann, Dieter Weichenhan, Rosalind J Wright, Irina Lehmann, Roland Eils
Psychological stress during pregnancy increases the risk of childhood wheeze and asthma. However, the transmitting mechanisms remain largely unknown. Since epigenetic alterations have emerged as a link between perturbations in the prenatal environment and an increased disease risk we used whole genome bisulfite sequencing (WGBS) to analyze changes in DNA methylation in mothers and their children related to prenatal psychosocial stress and assessed its role in the development of wheeze in the child. We evaluated genomic regions altered in their methylation level due to maternal stress based of WGBS data of 10 mother-child-pairs...
2016: Scientific Reports
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