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https://www.readbyqxmd.com/read/29327208/analysis-of-dna-modifications-in-aging-research
#1
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...
January 11, 2018: GeroScience
https://www.readbyqxmd.com/read/29288427/comparative-wgbs-identifies-genes-that-influence-non-ripe-phenotype-in-tomato-epimutant-colourless-non-ripening
#2
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...
December 27, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29224155/targeted-bisulfite-sequencing-using-the-seqcap-epi-enrichment-system
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/29224141/tagmentation-based-library-preparation-for-low-dna-input-whole-genome-bisulfite-sequencing
#6
Dieter Weichenhan, Qi Wang, Andrew Adey, Stephan Wolf, Jay Shendure, Roland Eils, Christoph Plass
Aberrations of the DNA methylome contribute to onset and progression of diseases. Whole genome bisulfite sequencing (WGBS) is the only analytical method covering the complete methylome. Alternative methods requiring less DNA than WGBS analyze only a minor portion of the methylome and do not cover important regulatory features like enhancers and noncoding RNAs. In tagmentation-based WGBS (TWGBS), several DNA and time-consuming steps of the conventional WGBS library preparation are circumvented by the use of a hyperactive transposase, which simultaneously fragments DNA and appends sequencing adapters...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224140/whole-genome-bisulfite-sequencing-using-the-ovation%C3%A2-ultralow-methyl-seq-protocol
#7
Christian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, Jörg Tost
The analysis of genome-wide epigenomic alterations including DNA methylation has become a subject of intensive research for many complex diseases. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies can be considered the gold standard for a comprehensive and quantitative analysis of cytosine methylation throughout the genome. Several approaches including tagmentation- and post bisulfite adaptor tagging (PBAT)-based WGBS have been devised. Here, we provide a detailed protocol based on a commercial kit for the preparation of libraries for WGBS from limited amounts of input DNA (50-100 ng) using the classical approach of WGBS by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222086/genome-wide-dna-methylation-profiling-using-the-methylation-dependent-restriction-enzyme-lpnpi
#8
Ruben Boers, Joachim Boers, Bas de Hoon, Christel Kockx, Zeliha Ozgur, Anco Molijn, Wilfred van IJcken, Joop Laven, Joost Gribnau
DNA methylation is a well-known epigenetic modification that plays a crucial role in gene regulation, but genome-wide analysis of DNA methylation remains technically challenging and costly. DNA methylation-dependent restriction enzymes can be used to restrict CpG methylation analysis to methylated regions of the genome only, which significantly reduces the required sequencing depth and simplifies subsequent bioinformatics analysis. Unfortunately, this approach has been hampered by complete digestion of DNA in CpG methylation-dense regions, resulting in fragments that are too small for accurate mapping...
December 8, 2017: Genome Research
https://www.readbyqxmd.com/read/29215068/integrated-dna-methylome-and-transcriptome-analysis-reveals-the-ethylene-induced-flowering-pathway-genes-in-pineapple
#9
Jiabin Wang, Zhiying Li, Ming Lei, Yunliu Fu, Jiaju Zhao, Mengfei Ao, Li Xu
Ethylene has long been used to promote flowering in pineapple production. Ethylene-induced flowering is dose dependent, with a critical threshold level of ethylene response factors needed to trigger flowering. The mechanism of ethylene-induced flowering is still unclear. Here, we integrated isoform sequencing (iso-seq), Illumina short-reads sequencing and whole-genome bisulfite sequencing (WGBS) to explore the early changes of transcriptomic and DNA methylation in pineapple following high-concentration ethylene (HE) and low-concentration ethylene (LE) treatment...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208987/genome-wide-dna-methylation-changes-associated-with-olfactory-learning-and-memory-in-apis-mellifera
#10
You Li, Li-Zhen Zhang, Yao Yi, Wan-Wan Hu, Ya-Hui Guo, Zhi-Jiang Zeng, Zachary-Y Huang, Zi-Long Wang
The honeybee is a model organism for studying learning and memory formation and its underlying molecular mechanisms. While DNA methylation is well studied in caste differentiation, its role in learning and memory is not clear in honeybees. Here, we analyzed genome-wide DNA methylation changes during olfactory learning and memory process in A. mellifera using whole genome bisulfite sequencing (WGBS) method. A total of 853 significantly differentially methylated regions (DMRs) and 963 differentially methylated genes (DMGs) were identified...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29145608/medreaders-a-database-for-transcription-factors-that-bind-to-methylated-dna
#11
Guohua Wang, Ximei Luo, Jianan Wang, Jun Wan, Shuli Xia, Heng Zhu, Jiang Qian, Yadong Wang
Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29099283/lowly-methylated-region-analysis-identifies-ebf1-as-a-potential-epigenetic-modifier-in-breast-cancer
#12
Nora Fernandez-Jimenez, Athena Sklias, Szilvia Ecsedi, Vincent Cahais, Davide Degli-Esposti, Antonin Jay, Pierre Benoit Ancey, Hae Dong Woo, Hector Hernandez-Vargas, Zdenko Herceg
Breast cancer (BC) encompasses heterogeneous pathologies with different subtypes exhibiting distinct molecular changes, including those related to DNA methylation. However, the role of these changes in mediating BC heterogeneity is poorly understood. Lowly methylated regions (LMRs), non-CpG island loci that usually contain transcription factor (TF) binding sites, have been suggested to act as regulatory elements that define cellular identity. In this study, we aimed to identify the key subtype-specific TFs that may lead to LMR generation and shape the BC methylome and transcription program...
November 3, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29052184/bisulfite-sequencing-using-small-dna-amounts
#13
Susanne Edelmann, Stefan Scholten
Bisulfite sequencing (BS-seq) enables the detection of DNA methylation at cytosine residues (5mC) at single-nucleotide resolution. For many applications, a limiting factor of conventional BS-seq protocols is the high amount of DNA required, since the treatment with bisulfite causes severe DNA fragmentation. Here, we describe a post-bisulfite tagging method that accounts for this problem. Illumina-compatible BS-seq libraries can be obtained from as little as five single haploid maize cells, enabling whole genome BS-seq (WGBS) for the generation of genome-wide, cell-type specific DNA methylation profiles...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28994822/whole-genome-dna-methylation-sequencing-of-the-chicken-retina-cornea-and-brain
#14
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/28986911/detection-of-dna-methylation-by-whole-genome-bisulfite-sequencing
#15
Qing Li, Peter J Hermanson, Nathan M Springer
DNA methylation plays an important role in the regulation of the expression of transposons and genes. Various methods have been developed to assay DNA methylation levels. Bisulfite sequencing is considered to be the "gold standard" for single-base resolution measurement of DNA methylation levels. Coupled with next-generation sequencing, whole-genome bisulfite sequencing (WGBS) allows DNA methylation to be evaluated at a genome-wide scale. Here, we described a protocol for WGBS in plant species with large genomes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28969601/genome-wide-analysis-of-dna-methylation-profiles-on-sheep-ovaries-associated-with-prolificacy-using-whole-genome-bisulfite-sequencing
#16
Yanli Zhang, Fengzhe Li, Xu Feng, Hua Yang, Aoxiang Zhu, Jing Pang, Le Han, Tingting Zhang, Xiaolei Yao, Feng Wang
BACKGROUND: Ovulation rate and litter size are important reproductive traits in sheep with high economic value. Recent work has revealed a potential link between DNA methylation and prolificacy. However, a genome-wide study that sought to identify potential DNA methylation sites involved in sheep prolificacy indicated that it is still unknown. Here, we aimed to investigate the genome-wide DNA methylation profiles of Hu sheep ovaries by comparing a high-prolificacy group (HP, litter size of three for at least 2 consecutive lambings) and low prolificacy group (LP, litter size of one for at least 2 consecutive lambings) using deep whole-genome bisulfite sequencing (WGBS)...
October 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28877971/genome-wide-analysis-of-dna-methylation-during-ovule-development-of-female-sterile-rice-fsv1
#17
Helian Liu, Ya Wu, Aqin Cao, Bigang Mao, Bingran Zhao, Jianbo Wang
The regulation of female fertility is an important field of rice sexual reproduction research. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during development processes. However, few reports have described the methylation profiles of female-sterile rice during ovule development. In this study, ovules were continuously acquired from the beginning of megaspore mother cell meiosis until the mature female gametophyte formation period, and global DNA methylation patterns were compared in the ovules of a high-frequency female-sterile line (fsv1) and a wild-type rice line (Gui99) using whole-genome bisulfite sequencing (WGBS)...
November 6, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28859663/sparse-conserved-under-methylated-cpgs-are-associated-with-high-order-chromatin-structure
#18
Xueqiu Lin, Jianzhong Su, Kaifu Chen, Benjamin Rodriguez, Wei Li
BACKGROUND: Whole-genome bisulfite sequencing (WGBS) is the gold standard for studying landscape DNA methylation. Current computational methods for WGBS are mainly designed for gene regulatory regions with multiple under-methylated CpGs (UMCs), such as promoters and enhancers. RESULTS: To reliably predict the functional importance of single isolated UMCs across the genome, which is usually not achievable using traditional methods, we develop a multi-sample-based method...
August 31, 2017: Genome Biology
https://www.readbyqxmd.com/read/28771560/comparative-genome-wide-methylation-analysis-of-longissimus-dorsi-muscles-between-japanese-black-wagyu-and-chinese-red-steppes-cattle
#19
COMPARATIVE STUDY
Xibi Fang, Zhihui Zhao, Haibin Yu, Guangpeng Li, Ping Jiang, Yuwei Yang, Runjun Yang, Xianzhong Yu
DNA methylation is an important epigenetic mechanism involved in expression of genes in many biological processes including muscle growth and development. Its effects on economically important traits are evinced from reported significant differences in meat quality traits between Japanese black (Wagyu) and Chinese Red Steppes cattle, thus presenting a unique model for analyzing the effects of DNA methylation on these traits. In the present study, we performed whole genome DNA methylation analysis in the two breeds by whole genome bisulfite sequencing (WGBS)...
2017: PloS One
https://www.readbyqxmd.com/read/28735485/genome-wide-analysis-of-dna-methylation-in-hematopoietic-cells-dna-methylation-analysis-by-wgbs
#20
Mira Jeong, Anna G Guzman, Margaret A Goodell
DNA methylation is a major epigenetic modification that regulates gene expression, genome imprinting, and development and has a role in diseases including cancer. There are various methods for whole-genome methylation profiling that differ in cost and resolution. Recent advances in high-throughput sequencing technologies coupled with bisulfite treatment enable absolute DNA methylation quantification and genome-wide single-nucleotide resolution analysis. In this chapter, we provide detailed protocols for whole-genome bisulfite sequencing (WGBS), which captures the complete methylome...
2017: Methods in Molecular Biology
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