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https://www.readbyqxmd.com/read/27646705/divergent-dna-methylation-provides-insights-into-the-evolution-of-duplicate-genes-in-zebrafish
#1
Zaixuan Zhong, Kang Du, Qian Yu, Yong E Zhang, Shunping He
The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish...
September 19, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27473283/dismiss-detection-of-stranded-methylation-in-medip-seq-data
#2
Umar Niazi, Kathrin K Geyer, Martin J Vickers, Karl F Hoffmann, Martin T Swain
BACKGROUND: DNA methylation is an important regulator of gene expression and chromatin structure. Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is commonly used to identify regions of DNA methylation in eukaryotic genomes. Within MeDIP-Seq libraries, methylated cytosines can be found in both double-stranded (symmetric) and single-stranded (asymmetric) genomic contexts. While symmetric CG methylation has been relatively well-studied, asymmetric methylation in any dinucleotide context has received less attention...
2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27443935/genome-wide-dna-methylation-profiling-in-zebrafish
#3
P J Murphy, B R Cairns
Genomic DNA methylation functions to repress gene expression by interfering with transcription factor binding and/or recruiting repressive chromatin machinery. Recent data support contribution of regulated DNA methylation to embryonic pluripotency, development, and tissue differentiation; this important epigenetic mark is chemically stable yet enzymatically reversible-and heritable through the germline. Importantly, all the major components involved in dynamic DNA methylation are conserved in zebrafish, including the factors that "write, read, and erase" this mark...
2016: Methods in Cell Biology
https://www.readbyqxmd.com/read/27212063/identification-of-methylated-genes-in-salivary-gland-adenoid-cystic-carcinoma-xenografts-using-global-demethylation-and-methylation-microarray-screening
#4
Shizhang Ling, Eleni M Rettig, Marietta Tan, Xiaofei Chang, Zhiming Wang, Mariana Brait, Justin A Bishop, Elana J Fertig, Michael Considine, Michael J Wick, Patrick K Ha
Salivary gland adenoid cystic carcinoma (ACC) is a rare head and neck malignancy without molecular biomarkers that can be used to predict the chemotherapeutic response or prognosis of ACC. The regulation of gene expression of oncogenes and tumor suppressor genes (TSGs) through DNA promoter methylation may play a role in the carcinogenesis of ACC. To identify differentially methylated genes in ACC, a global demethylating agent, 5-aza-2'-deoxycytidine (5-AZA) was utilized to unmask putative TSG silencing in ACC xenograft models in mice...
July 2016: International Journal of Oncology
https://www.readbyqxmd.com/read/27199997/analyses-of-methylomes-derived-from-meso-american-common-bean-phaseolus-vulgaris-l-using-medip-seq-and-whole-genome-sodium-bisulfite-sequencing
#5
Mollee Crampton, Venkateswara R Sripathi, Khwaja Hossain, Venu Kalavacharla
Common bean (Phaseolus vulgaris L.) is economically important for its high protein, fiber, and micronutrient contents, with a relatively small genome size of ∼587 Mb. Common bean is genetically diverse with two major gene pools, Meso-American and Andean. The phenotypic variability within common bean is partly attributed to the genetic diversity and epigenetic changes that are largely influenced by environmental factors. It is well established that an important epigenetic regulator of gene expression is DNA methylation...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27172168/base-resolution-profiling-of-active-dna-demethylation-using-mab-seq-and-camab-seq
#6
Hao Wu, Xiaoji Wu, Yi Zhang
A complete understanding of the function of the ten-eleven translocation (TET) family of dioxygenase-mediated DNA demethylation requires new methods to quantitatively map oxidized 5-methylcytosine (5mC) bases at high resolution. We have recently developed a methylase-assisted bisulfite sequencing (MAB-seq) method that allows base-resolution mapping of 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), two oxidized 5mC bases indicative of active DNA demethylation events. In standard bisulfite sequencing (BS-seq), unmodified C, 5fC and 5caC are read as thymine; thus 5fC and 5caC cannot be distinguished from C...
June 2016: Nature Protocols
https://www.readbyqxmd.com/read/27153660/brat-nova-fast-and-accurate-mapping-of-bisulfite-treated-reads
#7
Elena Y Harris, Rachid Ounit, Stefano Lonardi
UNLABELLED: In response to increasing amounts of sequencing data, faster and faster aligners need to become available. Here, we introduce BRAT-nova, a completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-Seq). BRAT-nova is very fast and accurate. On the human genome, BRAT-nova is 2-7 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2-8 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy and space efficiency...
September 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26961371/fast-accurate-and-lightweight-analysis-of-bs-treated-reads-with-erne-2
#8
Nicola Prezza, Francesco Vezzi, Max Käller, Alberto Policriti
BACKGROUND: Bisulfite treatment of DNA followed by sequencing (BS-seq) has become a standard technique in epigenetic studies, providing researchers with tools for generating single-base resolution maps of whole methylomes. Aligning bisulfite-treated reads, however, is a computationally difficult task: bisulfite treatment decreases the (lexical) complexity of low-methylated genomic regions, and C-to-T mismatches may reflect cytosine unmethylation rather than SNPs or sequencing errors. Further challenges arise both during and after the alignment phase: data structures used by the aligner should be fast and should fit into main memory, and the methylation-caller output should be somehow compressed, due to its significant size...
2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/26825949/single-base-resolution-analysis-of-dna-epigenome-via-high-throughput-sequencing
#9
Jinying Peng, Bo Xia, Chengqi Yi
Epigenetic changes caused by DNA methylation and histone modifications play important roles in the regulation of various cellular processes and development. Recent discoveries of 5-methylcytosine (5mC) oxidation derivatives including 5-hydroxymethylcytosine (5hmC), 5-formylcytsine (5fC) and 5-carboxycytosine (5caC) in mammalian genome further expand our understanding of the epigenetic regulation. Analysis of DNA modification patterns relies increasingly on sequencing-based profiling methods. A number of different approaches have been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing (BS-seq), TAB-seq (TET-assisted bisulfite sequencing), oxBS-seq (oxidative bisulfite sequencing) and etc...
March 2016: Science China. Life Sciences
https://www.readbyqxmd.com/read/26819470/differential-methylation-analysis-for-bs-seq-data-under-general-experimental-design
#10
Yongseok Park, Hao Wu
MOTIVATION: DNA methylation is an epigenetic modification with important roles in many biological processes and diseases. Bisulfite sequencing (BS-seq) has emerged recently as the technology of choice to profile DNA methylation because of its accuracy, genome coverage and higher resolution. Current statistical methods to identify differential methylation mainly focus on comparing two treatment groups. With an increasing number of experiments performed under a general and multiple-factor design, particularly in reduced representation bisulfite sequencing, there is a need to develop more flexible, powerful and computationally efficient methods...
May 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26798339/hbs-tools-for-hairpin-bisulfite-sequencing-data-processing-and-analysis
#11
Ming-An Sun, Karthik Raja Velmurugan, David Keimig, Hehuang Xie
The emerging genome-wide hairpin bisulfite sequencing (hairpin-BS-Seq) technique enables the determination of the methylation pattern for DNA double strands simultaneously. Compared with traditional bisulfite sequencing (BS-Seq) techniques, hairpin-BS-Seq can determine methylation fidelity and increase mapping efficiency. However, no computational tool has been designed for the analysis of hairpin-BS-Seq data yet. Here we present HBS-tools, a set of command line based tools for the preprocessing, mapping, methylation calling, and summarizing of genome-wide hairpin-BS-Seq data...
2015: Advances in Bioinformatics
https://www.readbyqxmd.com/read/26680022/methgo-a-comprehensive-tool-for-analyzing-whole-genome-bisulfite-sequencing-data
#12
Wen-Wei Liao, Ming-Ren Yen, Evaline Ju, Fei-Man Hsu, Larry Lam, Pao-Yang Chen
BACKGROUND: DNA methylation is a major epigenetic modification regulating several biological processes. A standard approach to measure DNA methylation is bisulfite sequencing (BS-Seq). BS-Seq couples bisulfite conversion of DNA with next-generation sequencing to profile genome-wide DNA methylation at single base resolution. The analysis of BS-Seq data involves the use of customized aligners for mapping bisulfite converted reads and the bioinformatic pipelines for downstream data analysis...
2015: BMC Genomics
https://www.readbyqxmd.com/read/26680004/loss-of-5-hydroxymethylcytosine-is-linked-to-gene-body-hypermethylation-in-kidney-cancer
#13
Ke Chen, Jing Zhang, Zhongqiang Guo, Qin Ma, Zhengzheng Xu, Yuanyuan Zhou, Ziying Xu, Zhongwu Li, Yiqiang Liu, Xiongjun Ye, Xuesong Li, Bifeng Yuan, Yuwen Ke, Chuan He, Liqun Zhou, Jiang Liu, Weimin Ci
Both 5-methylcytosine (5mC) and its oxidized form 5-hydroxymethylcytosine (5hmC) have been proposed to be involved in tumorigenesis. Because the readout of the broadly used 5mC mapping method, bisulfite sequencing (BS-seq), is the sum of 5mC and 5hmC levels, the 5mC/5hmC patterns and relationship of these two modifications remain poorly understood. By profiling real 5mC (BS-seq corrected by Tet-assisted BS-seq, TAB-seq) and 5hmC (TAB-seq) levels simultaneously at single-nucleotide resolution, we here demonstrate that there is no global loss of 5mC in kidney tumors compared with matched normal tissues...
January 2016: Cell Research
https://www.readbyqxmd.com/read/26648976/overexpression-of-the-heterochromatinization-factor-bahd1-in-hek293-cells-differentially-reshapes-the-dna-methylome-on-autosomes-and-x-chromosome
#14
Emanuele Libertini, Alice Lebreton, Goran Lakisic, Marie-Agnès Dillies, Stephan Beck, Jean-Yves Coppée, Pascale Cossart, Hélène Bierne
BAH domain-containing protein 1 (BAHD1) is involved in heterochromatin formation and gene repression in human cells. BAHD1 also localizes to the inactive X chromosome (Xi), but the functional significance of this targeting is unknown. So far, research on this protein has been hampered by its low endogenous abundance and its role in epigenetic regulation remains poorly explored. In this work, we used whole-genome bisulfite sequencing (BS-seq) to compare the DNA methylation profile of HEK293 cells expressing low levels of BAHD1 (HEK-CT) to that of isogenic cells stably overexpressing BAHD1 (HEK-BAHD1)...
2015: Frontiers in Genetics
https://www.readbyqxmd.com/read/26615747/genome-wide-analysis-of-dna-methylation-in-the-sexual-stage-of-the-insect-pathogenic-fungus-cordyceps-militaris
#15
Yu-long Wang, Zhang-xun Wang, Chun Liu, Si-bao Wang, Bo Huang
DNA methylation is a basic epigenetic mechanism found in eukaryotes, but its patterns and roles vary significantly among diverse taxa. In fungi, DNA methylation has various effects on diverse biological processes. However, its function in the sexual development of fungi remains unclear. Cordyceps militaris, readily performs sexual reproduction and thus provides a remarkably rich model for understanding epigenetic processes in sexual development. Here, we surveyed the methylome of C. militaris at single-base resolution to assess DNA methylation patterns during sexual development using genomic bisulfite sequencing (BS-Seq)...
December 2015: Fungal Biology
https://www.readbyqxmd.com/read/26334796/hicdat-a-fast-and-easy-to-use-hi-c-data-analysis-tool
#16
Marc W Schmid, Stefan Grob, Ueli Grossniklaus
BACKGROUND: The study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear architecture as a phenotype is only about to unfold. To use Hi-C for phenotypic comparisons among different cell types, conditions, or genetic backgrounds, Hi-C data processing needs to be more accessible to biologists. RESULTS: HiCdat provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R...
2015: BMC Bioinformatics
https://www.readbyqxmd.com/read/26319221/bs-snper-snp-calling-in-bisulfite-seq-data
#17
Shengjie Gao, Dan Zou, Likai Mao, Huayu Liu, Pengfei Song, Youguo Chen, Shancen Zhao, Changduo Gao, Xiangchun Li, Zhibo Gao, Xiaodong Fang, Huanming Yang, Torben F Ørntoft, Karina D Sørensen, Lars Bolund
UNLABELLED: Sodium bisulfite conversion followed by sequencing (BS-Seq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. However, SNP calling in such data is complex and time consuming. Here, we present an ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data...
December 15, 2015: Bioinformatics
https://www.readbyqxmd.com/read/25514978/genome-wide-and-single-base-resolution-dna-methylomes-of-the-pacific-oyster-crassostrea-gigas-provide-insight-into-the-evolution-of-invertebrate-cpg-methylation
#18
Xiaotong Wang, Qiye Li, Jinmin Lian, Li Li, Lijun Jin, Huimin Cai, Fei Xu, Haigang Qi, Linlin Zhang, Fucun Wu, Jie Meng, Huayong Que, Xiaodong Fang, Ximing Guo, Guofan Zhang
BACKGROUND: Studies of DNA methylomes in a wide range of eukaryotes have revealed both conserved and divergent characteristics of DNA methylation among phylogenetic groups. However, data on invertebrates particularly molluscs are limited, which hinders our understanding of the evolution of DNA methylation in metazoa. The sequencing of the Pacific oyster Crassostrea gigas genome provides an opportunity for genome-wide profiling of DNA methylation in this model mollusc. RESULTS: Homologous searches against the C...
2014: BMC Genomics
https://www.readbyqxmd.com/read/25378318/dbtss-as-an-integrative-platform-for-transcriptome-epigenome-and-genome-sequence-variation-data
#19
Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, Kenta Nakai
DBTSS (http://dbtss.hgc.jp/) was originally constructed as a collection of uniquely determined transcriptional start sites (TSSs) in humans and some other species in 2002. Since then, it has been regularly updated and in recent updates epigenetic information has also been incorporated because such information is useful for characterizing the biological relevance of these TSSs/downstream genes. In the newest release, Release 9, we further integrated public and original single nucleotide variation (SNV) data into our database...
January 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25326660/bison-bisulfite-alignment-on-nodes-of-a-cluster
#20
Devon Patrick Ryan, Dan Ehninger
BACKGROUND: DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation at single-base resolution. The relative slowness of most commonly used aligners for processing such data introduces an unnecessarily long delay between receipt of raw data and statistical analysis. While this process can be sped-up by using computer clusters, current tools are not designed with them in mind and end-users must create such implementations themselves...
2014: BMC Bioinformatics
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