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https://www.readbyqxmd.com/read/29775621/methylation-of-nbpf1-as-a-novel-marker-for-the-detection-of-plasma-cell-free-dna-of-breast-cancer-patients
#1
REVIEW
Dandan Li, Pengchang Li, Jie Yi, Yaling Dou, Xiuzhi Guo, Yicong Yin, Danchen Wang, Chaochao Ma, Jie Wu, Ling Qiu
BACKGROUND: Recent studies revealed that tumor-specific gene methylation can be detected in the circulating cell-free DNA (cfDNA) of cancer patients; therefore, methylated cfDNA is considered a promising biomarker. Human neuroblastoma breakpoint family member 1 (NBPF1) was originally identified in a neuroblastoma (NB) patient. The present study is the first to evaluate the presence of NBPF1 gene methylation in cell-free DNA (cfDNA) in plasma of breast cancer patients. METHODS: Differentially methylated cfDNA was screened using bisulfite sequencing with a next-generation sequencer (BS-seq) among 25 breast cancer patients, 25 patients with a benign breast disease and 25 healthy female volunteers...
May 15, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
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/29554207/arioc-gpu-accelerated-alignment-of-short-bisulfite-treated-reads
#3
Richard Wilton, Xin Li, Andrew P Feinberg, Alexander S Szalay
Motivation: The alignment of bisulfite-treated DNA sequences (BS-seq reads) to a large genome involves a significant computational burden beyond that required to align non-bisulfite-treated reads. In the analysis of BS-seq data, this can present an important performance bottleneck that can be mitigated by appropriate algorithmic and software-engineering improvements. One strategy is to modify the read-alignment algorithms by integrating the logic related to BS-seq alignment, with the goal of making the software implementation amenable to optimizations that lead to higher speed and greater sensitivity than might otherwise be attainable...
March 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29409498/dna-methylome-profiling-at-single-base-resolution-through-bisulfite-sequencing-of-5mc-immunoprecipitated-dna
#4
Zhen Jia, Yueyi Shi, Lei Zhang, Yipeng Ren, Tong Wang, Lejun Xing, Baorong Zhang, Guolan Gao, Rongfa Bu
BACKGROUND: Detection of DNA methylome at single-base resolution is a significant challenge but promises to shed considerable light on human disease etiology. Current technologies could not detect DNA methylation genome-wide at single-base resolution with small amount of sequencing data and could not avoid detecting the methylation of repetitive elements which are considered as "junk DNA". METHODS: In this study, we have developed a novel DNA methylome profiling technology named MB-seq with its ability to identify genome-wide 5mC and quantify DNA methylation levels by introduced an assistant adapter AluI-linker This linker can be ligated to sonicated DNA and then be digested after the bisulfite treatment and amplification, which has no effect of MeDIP enrichment...
February 6, 2018: BMC Biotechnology
https://www.readbyqxmd.com/read/29302919/erratum-to-whole-genome-dna-methylation-analysis-of-brachypodium-distachyon-using-next-generation-sequencing-bs-seq
#5
I-Hsuan Lin
No abstract text is available yet for this article.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29115936/analyses-of-methylomes-of-upland-and-lowland-switchgrass-panicum-virgatum-ecotypes-using-medip-seq-and-bs-seq
#6
Mollee Dworkin, Shaojun Xie, Malay Saha, Jyothi Thimmapuram, Venu Kal Kalavacharla
BACKGROUND: Switchgrass is a crop with many desirable traits for bioenergy production. Plant genomes have high DNA methylation levels throughout genes and transposable elements and DNA methylation is known to play a role in silencing transposable elements. Here we analyzed methylomes in two switchgrass genotypes AP13 and VS16. AP13 is derived from a lowland ecotype and VS16, typically considered drought-tolerant, is derived from an upland ecotype, both genotypes are tetraploid (2n = 4× = 36)...
November 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29052184/bisulfite-sequencing-using-small-dna-amounts
#7
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/29052183/profiling-dna-methylation-using-bisulfite-sequencing-bs-seq
#8
Yun-Ru Chen, Sheng Yu, Silin Zhong
DNA cytosine methylation is one of the most abundant epigenetic marks found in the plant nuclear genome. Bisulfite sequencing (BS-Seq) is the method of choice for profiling DNA cytosine methylation genome-wide at a single nucleotide resolution. The basis of this technique is that the unmethylated cytosine can be deaminated to uracil by sodium bisulfite, while the methylated cytosine is resistant to the treatment. By deep sequencing of the bisulfite converted genomic DNA, the methylation level of each mappable cytosine position in the genome could be measured...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29039015/whole-genome-dna-methylation-analysis-using-next-generation-sequencing-bs-seq
#9
I-Hsuan Lin
Plant methylation is widely evident and has played crucial roles ranging in defining the epi-genome variations during abiotic and biotic stress. Variations in epi-genomic level has observed not only in the symmetrical as well as the non-symmetrical sequences. Plethora of these epi-genomic variations have been widely also demonstrated at the flowering, tissue-specific, and also at developmental stages revealing a strong association of the observed epi-alleles to the physiological state. In the present chapter, epi-genomic analysis of the s has been described with functional workflow and illustrated methodology...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28621722/comparative-analysis-of-genome-wide-dna-methylation-profiles-for-the-genic-male-sterile-cabbage-line-01-20s-and-its-maintainer-line
#10
Fengqing Han, Xiaoli Zhang, Xing Liu, Henan Su, Congcong Kong, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yumei Liu, Zhansheng Li, Honghao Lv
Methylation modifications play an important role in multiple biological processes. Several studies have reported altered methylation patterns in male sterile plants such as rice and wheat, but little is known about the global methylation profiles and their possible roles in the cabbage (Brassicaoleracea) male sterile line. In this study, single-base-resolution bisulfite sequencing (BS-Seq) was adopted to identify the pattern and degree of cytosine methylation in the male sterile line 01-20S and its near-isogenic fertile line 01-20F...
June 16, 2017: Genes
https://www.readbyqxmd.com/read/28510608/the-biomphalaria-glabrata-dna-methylation-machinery-displays-spatial-tissue-expression-is-differentially-active-in-distinct-snail-populations-and-is-modulated-by-interactions-with-schistosoma-mansoni
#11
Kathrin K Geyer, Umar H Niazi, David Duval, Céline Cosseau, Chad Tomlinson, Iain W Chalmers, Martin T Swain, David J Cutress, Utibe Bickham-Wright, Sabrina E Munshi, Christoph Grunau, Timothy P Yoshino, Karl F Hoffmann
BACKGROUND: The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS: Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions...
May 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28449092/genome-wide-dna-methylomes-from-discrete-developmental-stages-reveal-the-predominance-of-non-cpg-methylation-in-tribolium-castaneum
#12
Xiaowen Song, Fei Huang, Juanjuan Liu, Chengjun Li, Shanshan Gao, Wei Wu, Mengfan Zhai, Xiaojuan Yu, Wenfeng Xiong, Jia Xie, Bin Li
Cytosine DNA methylation is a vital epigenetic regulator of eukaryotic development. Whether this epigenetic modification occurs in Tribolium castaneum has been controversial, its distribution pattern and functions have not been established. Here, using bisulphite sequencing (BS-Seq), we confirmed the existence of DNA methylation and described the methylation profiles of the four life stages of T. castaneum. In the T. castaneum genome, both symmetrical CpG and non-CpG methylcytosines were observed. Symmetrical CpG methylation, which was catalysed by DNMT1 and occupied a small part in T...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28349457/detection-of-5-methylcytosine-in-specific-poly-a-rnas-by-bisulfite-sequencing
#13
Thomas Amort, Alexandra Lusser
RNA bisulfite sequencing (RNA-BS-seq) represents a method for the detection of methylated cytosines in RNA. Developed originally for the analysis of DNA methylation, a modified version of this method can be used for the analysis of methylated cytosine in RNA. Treatment of nucleic acids with HSO3 -ions under acidic conditions results in deamination of cytosine (C) to uracil, while 5-methylcytosine (m5C) or 5-hydroxymethylcytosine (hm5C) exhibit low reactivity in this reaction and remain unchanged. Subsequent PCR amplification and sequencing of specific targets allows for the assessment of the methylation status of single Cs in their native sequence context at nucleotide resolution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28155665/tea-the-epigenome-platform-for-arabidopsis-methylome-study
#14
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/28064247/genome-wide-analysis-of-the-distinct-types-of-chromatin-interactions-in-arabidopsis-thaliana
#15
Jingjing Wang, Yincong Zhou, Xue Li, Xianwen Meng, Miao Fan, Hongjun Chen, Jitong Xue, Ming Chen
The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors...
January 1, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28055034/applying-the-intact-method-to-purify-endosperm-nuclei-and-to-generate-parental-specific-epigenome-profiles
#16
Jordi Moreno-Romero, Juan Santos-González, Lars Hennig, Claudia Köhler
The early endosperm tissue of dicot species is very difficult to isolate by manual dissection. This protocol details how to apply the INTACT (isolation of nuclei tagged in specific cell types) system for isolating early endosperm nuclei of Arabidopsis at high purity and how to generate parental-specific epigenome profiles. As a Protocol Extension, this article describes an adaptation of an existing Nature Protocol that details the use of the INTACT method for purification of root nuclei. We address how to obtain the INTACT lines, generate the starting material and purify the nuclei...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/27646705/divergent-dna-methylation-provides-insights-into-the-evolution-of-duplicate-genes-in-zebrafish
#17
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
#18
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...
July 29, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27443935/genome-wide-dna-methylation-profiling-in-zebrafish
#19
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
#20
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
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