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https://www.readbyqxmd.com/read/27926823/aliidiomarina-soli-sp-nov-isolated-from-saline-alkaline-soil
#1
Lian Xu, Ji-Quan Sun, Li-Juan Wang, Xiao-Zhen Liu, Yin-Yao Ji, Zhong-Qiu Shao, Xiao-Lei Wu
A Gram-staining-negative, motile, non-spore-forming bacterium designated strain Y4G10-17T was isolated from the saline-alkali farmland top soil, Inner Mongolia, northern China. Strain Y4G10-17T could grow at 4-45°C (with 30°C as the optimal temperature), pH 6.0-12.0 (optimal at pH 9.0), and in the presence of 1.0-12.0 % (w/v) NaCl (optimal at 4.0-6.0 %). Phylogenetic analysis based on the eight different copies of the 16S rRNA gene sequences revealed that strain Y4G10-17T shared the highest sequence similarities with Aliidiomarina maris CF12-14T, 97...
December 7, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926821/algoriphagus-aestuariicola-sp-nov-isolated-from-estuary-sediment
#2
Xiaomeng Jia, Baolei Jia, Kyung Hyun Kim, Che Ok Jeon
A Gram-staining-negative and strictly aerobic bacterium, designated strain S2-A1T, was isolated from estuary sediment in South Korea. Cells of strain S2-A1T were oxidase- and catalase-positive rods without a gliding motility. Growth was observed at 15-40 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum, pH 7.0-7.5) and in the presence of 0-4.0 % (w/v) NaCl (optimum, 0.5-1.0 %). The sole respiratory quinone was MK-7. Iso-C15:0, summed feature 3 (comprising C16:1 ω7c/C16:1 ω6c) and summed feature 9 (comprising iso-C17:1 ω9c/C16:0 10-methyl) were found as the major fatty acids (>5 % of the total fatty acids)...
December 7, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926820/altererythrobacter-salegens-sp-nov-a-slightly-halophilic-bacterium-isolated-from-surface-sediment
#3
Xiaoyan Liang, Huina Lin, Kailing Wang, Yunjing Liao, Qiliang Lai, Ying Xu, Changyun Wang
A Gram-negative, rod-shaped and slightly halophilic bacterium, strain XY-R17T, was isolated from the surface sediment of Mai Po Inner Deep Bay Ramsar Site birdwatch in Hong Kong. The 16S rRNA gene sequence of strain XY-R17T exhibited a 96.5% similarity to that of the type strain Altererythrobacter atlanticus. Optimal growth occurred at pH 7.0-7.5, 3%-8% (w/v) NaCl, 28-30˚C. The major respiratory quinone was Ubiquinone-10. The principal fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and 11-methyl C18:1ω7c...
December 5, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926531/an-annotated-list-of-bivalent-chromatin-regions-in-human-es-cells-a-new-tool-for-cancer-epigenetic-research
#4
Franck Court, Philippe Arnaud
CpG islands (CGI) marked by bivalent chromatin in stem cells are believed to be more prone to aberrant DNA methylation in tumor cells. The robustness and genome-wide extent of this instructive program in different cancer types remain to be determined. To address this issue we developed a user-friendly approach to integrate the stem cell chromatin signature in customized DNA methylation analyses. We used publicly available ChIP-sequencing datasets of several human embryonic stem cell (hESC) lines to determine the extent of bivalent chromatin genome-wide...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27926527/meqtl-analysis-of-childhood-obesity-links-epigenetics-with-a-risk-snp-rs17782313-near-mc4r-from-meta-analysis
#5
Yuping Tang, Bo Jin, Lingling Zhou, Weifeng Lu
Earlier GWAS has identified that rs17782313 near MC4R was associated with obesity. However, subsequent studies showed conflicting results, especially among childhood. Besides, the mechanisms underlying the association between rs17782313 and childhood obesity remain largely unexplored, and genetic and epigenetic may interact and together affect the development of childhood obesity. We conducted a comprehensive meta-analysis to assess the association between rs17782313 and childhood obesity. MeQTL and eQTL analysis was applied to explore the effect of rs17782313 on DNA methylation and MC4R expression...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27925358/castration-induced-changes-in-the-expression-profiles-and-promoter-methylation-of-the-ghr-gene-in-huainan-male-pigs
#6
Jing Wang, Junfeng Chen, Jiaqing Zhang, Binwen Gao, Xianxiao Bai, Yali Lan, Ping Lin, Hongxia Guo, Yuan Gao, Baosong Xing
Castration plays a regulatory role in growth and carcass traits, particularly in fat deposition, but its molecular mechanisms are still not clear. The present study showed that castration significantly reduced the serum growth hormone and the responses of the growth hormone receptor (GHR), insulin-like growth factor 1 (IGF-I), IGF-IR and peroxisome proliferator-activated receptor gamma (PPARγ) to castration were similar in different adipose tissues. However, the GHR expression trends were opposite between the liver and the adipose tissues; bisulfite sequencing PCR (BSP) showed that its methylation in these two tissues was different...
December 7, 2016: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/27925355/epigenetic-analysis-of-the-ifn%C3%AE-3-gene-identifies-a-novel-marker-for-response-to-therapy-in-hcv-infected-subjects
#7
Jeffrey F Waring, J Wade Davis, Emily Dumas, Daniel Cohen, Kenneth Idler, Stephen Abel, Robert Georgantas, Thomas Podsadecki, Sandeep Dutta
Chronic hepatitis C virus (HCV) infection is characterized by high inter-individual variability in response to pegylated interferon and ribavirin. A genetic polymorphism on chromosome 19 (rs12979860) upstream of interferon-λ-3 (IFNλ3) is associated with a 2-fold change in sustained virologic response rate after 48 weeks of treatment with pegylated interferon/ribavirin in HCV genotype 1 (GT1) treatment-naïve patients. We conducted epigenetic analysis on the IFNλ3 promoter to investigate whether DNA methylation is associated with response to HCV therapy...
December 7, 2016: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/27924603/differential-expression-and-functional-analysis-of-high-throughput-omics-data-using-open-source-tools
#8
Moritz Kebschull, Melanie Julia Fittler, Ryan T Demmer, Panos N Papapanou
Today, -omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ, or tissue sample, allow for an unbiased, comprehensive genome-level analysis of complex diseases, offering a large advantage over earlier "candidate" gene or pathway analyses. A primary goal in the analysis of these high-throughput assays is the detection of those features among several thousand that differ between different groups of samples. In the context of oral biology, our group has successfully utilized -omics technology to identify key molecules and pathways in different diagnostic entities of periodontal disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924602/genome-wide-analysis-of-periodontal-and-peri-implant-cells-and-tissues
#9
Moritz Kebschull, Claudia Hülsmann, Per Hoffmann, Panos N Papapanou
Omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ or tissue sample, are powerful means of generating comprehensive genome-level data sets on complex diseases. We have systematically assessed the transcriptome, miRNome and methylome of gingival tissues from subjects with different diagnostic entities of periodontal disease, and studied the transcriptome of primary cells ex vivo, or in vitro after infection with periodontal pathogens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924601/a-protocol-for-the-determination-of-the-methylation-status-of-gingival-tissue-dna-at-specific-cpg-islands
#10
Trudy J Milne
Tissue biopsies are very precious. A method that allows the isolation of a high quality and quantity of genomic DNA, total RNA, and total protein from a single biopsy that is suitable for downstream applications (e.g., DNA methylation analysis, quantitative PCR, and gel electrophoresis techniques) is very desirable. The method described here combines a tissue stabilization reagent combined with a spin-column method for the simultaneous purification of gingival tissue DNA, RNA, and protein. The genomic DNA is then used for quantitative analysis of DNA methylation using real-time PCR (the qAMP method)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924600/generating-multiple-base-resolution-dna-methylomes-using-reduced-representation-bisulfite-sequencing
#11
Aniruddha Chatterjee, Euan J Rodger, Peter A Stockwell, Gwenn Le Mée, Ian M Morison
Reduced representation bisulfite sequencing (RRBS) is an effective technique for profiling genome-wide DNA methylation patterns in eukaryotes. RRBS couples size selection, bisulfite conversion, and second-generation sequencing to enrich for CpG-dense regions of the genome. The progressive improvement of second-generation sequencing technologies and reduction in cost provided an opportunity to examine the DNA methylation patterns of multiple genomes. Here, we describe a protocol for sequencing multiple RRBS libraries in a single sequencing reaction to generate base-resolution methylomes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924599/tools-and-strategies-for-analysis-of-genome-wide-and-gene-specific-dna-methylation-patterns
#12
Aniruddha Chatterjee, Euan J Rodger, Ian M Morison, Michael R Eccles, Peter A Stockwell
DNA methylation is a stable epigenetic mechanism that has important roles in the normal function of a cell and therefore also in disease etiology. Accurate measurements of normal and altered DNA methylation patterns are important to understand its role in regulating gene expression and cell phenotype. Remarkable progress has been made over the last decade in developing methodologies to investigate DNA methylation. The availability of next-generation sequencing has enabled the profiling of methylation marks at an unprecedented scale...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924165/assessment-of-global-dna-methylation-in-the-first-trimester-fetal-tissues-exposed-to-maternal-cigarette-smoking
#13
Svetlana Fa, Trine Vilsbøll Larsen, Katrine Bilde, Tina F Daugaard, Emil H Ernst, Rasmus H Olesen, Linn S Mamsen, Erik Ernst, Agnete Larsen, Anders L Nielsen
AIMS: Maternal cigarette smoking during pregnancy increases the risk of negative health consequences for the exposed child. Epigenetic mechanisms constitute a likely link between the prenatal exposure to maternal cigarette smoking and the increased risk in later life for diverse pathologies. Maternal smoking induces gene-specific DNA methylation alterations as well as global DNA hypermethylation in the term placentas and hypomethylation in the cord blood. Early pregnancy represents a developmental time where the fetal epigenome is remodeled and accordingly can be expected to be highly prone to exposures with an epigenetic impact...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27924164/smoking-associated-dna-methylation-markers-predict-lung-cancer-incidence
#14
Yan Zhang, Magdeldin Elgizouli, Ben Schöttker, Bernd Holleczek, Alexandra Nieters, Hermann Brenner
BACKGROUND: Newly established blood DNA methylation markers that are strongly associated with smoking might open new avenues for lung cancer (LC) screening. We aimed to assess the performance of the top hits from previous epigenome-wide association studies in prediction of LC incidence. In a prospective nested case-control study, DNA methylation at AHRR (cg05575921), 6p21.33 (cg06126421), and F2RL3 (cg03636183) were measured by pyrosequencing in baseline whole blood samples of 143 incident LC cases identified during 11 years of follow-up and 457 age- and sex-matched controls without diagnosis of LC until the end of follow-up...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27924045/a-novel-method-for-the-simultaneous-identification-of-methylcytosine-and-hydroxymethylcytosine-at-a-single-base-resolution
#15
Yuki Kawasaki, Yukiko Kuroda, Isao Suetake, Shoji Tajima, Fumitoshi Ishino, Takashi Kohda
Since the discovery of oxidative demethylation of methylcytosine (mC) by Tet enzymes, an analytical method has been urgently needed that would enable the identification of mC and hydroxymethylcytosine (hmC) at the single base resolution level, because their roles in gene regulation are quite different from each other. However, the bisulfite sequencing method, the gold standard for DNA methylation analysis at present, does not distinguish them. Recently reported alternative methods, such as oxBS-seq and TAB-seq, are not even capable of determining mC and hmC simultaneously...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924040/kdm2a-integrates-dna-and-histone-modification-signals-through-a-cxxc-phd-module-and-direct-interaction-with-hp1
#16
Julie Borgel, Marek Tyl, Karin Schiller, Zsofia Pusztai, Christopher M Dooley, Wen Deng, Carol Wooding, Richard J White, Tobias Warnecke, Heinrich Leonhardt, Elisabeth M Busch-Nentwich, Till Bartke
Functional genomic elements are marked by characteristic DNA and histone modification signatures. How combinatorial chromatin modification states are recognized by epigenetic reader proteins and how this is linked to their biological function is largely unknown. Here we provide a detailed molecular analysis of chromatin recognition by the lysine demethylase KDM2A. Using biochemical approaches we identify a nucleosome interaction module within KDM2A consisting of a CXXC type zinc finger, a PHD domain and a newly identified Heterochromatin Protein 1 (HP1) interaction motif that mediates direct binding between KDM2A and HP1...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924034/comprehensive-characterization-annotation-and-innovative-use-of-infinium-dna-methylation-beadchip-probes
#17
Wanding Zhou, Peter W Laird, Hui Shen
Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3' nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924023/methsmrt-an-integrative-database-for-dna-n6-methyladenine-and-n4-methylcytosine-generated-by-single-molecular-real-time-sequencing
#18
Pohao Ye, Yizhao Luan, Kaining Chen, Yizhi Liu, Chuanle Xiao, Zhi Xie
DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. Previous efforts have been largely focused on 5mC, providing invaluable insights into epigenetic regulation through DNA methylation. Recently developed single-molecule real-time (SMRT) sequencing technology provides a unique opportunity to detect the less studied DNA 6mA and 4mC modifications at single-nucleotide resolution. With a rapidly increased amount of SMRT sequencing data generated, there is an emerging demand to systematically explore DNA 6mA and 4mC modifications from these data sets...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924004/temporal-association-of-orca-lrwd1-to-late-firing-origins-during-g1-dictates-heterochromatin-replication-and-organization
#19
Yating Wang, Abid Khan, Anna B Marks, Owen K Smith, Sumanprava Giri, Yo-Chuen Lin, Rachel Creager, David M MacAlpine, Kannanganattu V Prasanth, Mirit I Aladjem, Supriya G Prasanth
DNA replication requires the recruitment of a pre-replication complex facilitated by Origin Recognition Complex (ORC) onto the chromatin during G1 phase of the cell cycle. The ORC-associated protein (ORCA/LRWD1) stabilizes ORC on chromatin. Here, we evaluated the genome-wide distribution of ORCA using ChIP-seq during specific time points of G1. ORCA binding sites on the G1 chromatin are dynamic and temporally regulated. ORCA association to specific genomic sites decreases as the cells progressed towards S-phase...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923996/binding-of-mbd-proteins-to-dna-blocks-tet1-function-thereby-modulating-transcriptional-noise
#20
Anne K Ludwig, Peng Zhang, Florian D Hastert, Stephanie Meyer, Cathia Rausch, Henry D Herce, Udo Müller, Anne Lehmkuhl, Ines Hellmann, Carina Trummer, Christian Storm, Heinrich Leonhardt, M Cristina Cardoso
Aberrant DNA methylation is a hallmark of various human disorders, indicating that the spatial and temporal regulation of methylation readers and modifiers is imperative for development and differentiation. In particular, the cross-regulation between 5-methylcytosine binders (MBD) and modifiers (Tet) has not been investigated. Here, we show that binding of Mecp2 and Mbd2 to DNA protects 5-methylcytosine from Tet1-mediated oxidation. The mechanism is not based on competition for 5-methylcytosine binding but on Mecp2 and Mbd2 directly restricting Tet1 access to DNA...
December 6, 2016: Nucleic Acids Research
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