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Methylation enrichment

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https://www.readbyqxmd.com/read/29237241/the-p-patens-chromosome-scale-assembly-reveals-moss-genome-structure-and-evolution
#1
Daniel Lang, Kristian K Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, Fabian B Haas, Mathieu Piednoel, Heidrun Gundlach, Michiel Van Bel, Rabea Meyberg, Cristina Vives, Jordi Morata, Aikaterini Symeonidi, Manuel Hiss, Wellington Muchero, Yasuko Kamisugi, Omar Saleh, Guillaume Blanc, Eva L Decker, Nico van Gessel, Jane Grimwood, Richard D Hayes, Sean W Graham, Lee E Gunter, Stuart McDaniel, Sebastian N W Hoernstein, Anders Larsson, Fay-Wei Li, Pierre-Francois Perroud, Jeremy Phillips, Priya Ranjan, Daniel S Rokshar, Carl J Rothfels, Lucas Schneider, Shengqiang Shu, Dennis W Stevenson, Fritz Thümmler, Michael Tillich, Juan Carlos Villarreal A, Thomas Widiez, Gane Ka-Shu Wong, Ann Wymore, Yong Zhang, Andreas D Zimmer, Ralph S Quatrano, Klaus F X Mayer, David Goodstein, Josep M Casacuberta, Klaas Vandepoele, Ralf Reski, Andrew C Cuming, Jerry Tuskan, Florian Maumus, Jérome Salse, Jeremy Schmutz, Stefan A Rensing
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2,000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes...
December 13, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29234590/an-integrative-analysis-of-dna-methylation-in-osteosarcoma
#2
Jie Xu, Deng Li, Zhiqing Cai, Yingbin Zhang, Yulin Huang, Baohua Su, Ruofan Ma
Background: The study aimed to analyze aberrantly methylated genes, relevant pathways and transcription factors (TFs) in osteosarcoma (OS) development. Methods: Based on the DNA methylation microarray data GSE36002 that were downloaded from GEO database, the differentially methylated genes in promoter regions were identified between OS and normal samples. Pathway and function enrichment analyses of differentially methylated genes was performed. Subsequently, protein-protein interaction (PPI) network was constructed, followed by identification of cancer-associated differentially methylated genes and significant differentially methylated TFs...
November 2017: Journal of Bone Oncology
https://www.readbyqxmd.com/read/29234463/xylan-extraction-from-pretreated-sugarcane-bagasse-using-alkaline-and-enzymatic-approaches
#3
Daniele Sporck, Felipe A M Reinoso, Jorge Rencoret, Ana Gutiérrez, José C Del Rio, André Ferraz, Adriane M F Milagres
Background: New biorefinery concepts are necessary to drive industrial use of lignocellulose biomass components. Xylan recovery before enzymatic hydrolysis of the glucan component is a way to add value to the hemicellulose fraction, which can be used in papermaking, pharmaceutical, and food industries. Hemicellulose removal can also facilitate subsequent cellulolytic glucan hydrolysis. Results: Sugarcane bagasse was pretreated with an alkaline-sulfite chemithermomechanical process to facilitate subsequent extraction of xylan by enzymatic or alkaline procedures...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29234025/h3k14ac-is-linked-to-methylation-of-h3k9-by-the-triple-tudor-domain-of-setdb1
#4
Renata Z Jurkowska, Su Qin, Goran Kungulovski, Wolfram Tempel, Yanli Liu, Pavel Bashtrykov, Judith Stiefelmaier, Tomasz P Jurkowski, Srikanth Kudithipudi, Sara Weirich, Raluca Tamas, Hong Wu, Ludmila Dombrovski, Peter Loppnau, Richard Reinhardt, Jinrong Min, Albert Jeltsch
SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. Structural and biochemical data demonstrate a pocket switch mechanism in histone code reading, because K9me1 or K9me2 is preferentially recognized by the aromatic cage of TD3, while K9me3 selectively binds to TD2...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233090/dna-methylation-regulates-discrimination-of-enhancers-from-promoters-through-a-h3k4me1-h3k4me3-seesaw-mechanism
#5
Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J Taft, Hans R Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J Araúzo-Bravo
BACKGROUND: DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. RESULTS: We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci...
December 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29229679/epigenetic-and-posttranscriptional-regulation-of-cd16-expression-during-human-nk-cell-development
#6
Aaron R Victor, Christoph Weigel, Steven D Scoville, Wing Keung Chan, Kelsey Chatman, Mary M Nemer, Charlene Mao, Karen A Young, Jianying Zhang, Jianhua Yu, Aharon G Freud, Christopher C Oakes, Michael A Caligiuri
The surface receptor FcγRIIIA (CD16a) is encoded by the FCGR3A gene and is acquired by human NK cells during maturation. NK cells bind the Fc portion of IgG via CD16a and execute Ab-dependent cell-mediated cytotoxicity, which is critical for the effectiveness of several antitumor mAb therapies. The role of epigenetic regulatory mechanisms controlling transcriptional and posttranscriptional CD16 expression in NK cells is unknown. In this study, we compared specific patterns of DNA methylation and expression of FCGR3A with FCGR3B, which differ in cell type-specific expression despite displaying nearly identical genomic sequences...
December 11, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29228771/curcumin-derivative-epigenetically-reactivates-nrf2-antioxidative-stress-signaling-in-mouse-prostate-cancer-tramp-c1-cells
#7
Wenji Li, Zheng-Yuan Su, Yue Guo, Chengyue Zhang, RenYi Wu, Linbo Gao, Xi Zheng, Zhi-Yun Du, Kun Zhang, Ah-Ng Kong
The carcinogenesis of prostate cancer (PCa) in TRAMP model is highly correlated with hypermethylation in the promoter region of Nrf2 and the accompanying reduced transcription of Nrf2 and its regulated detoxifying genes. We aimed to investigate the effects of (3E,5E)-3,5-Bis(3,4,5-trimethoxybenzylidene) -tetrahydrothiopyran-4-one (F10) and (3E,5E)-3,5-Bis(3,4,5-trimethoxybenzylidene) -tetrahydropyran-4-one (E10), two synthetic curcumin derivatives, on restoring Nrf2 activity in TRAMP C1 cells. HepG2-C8 cells transfected with an antioxidant-response element (ARE)-luciferase vector were treated with F10, E10, curcumin and sulforaphane (SFN) to compare their effects on Nrf2-ARE pathways...
December 11, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/29228717/somatic-prdm2-c-4467dela-mutations-in-colorectal-cancers-control-histone-methylation-and-tumor-growth
#8
Tatjana Pandzic, Veronica Rendo, Jinyeong Lim, Chatarina Larsson, Jimmy Larsson, Ivaylo Stoimenov, Snehangshu Kundu, Muhammad Akhtar Ali, Mats Hellström, Liqun He, Anders M Lindroth, Tobias Sjöblom
The chromatin modifier PRDM2/RIZ1 is inactivated by mutation in several forms of cancer and is a putative tumor suppressor gene. Frameshift mutations in the C-terminal region of PRDM2, affecting (A)8 or (A)9 repeats within exon 8, are found in one third of colorectal cancers with microsatellite instability, but the contribution of these mutations to colorectal tumorigenesis is unknown. To model somatic mutations in microsatellite unstable tumors, we devised a general approach to perform genome editing while stabilizing the mutated nucleotide repeat...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228692/epigenetic-landscape-change-analysis-during-human-emt-sheds-light-on-a-key-emt-mediator-trim29
#9
Sung Kyung Choi, Kurinji Pandiyan, Jung Woo Eun, Xiaojing Yang, Seong Hwi Hong, Suk Woo Nam, Peter A Jones, Gangning Liang, Jueng Soo You
Epithelial to mesenchymal transition (EMT) is a key trans-differentiation process, which plays a critical role in physiology and pathology. Although gene expression changes in EMT have been scrutinized, study of epigenome is in its infancy. To understand epigenetic changes during TWIST-driven EMT, we used the AcceSssIble assay to study DNA methylation and chromatin accessibility in human mammary epithelial cells (HMECs). The DNA methylation changes were found to have functional significance in EMT - i.e. methylated genes were enriched for E-box motifs that can be recognized by TWIST, at the promoters suggesting a potential targeting phenomenon, whereas the demethylated regions were enriched for pro-metastatic genes, supporting the role of EMT in metastasis...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228658/dna-methylation-landscape-of-hepatoblastomas-reveals-arrest-at-early-stages-of-liver-differentiation-and-cancer-related-alterations
#10
Mariana Maschietto, Tatiane Cristina Rodrigues, André Yoshiaki Kashiwabara, Érica Sara Souza de Araujo, Talita Ferreira Marques Aguiar, Cecilia Maria Lima da Costa, Isabela Werneck da Cunha, Luciana Dos Reis Vasques, Monica Cypriano, Helena Brentani, Silvia Regina Caminada de Toledo, Peter Lees Pearson, Dirce Maria Carraro, Carla Rosenberg, Ana C V Krepischi
Hepatoblastomas are uncommon embryonal liver tumors accounting for approximately 80% of childhood hepatic cancer. We hypothesized that epigenetic changes, including DNA methylation, could be relevant to hepatoblastoma onset. The methylomes of eight matched hepatoblastomas and non-tumoral liver tissues were characterized, and data were validated in an independent group (11 hepatoblastomas). In comparison to differentiated livers, hepatoblastomas exhibited a widespread and non-stochastic pattern of global low-level hypomethylation...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29227285/shifts-in-podocyte-histone-h3k27me3-regulate-mouse-and-human-glomerular-disease
#11
Syamantak Majumder, Karina Thieme, Sri N Batchu, Tamadher A Alghamdi, Bridgit B Bowskill, M Golam Kabir, Youan Liu, Suzanne L Advani, Kathryn E White, Laurette Geldenhuys, Karthik K Tennankore, Penelope Poyah, Ferhan S Siddiqi, Andrew Advani
Histone protein modifications control fate determination during normal development and dedifferentiation during disease. Here, we set out to determine the extent to which dynamic changes to histones affect the differentiated phenotype of ordinarily quiescent adult glomerular podocytes. To do this, we examined the consequences of shifting the balance of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark in podocytes. Adriamycin nephrotoxicity and subtotal nephrectomy (SNx) studies indicated that deletion of the histone methylating enzyme EZH2 from podocytes decreased H3K27me3 levels and sensitized mice to glomerular disease...
December 11, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29227020/determination-of-herbicides-in-environmental-water-samples-by-simultaneous-in-syringe-magnetic-stirring-assisted-dispersive-liquid-liquid-microextraction-and-silylation-followed-by-gc-ms
#12
Ruth Suárez, Sabrina Clavijo, Alba González, Víctor Cerdà
An on line, fast, simple, selective and sensitive method has been developed for the determination of three herbicides belonging to the following families: triazines (atrazine), chloroacetamide (alachlor) and phenoxy (2,4-dichlorophenoxyacetic acid) in water samples. The method involves an in-syringe magnetic stirring-assisted dispersive liquid-liquid microextraction along with simultaneous silylation prior to their determination by gas chromatography with mass spectrometry. Extraction, derivatization and preconcentration have been simultaneously performed using acetone as dispersive solvent, N-methyl-N-tert-butyldimethylsilyltrifluoroacetamide as derivatization agent and trichloroethylene as extraction solvent...
December 11, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/29225717/feasibility-of-quantifying-sdc2-methylation-in-stool-dna-for-early-detection-of-colorectal-cancer
#13
Tae Jeong Oh, Hyun Il Oh, Yang Yei Seo, Dongjun Jeong, Changjin Kim, Hyoun Woo Kang, Yoon Dae Han, Hyun Cheol Chung, Nam Kyu Kim, Sungwhan An
Background: Colorectal cancer (CRC) screening is the most efficient strategy to reduce disease-related mortality. Frequent aberrant DNA methylation is known to occur in selected genes and early during CRC development, which has emerged as a new epigenetic biomarker for early detection of CRC. Previously, we reported that we identified that CpG sites of SDC2 were aberrantly methylated in tumor tissues of most CRC patients through comprehensive methylation analysis and demonstrated a high potential of quantification of SDC2 methylation in blood for early detection of colorectal cancer...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29225663/high-throughput-detection-of-antioxidants-in-mulberry-fruit-using-correlations-between-high-resolution-mass-and-activity-profiles-of-chromatographic-fractions
#14
Ye Ji Park, Si Hyun Seong, Min Sun Kim, Sang Wan Seo, Mee Ree Kim, Hyun Sik Kim
Background: Plant extracts contain a huge variety of pharmacologically active substances. Conventionally, various chromatographic methods must be applied several times to purify functional compounds to measure their functional activity. However, conventional purification methods are time-consuming and expensive due to the laborious purification process. Recently, a high-throughput discovery method that replaces such time-consuming purification processes was introduced; this method uses 15 T ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry (15 T FT-ICR MS) and a high-throughput screening method...
2017: Plant Methods
https://www.readbyqxmd.com/read/29225348/a-multi-dimensional-characterization-of-anxiety-in-monozygotic-twin-pairs-reveals-susceptibility-loci-in-humans
#15
Reid S Alisch, Carol Van Hulle, Pankaj Chopra, Anita Bhattacharyya, Su-Chun Zhang, Richard J Davidson, Ned H Kalin, H Hill Goldsmith
The etiology of individual differences in human anxiousness is complex and includes contributions from genetic, epigenetic (i.e., DNA methylation) and environmental factors. Past genomic approaches have been limited in their ability to detect human anxiety-related differences in these factors. To overcome these limitations, we employed both a multi-dimensional characterization method, to select monozygotic twin pairs discordant for anxiety, and whole genome DNA methylation sequencing. This approach revealed 230 anxiety-related differentially methylated loci that were annotated to 183 genes, including several known stress-related genes such as NAV1, IGF2, GNAS, and CRTC1...
December 11, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/29224170/affinity-based-enrichment-techniques-for-the-genome-wide-analysis-of-5-hydroxymethylcytosine
#16
John P Thomson, Richard R Meehan
Since its initial characterization in 2009 there has been a great degree of interest in comparative profiling of 5-hydroxymethylcytosine (5hmC) nucleotides in vertebrate DNA. Through a host of genome-wide studies the distribution of 5hmC has been mapped in a range of cell lines, tissue types and organisms; the majority of which have been generated through affinity-based methods for 5hmC enrichment. Although recent advances in the field have resulted in the ability to investigate the levels of both methylated and hydroxymethylated cytosines at single base resolution, such studies are still relatively cost-prohibitive as well as technically challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224167/dna-methylation-analysis-of-free-circulating-dna-in-body-fluids
#17
Maria Jung, Glen Kristiansen, Dimo Dietrich
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224156/multiplexed-and-sensitive-dna-methylation-testing-using-methylation-sensitive-restriction-enzymes-msre-qpcr
#18
Gabriel Beikircher, Walter Pulverer, Manuela Hofner, Christa Noehammer, Andreas Weinhaeusel
DNA methylation is a chemically stable key-player in epigenetics. In the vertebrate genome the 5-methyl cytosine (5mC) has been found almost exclusively in the CpG dinucleotide context. CpG dinucleotides are enriched in CpG islands very frequently located within or close to gene promoters. Analyses of DNA methylation changes in human diagnostics have been conducted classically using methylation-sensitive restriction enzymes (MSRE). Since the discovery of bisulfite conversion-based sequencing and PCR assays, MSRE-based PCR assays have been less frequently used, although especially in the field of cancer epigenetics MSRE-based genome-wide discovery and targeted screening applications have been and are still performed successfully...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224155/targeted-bisulfite-sequencing-using-the-seqcap-epi-enrichment-system
#19
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
#20
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
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