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single cell methylation

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https://www.readbyqxmd.com/read/28106918/divergent-cytosine-dna-methylation-patterns-in-single-cell-soybean-root-hairs
#1
Md Shakhawat Hossain, Taiji Kawakatsu, Kyung Do Kim, Zhang Ning, Cuong T Nguyen, Saad M Khan, Josef M Batek, Trupti Joshi, Jeremy Schmutz, Jane Grimwood, Robert J Schmitz, Dong Xu, Scott A Jackson, Joseph R Ecker, Gary Stacey
Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single-cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single-cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single-cell root hairs as compared with multicellular stripped roots, as well as in response to heat stress...
January 20, 2017: New Phytologist
https://www.readbyqxmd.com/read/28105783/plateau-rayleigh-instability-morphology-evolution-prime-from-electrospun-core-shell-polymer-fibers-to-polymer-microbowls
#2
Yu-Jing Chiu, Hsiao-Fan Tseng, Yu-Ching Lo, Bo-Hao Wu, Jiun-Tai Chen
Electrospun core-shell fibers have great potentials in many areas, such as tissue engineering, drug delivery, and organic solar cells. Although many core-shell fibers have been prepared and studied, the morphology transformation of core-shell fibers have been rarely studied. In this work, the morphology evolution of electrospun core-shell polymer fibers driven by the Plateau-Rayleigh instability is investigated. Polystyrene/poly(methyl methacrylate) (PS/PMMA) core-shell fibers are first prepared by using blend solutions and a single axial electrospinning setup...
January 20, 2017: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/28103133/role-of-choline-in-the-modulation-of-degenerative-processes-in-vivo-and-in-vitro-studies
#3
Tania Merinas-Amo, Inmaculada Tasset-Cuevas, Antonio M Díaz-Carretero, Ángeles Alonso-Moraga, Fernando Calahorro
The purpose of the present study was to examine the nutraceutical potential of choline as an added value to its well-known brain nutrient role. Several toxicity, antitoxicity, genotoxicity, antigenotoxicity, and longevity endpoints were checked in the somatic mutation and recombination test in in vivo Drosophila animal model. Cytotoxicity in human leukemia-60 cell line (HL-60) promyelocytic and NIH3T3 mouse fibroblast cells, proapoptotic DNA fragmentation, comet assay, methylation status, and macroautophagy (MA) activity were tested in in vitro assays...
January 19, 2017: Journal of Medicinal Food
https://www.readbyqxmd.com/read/28098555/nematophagous-fungus-arthrobotrys-oligospora-mimics-olfactory-cues-of-sex-and-food-to-lure-its-nematode-prey
#4
Yen-Ping Hsueh, Matthew R Gronquist, Erich M Schwarz, Ravi David Nath, Ching-Han Lee, Shalha Gharib, Frank C Schroeder, Paul W Sternberg
To study the molecular basis for predator-prey coevolution, we investigated how Caenorhabditis elegans responds to the predatory fungus Arthrobotrys oligospora. C. elegans and other nematodes were attracted to volatile compounds produced by A. oligospora. Gas-chromatographic mass-spectral analyses of A. oligospora-derived volatile metabolites identified several odors mimicking food cues attractive to nematodes. One compound, methyl 3-methyl-2-butenoate (MMB) additionally triggered strong sex- and stage-specific attraction in several Caenorhabditis species...
January 18, 2017: ELife
https://www.readbyqxmd.com/read/28094813/a-methylome-wide-mqtl-analysis-reveals-associations-of-methylation-sites-with-gad1-and-hdac3-snps-and-a-general-psychiatric-risk-score
#5
D M Ciuculete, A E Boström, S Voisin, H Philipps, O E Titova, M Bandstein, L Nikontovic, M J Williams, J Mwinyi, H B Schiöth
Genome-wide association studies have identified a number of single-nucleotide polymorphisms (SNPs) that are associated with psychiatric diseases. Increasing body of evidence suggests a complex connection of SNPs and the transcriptional and epigenetic regulation of gene expression, which is poorly understood. In the current study, we investigated the interplay between genetic risk variants, shifts in methylation and mRNA levels in whole blood from 223 adolescents distinguished by a risk for developing psychiatric disorders...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28093566/estrogen-dependent-association-of-hdac4-with-fear-in-female-mice-and-women-with-ptsd
#6
S A Maddox, V Kilaru, J Shin, T Jovanovic, L M Almli, B G Dias, S D Norrholm, N Fani, V Michopoulos, Z Ding, K N Conneely, E B Binder, K J Ressler, A K Smith
Women are at increased risk of developing post-traumatic stress disorder (PTSD) following a traumatic event. Recent studies suggest that this may be mediated, in part, by circulating estrogen levels. This study evaluated the hypothesis that individual variation in response to estrogen levels contributes to fear regulation and PTSD risk in women. We evaluated DNA methylation from blood of female participants in the Grady Trauma Project and found that serum estradiol levels associates with DNA methylation across the genome...
January 17, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28089370/single-cell-multiomics-multiple-measurements-from-single-cells
#7
REVIEW
Iain C Macaulay, Chris P Ponting, Thierry Voet
Single-cell sequencing provides information that is not confounded by genotypic or phenotypic heterogeneity of bulk samples. Sequencing of one molecular type (RNA, methylated DNA or open chromatin) in a single cell, furthermore, provides insights into the cell's phenotype and links to its genotype. Nevertheless, only by taking measurements of these phenotypes and genotypes from the same single cells can such inferences be made unambiguously. In this review, we survey the first experimental approaches that assay, in parallel, multiple molecular types from the same single cell, before considering the challenges and opportunities afforded by these and future technologies...
January 12, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28077880/interleukin-2-receptor-%C3%AE-proximal-promoter-hypomethylation-is-associated-with-multiple-sclerosis
#8
J Field, A Fox, M A Jordan, A G Baxter, T Spelman, M Gresle, H Butzkueven, T J Kilpatrick, J P Rubio
Genetic studies have demonstrated association between single-nucleotide polymorphisms within the IL2RA (interleukin-2 receptor α-subunit) gene and risk of developing multiple sclerosis (MS); however, these variants do not have obvious functional consequences. DNA methylation is a source of genetic variation that could impact on autoimmune disease risk. We investigated DNA methylation of the IL2RA promoter in genomic DNA obtained from peripheral blood mononuclear cells and neural tissue using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry...
January 12, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28069706/dna-sequence-properties-that-predict-susceptibility-to-epiallelic-switching
#9
Marco Catoni, Jayne Griffiths, Claude Becker, Nicolae Radu Zabet, Carlos Bayon, Mélanie Dapp, Michal Lieberman-Lazarovich, Detlef Weigel, Jerzy Paszkowski
Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon-derived, methylated at all cytosines, which may or may not form epialleles...
January 9, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28069692/genes-involved-in-development-and-differentiation-are-commonly-methylated-in-cancers-derived-from-multiple-organs-a-single-institutional-methylome-analysis-using-1007-tissue-specimens
#10
Kentaro Ohara, Eri Arai, Yoriko Takahashi, Nanako Ito, Ayako Shibuya, Koji Tsuta, Ryoji Kushima, Hitoshi Tsuda, Hidenori Ojima, Hiroyuki Fujimoto, Shun-Ichi Watanabe, Hitoshi Katai, Takayuki Kinoshita, Tatsuhiro Shibata, Takashi Kohno, Yae Kanai
The aim of this study was to clarify the significance of DNA methylation alterations shared by cancers derived from multiple organs. We analyzed single-institutional methylome data by single-CpG-resolution Infinium assay for 1,007 samples of non-cancerous tissue (N) and corresponding cancerous tissue (T) obtained from lung, stomach, kidney, breast and liver. Principal component analysis revealed that N samples of each organ showed distinct DNA methylation profiles, DNA methylation profiles of N samples of each organ being inherited by the corresponding T samples and DNA methylation profiles of T samples being more similar to those of N samples in the same organ than those of T samples in other organs...
January 9, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28068321/analysis-of-dna-methylation-in-single-circulating-tumor-cells
#11
C F Pixberg, K Raba, F Müller, B Behrens, E Honisch, D Niederacher, H Neubauer, T Fehm, W Goering, W A Schulz, P Flohr, G Boysen, M Lambros, J S De Bono, W T Knoefel, C Sproll, N H Stoecklein, R P L Neves
Direct analysis of circulating tumor cells (CTCs) can inform on molecular mechanisms underlying systemic spread. Here we investigated promoter methylation of three genes regulating epithelial-to-mesenchymal transition (EMT), a key mechanism enabling epithelial tumor cells to disseminate and metastasize. For this, we developed a single-cell protocol based on agarose-embedded bisulfite treatment, which allows investigating DNA methylation of multiple loci via a multiplex PCR (multiplexed-scAEBS). We established our assay for the simultaneous analysis of three EMT-associated genes miR-200c/141, miR-200b/a/429 and CDH1 in single cells...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28067485/honokiol-inhibits-dna-polymerases-%C3%AE-and-%C3%AE-and-increases-bleomycin-sensitivity-of-human-cancer-cells
#12
A S Prakasha Gowda, Zucai Suo, Thomas E Spratt
A major concept to sensitize cancer cells to DNA damaging agents is by inhibiting proteins in the DNA repair pathways. X-family DNA polymerases play critical roles in both base excision repair (BER) and nonhomologous end joining (NHEJ). In this study, we examined the effectiveness of honokiol to inhibit human DNA polymerase β (pol β), which is involved in BER, and DNA polymerase λ (pol λ), which is involved in NHEJ. Kinetic analysis with purified polymerases showed that honokiol inhibited DNA polymerase activity...
January 19, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28063892/an-intraocular-drug-delivery-system-using-targeted-nanocarriers-attenuates-retinal-ganglion-cell-degeneration
#13
Lei Zhao, Guojun Chen, Jun Li, Yingmei Fu, Timur A Mavlyutov, Annie Yao, Robert W Nickells, Shaoqin Gong, Lian-Wang Guo
Glaucoma is a common blinding disease characterized by loss of retinal ganglion cells (RGCs). To date, there is no clinically available treatment directly targeting RGCs. We aim to develop an RGC-targeted intraocular drug delivery system using unimolecular micelle nanoparticles (unimNPs) to prevent RGC loss. The unimNPs were formed by single/individual multi-arm star amphiphilic block copolymer poly(amidoamine)-polyvalerolactone-poly(ethylene glycol) (PAMAM-PVL-PEG). While the hydrophobic PAMAM-PVL core can encapsulate hydrophobic drugs, the hydrophilic PEG shell provides excellent water dispersity...
January 4, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28063323/genetic-and-epigenetic-regulation-on-the-transcription-of-gabrb2-genotype-dependent-hydroxymethylation-and-methylation-alterations-in-schizophrenia
#14
Lu Zong, Lin Zhou, Yu Hou, Lulu Zhang, Wei Jiang, Wenwei Zhang, Lijuan Wang, Xia Luo, Shiqing Wang, Cong Deng, Zhizhen Peng, Shufen Li, Jiming Hu, Hu Zhao, Cunyou Zhao
To improve our understanding of the abnormalities and non-Mendelian inheritance characteristics of schizophrenia, this study examined DNA methylation (5mC) and hydroxymethylation (5hmC) in the schizophrenia-associated GABRB2 gene encoding the type A γ-aminobutyric acid receptor β2 subunit. DNAs from the peripheral white blood cells of 279 schizophrenic patients and 256 controls from the Chinese Han population were examined to reveal that the GABRB2 promoter P1-5mC level which was correlated with olanzapine administration, P2-5mC/5hmC level, and Alu-5mC level which was correlated with administration of ziprasidone or oxcarbazepine, were increased in schizophrenic patients...
December 28, 2016: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28055034/applying-the-intact-method-to-purify-endosperm-nuclei-and-to-generate-parental-specific-epigenome-profiles
#15
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/28053122/a-semi-protected-oligonucleotide-recombination-assay-for-dna-mismatch-repair-in-vivo-suggests-different-modes-of-repair-for-lagging-strand-mismatches
#16
Eric A Josephs, Piotr E Marszalek
In Escherichia coli, a DNA mismatch repair (MMR) pathway corrects errors that occur during DNA replication by coordinating the excision and re-synthesis of a long tract of the newly-replicated DNA between an epigenetic signal (a hemi-methylated d(GATC) site or a single-stranded nick) and the replication error after the error is identified by protein MutS. Recent observations suggest that this 'long-patch repair' between these sites is coordinated in the same direction of replication by the replisome. Here, we have developed a new assay that uniquely allows us to introduce targeted 'mismatches' directly into the replication fork via oligonucleotide recombination, examine the directionality of MMR, and quantify the nucleotide-dependence, sequence context-dependence, and strand-dependence of their repair in vivo-something otherwise nearly impossible to achieve...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28052964/whole-genome-bisulfite-sequencing-of-human-pancreatic-islets-reveals-novel-differentially-methylated-regions-in-type-2-diabetes-pathogenesis
#17
Petr Volkov, Karl Bacos, Jones K Ofori, Jonathan Lou S Esguerra, Lena Eliasson, Tina Rönn, Charlotte Ling
Current knowledge about the role of epigenetics in type 2 diabetes (T2D) remains limited. Only a few studies have investigated DNA methylation of selected candidate genes or a very small fraction of genomic CpG sites in human pancreatic islets, the tissue of primary pathogenic importance for diabetes. Our aim was to characterize the whole-genome DNA methylation landscape in human pancreatic islets, to identify differentially methylated regions (DMRs) in diabetic islets, and to investigate the function of DMRs in islet biology...
January 4, 2017: Diabetes
https://www.readbyqxmd.com/read/28049248/nestin-expression-in-the-adult-mouse-retina-with-pharmaceutically-induced-retinal-degeneration
#18
Chan Hee Moon, Heeyoon Cho, Yoon Kyung Kim, Tae Kwann Park
The present study investigated the temporal pattern and cellular localization of nestin in the adult mouse retina with pharmaceutically induced retinal degeneration using N-methyl-N-nitrosourea (MNU). After a single intraperitoneal injection of MNU in 8-week-old C57BL/6 mice, the animals were sacrificed at 1, 3, 5, 7, and 21 days (n = 6, in each stage). The eyes were examined by means of immunohistochemical tests using nestin, ionized calcium-binding adaptor molecule (Iba-1), CD11b, F4/80, and glial fibrillary acidic protein (GFAP)...
February 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/28042858/how-does-thymine-dna-survive-ultrafast-dimerization-damage
#19
Hongjuan Wang, Xuebo Chen
The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction takes place on a picosecond time scale along barrierless or low barrier singlet/triplet pathways. However, the observed dimerization quantum yield in different thymine multimer is considerable lower than might be expected. A reasonable explanation is required to understand why thymine in DNA is able to survive ultrafast dimerization damage...
December 31, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28039772/synthesis-crystal-structures-and-antitumor-activity-of-two-platinum-ii-complexes-with-methyl-hydrazinecarbodithioate-derivatives-of-indolin-2-one
#20
You-Shan Li, Bin Peng, Li Ma, Sheng-Li Cao, Lu-Lu Bai, Chao-Rui Yang, Chong-Qing Wan, Hao-Jie Yan, Pan-Pan Ding, Zhong-Feng Li, Ji Liao, Ying-Ying Meng, Hai-Long Wang, Jing Li, Xingzhi Xu
Two new platinum(II) complexes 7a and 7b with methyl hydrazinecarbodithioate derivatives of indolin-2-one have been prepared and characterized by single-crystal X-ray diffraction, NMR spectroscopy and mass spectrometry. Antiproliferative activity of the two complexes and their ligands 6a and 6b against HCT-116, MCF-7 and MDA-MB-231 cell lines was determined by the MTS assay. Complexes 7a and 7b exhibited stronger antiproliferative activity against three cell lines than compounds 6a and 6b (IC50, 1.89-5.60 versus 6...
December 26, 2016: European Journal of Medicinal Chemistry
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