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Plant dna methylation

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https://www.readbyqxmd.com/read/28819832/protective-role-of-humic-acids-against-picloram-induced-genomic-instability-and-dna-methylation-in-phaseolus-vulgaris
#1
Mahmut Sinan Taspinar, Murat Aydin, Burcu Sigmaz, Nalan Yildirim, Guleray Agar
Picloram (4-amino-3,5,6-trichloropicolinic acid) is a liquid auxinic herbicide used to control broad-leaved weeds. Picloram is representing a possible hazard to ecosystems and human health. Therefore, in this study, DNA methylation changes and DNA damage levels in Phaseolus vulgaris exposed to picloram, as well as whether humic acid (HA) has preventive effects on these changes were investigated. Random amplified polymorphic DNA (RAPD) techniques were used for identification of DNA damage and coupled restriction enzyme digestion-random amplification (CRED-RA) techniques were used to detect the changed pattern of DNA methylation...
August 17, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28818371/assessment-of-molecular-and-epigenetic-changes-in-the-albinism-of-agave-angustifolia-haw
#2
Rosa Us-Camas, Eduardo Castillo-Castro, Margarita Aguilar-Espinosa, Verónica Limones-Briones, Renata Rivera-Madrid, Manuel L Robert-Díaz, Clelia De-la-Peña
Albinism in plants is a rare phenomenon that occurs in nature and is characterized by the total or partial loss of photosynthetic pigments. Although progress has been made in understanding the nature of this phenomenon, the precise causes and biological basis are still unexplored. Here, we study the genetic and epigenetic differences between green (G), variegated (V) and albino (A) A. angustifolia Haw. plantlets obtained by in vitro propagation in order to present new insights into albinism from a plant system that offers a unique set of biological phenotypic characteristics...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28815539/long-noncoding-rnas-in-plants
#3
Hsiao-Lin V Wang, Julia A Chekanova
The eukaryotic genomes are pervasively transcribed. In addition to protein-coding RNAs, thousands of long noncoding RNAs (lncRNAs) modulate key molecular and biological processes. Most lncRNAs are found in the nucleus and associate with chromatin, but lncRNAs can function in both nuclear and cytoplasmic compartments. Emerging work has found that many lncRNAs regulate gene expression and can affect genome stability and nuclear domain organization both in plant and in the animal kingdom. Here, we describe the major plant lncRNAs and how they act, with a focus on research in Arabidopsis thaliana and our emerging understanding of lncRNA functions in serving as molecular sponges and decoys, functioning in regulation of transcription and silencing, particularly in RNA-directed DNA methylation, and in epigenetic regulation of flowering time...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28812058/environmental-pollutants-and-neurodevelopment-review-of-benefits-from-closure-of-a-coal-burning-power-plant-in-tongliang-china
#4
Vrinda Kalia, Frederica Perera, Deliang Tang
Background. Understanding preventable causes of neurodevelopmental disorders is a public health priority. Polycyclic aromatic hydrocarbons (PAH) from combustion of fossil fuel, lead, and mercury are among known neurodevelopmental toxicants. Method. For the first time, we comprehensively review the findings from a study by the Columbia Center for Children's Environmental Health and Chinese partners that followed 2 groups of mother-child pairs, one from 2002 and another from 2005, in Tongliang County, China. Pregnant mothers in the 2 cohorts experienced different exposure to PAH because a local coal-burning power plant was shut down in 2004...
2017: Global Pediatric Health
https://www.readbyqxmd.com/read/28811333/arabidopsis-lorelei-a-maternally-expressed-imprinted-gene-promotes-early-seed-development
#5
Yanbing Wang, Tatsuya Tsukamoto, Jennifer Ashley Noble, Xunliang Liu, Rebecca Mosher, Ravishankar Palanivelu
n flowering plants the female gametophyte controls pollen tube reception immediately before fertilization and regulates seed development immediately after fertilization, although controlling mechanisms remain poorly understood. Previously, we showed that LORELEI (LRE), which encodes a putative glycosylphosphatidylinositol (GPI)-anchored membrane protein, is critical for pollen tube reception by the female gametophyte before fertilization and initiation of seed development after fertilization. Here, we show that LRE is expressed in the synergid, egg, and central cells of the female gametophyte and in the zygote and proliferating endosperm of the seed...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28796917/single-base-methylome-analysis-reveals-dynamic-epigenomic-differences-associated-with-water-deficit-in-apple
#6
Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan
Cytosine methylation is an essential feature of epigenetic regulation and is involved in various biological processes. Although cytosine methylation has been analyzed at the genomic scale for several plant species, there is a general lack of understanding of the dynamics of global and genic DNA methylation in plants growing in environments challenged with biotic and abiotic stresses. In this study, we mapped cytosine methylation at single-base resolution in the genome of commercial apple (Malus x domestica), and analyzed changes in methylation patterns associated with water deficit in representative drought-sensitive and drought-tolerant cultivars...
August 10, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28796823/assessment-of-photocatalytic-potentiality-and-determination-of-ecotoxicity-using-plant-model-for-better-environmental-applicability-of-synthesized-copper-copper-oxide-and-copper-doped-zinc-oxide-nanoparticles
#7
Debadrito Das, Animesh Kumar Datta, Divya Vishambhar Kumbhakar, Bapi Ghosh, Ankita Pramanik, Sudha Gupta, Aninda Mandal
NPS SYNTHESIS, CHARACTERIZATION AND AZO-DYE DEGRADATION: A facile cost effective wet chemical method of synthesis is proposed for Cu-NPs, CuO-NPs and Cu-doped ZnO-NPs. The nanomaterials are opto-physically characterized for nano standard quality. Cu-doped ZnO-NPs based catalytic system is found to possess most efficient photocatalytic activity in degradation of two organic azo-dyes namely methyl red (MR) and malachite green (MG) that are released as industrial effluents in eco-environment intercollegium...
2017: PloS One
https://www.readbyqxmd.com/read/28783101/analysis-of-argonaute-4-associated-long-non-coding-rna-in-arabidopsis-thaliana-sheds-novel-insights-into-gene-regulation-through-rna-directed-dna-methylation
#8
Phil Chi Khang Au, Elizabeth S Dennis, Ming-Bo Wang
RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28780454/nicotinamide-antioxidative-and-dna-hypomethylation-effects-in-plant-cells
#9
Torkel Berglund, Anders Wallström, Tuong-Van Nguyen, Cecilia Laurell, Anna B Ohlsson
The effects of nicotinamide (NIC) and its natural plant metabolites nicotinic acid (NIA) and trigonelline (TRIG) were studied with respect to defense in plant cell cultures. NIC and NIA could protect against oxidative stress damage caused by 2,2'-azobis(2-amidinopropane) dihydrochloride (AAPH), which generates free radicals. Damage was analyzed as DNA strand breaks in cell cultures of Pisum sativum (garden pea), Daucus carota (carrot), Populus tremula L. × P. tremuloides (hybrid aspen) and Catharanthus roseus (Madagascar periwinkle), monitored by single cell gel electrophoresis (comet assay), and assays of cell leakage in C...
July 29, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28769976/new-insights-into-5hmc-dna-modification-generation-distribution-and-function
#10
REVIEW
Dong-Qiao Shi, Iftikhar Ali, Jun Tang, Wei-Cai Yang
Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition to the common methylation on the 5th position of the pyrimidine ring of cytosine (5mC), other types of modifications at the same position, such as 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC), are also important. Recently, 5hmC, a product of 5mC demethylation by the Ten-Eleven Translocation family proteins, was shown to regulate many cellular and developmental processes, including the pluripotency of embryonic stem cells, neuron development, and tumorigenesis in mammals...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28761142/methylation-profile-of-a-satellite-dna-constituting-the-intercalary-g-c-rich-heterochromatin-of-the-cut-trough-shell-spisula-subtruncata-bivalvia-mactridae
#11
Daniel García-Souto, Brankica Mravinac, Eva Šatović, Miroslav Plohl, Paloma Morán, Juan J Pasantes
Tandemly repeated DNAs usually constitute significant portions of eukaryotic genomes. In bivalves, however, repetitive DNAs are habitually not widespread. In our search for abundant repetitive DNAs in trough shells, we discovered a novel satellite DNA, SSUsat, which constitutes at least 1.3% of the genome of Spisula subtruncata. As foreseen by the satellite DNA library hypothesis, we confirmed that this satellite DNA is also present in two other Mactridae species, showing a highly conserved nucleotide sequence together with a dramatic diminution in the number of repeats...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28758879/genome-wide-analysis-of-cytosine-dna-methylation-revealed-salicylic-acid-promotes-defense-pathways-over-seedling-development-in-pearl-millet
#12
Baba Ngom, Ibrahima Sarr, Josphert Kimatu, Edward Mamati, Ndjido Ardo Kane
Cytosine DNA methylation is an epigenetic regulatory system used by plants to control gene expression. Methylation pattern always changes after abiotic stresses, pathogens and pest infections or after a treatment with salicylic acid (SA). The latter is a key player in plant development and defense against insect herbivores, pathogens, and abiotic stresses. The roles of SA on the methylation patterns and the plant development were carried out in four pearl millet (Pennisetum glaucum) varieties. Seedlings of four early-flowering photosensitive genotypes (PMS3, PMI8, PMG, and PMT2) were grown on MS medium supplemented with null or different doses of SA...
July 31, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28756583/phytopathogen-induced-changes-to-plant-methylomes
#13
REVIEW
Tarek Hewezi, Vince Pantalone, Morgan Bennett, C Neal Stewart, Tessa M Burch-Smith
DNA methylation is a dynamic and reversible type of epigenetic mark that contributes to cellular physiology by affecting transcription activity, transposon mobility and genome stability. When plants are infected with pathogens, plant DNA methylation patterns can change, indicating an epigenetic interplay between plant host and pathogen. In most cases methylation can change susceptibility. While DNA hypomethylation appears to be a common phenomenon during the susceptible interaction, the levels and patterns of hypomethylation in transposable elements and genic regions may mediate distinct responses against various plant pathogens...
July 29, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28755698/non-target-site-resistance-to-als-inhibiting-herbicides-in-a-sagittaria-trifolia-l-population
#14
Bochui Zhao, Danni Fu, Yang Yu, Chengtian Huang, Kecheng Yan, Pingsheng Li, Jamil Shafi, He Zhu, Songhong Wei, Mingshan Ji
Sagittaria trifolia L. is one of the most competitive weeds in rice fields in northeastern China. The continuous use of acetolactate synthase (ALS)-inhibitors has led to the evolution of herbicide resistant S. trifolia. A subpopulation BC1, which was derived from the L1 population, was analyzed using DNA sequencing and ALS enzyme activity assays and levels of resistance to five ALS-inhibiting herbicides was determined. DNA sequencing and ALS enzyme assays revealed no amino acid substitutions and no significant differences in enzyme sensitivity between susceptible and resistant populations...
August 2017: Pesticide Biochemistry and Physiology
https://www.readbyqxmd.com/read/28746368/the-genome-wide-identification-and-transcriptional-levels-of-dna-methyltransferases-and-demethylases-in-globe-artichoke
#15
Silvia Gianoglio, Andrea Moglia, Alberto Acquadro, Cinzia Comino, Ezio Portis
Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var...
2017: PloS One
https://www.readbyqxmd.com/read/28742090/t-dna-genome-junctions-form-early-after-infection-and-are-influenced-by-the-chromatin-state-of-the-host-genome
#16
Shay Shilo, Pooja Tripathi, Cathy Melamed-Bessudo, Oren Tzfadia, Theodore R Muth, Avraham A Levy
Agrobacterium tumefaciens mediated T-DNA integration is a common tool for plant genome manipulation. However, there is controversy regarding whether T-DNA integration is biased towards genes or randomly distributed throughout the genome. In order to address this question, we performed high-throughput mapping of T-DNA-genome junctions obtained in the absence of selection at several time points after infection. T-DNA-genome junctions were detected as early as 6 hours post-infection. T-DNA distribution was apparently uniform throughout the chromosomes, yet local biases toward AT-rich motifs and T-DNA border sequence micro-homology were detected...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28741224/comparative-analysis-of-histone-modifications-and-dna-methylation-at-osbz8-locus-under-salinity-stress-in-ir64-and-nonabokra-rice-varieties
#17
Amit Paul, Pratiti Dasgupta, Dipan Roy, Shubho Chaudhuri
Rice being an important cereal crop is highly sensitive to salinity stress causing growth retardation and loss in productivity. However, certain rice genotypes like Nonabokra and Pokkali show a high level of tolerance towards salinity stress compared to IR64 variety. This differential response of tolerant varieties towards salinity stress may be a cumulative effect of genetic and epigenetic factors. In this study, we have compared the salinity-induced changes in chromatin modifications at the OsBZ8 locus in salt-tolerant Nonabokra and salt-sensitive IR64 rice varieties...
July 24, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28740750/herbicide-injury-induces-dna-methylome-alterations-in-arabidopsis
#18
Gunjune Kim, Christopher R Clarke, Hailey Larose, Hong T Tran, David C Haak, Liqing Zhang, Shawn Askew, Jacob Barney, James H Westwood
The emergence of herbicide-resistant weeds is a major threat facing modern agriculture. Over 470 weedy-plant populations have developed resistance to herbicides. Traditional evolutionary mechanisms are not always sufficient to explain the rapidity with which certain weed populations adapt in response to herbicide exposure. Stress-induced epigenetic changes, such as alterations in DNA methylation, are potential additional adaptive mechanisms for herbicide resistance. We performed methylC sequencing of Arabidopsis thaliana leaves that developed after either mock treatment or two different sub-lethal doses of the herbicide glyphosate, the most-used herbicide in the history of agriculture...
2017: PeerJ
https://www.readbyqxmd.com/read/28735394/detection-of-differential-dna-methylation-under-stress-conditions-using-bisulfite-sequence-analysis
#19
Ibtisam Al Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
DNA methylation is the most important epigenetic change affecting gene expression in plants grown under normal as well as under stress conditions. Therefore, researchers study differential DNA methylation under distinct environmental conditions and their relationship with transcriptome abundance. Up to date, more than 25 methods and techniques are available to detect DNA methylation based on different principles. Bisulfite sequencing method is considered as a gold standard since it is able to distinguish 5-methylcytosine from cytosine using the bisulfite treatment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28732548/genome-wide-mapping-of-transcriptional-enhancer-candidates-using-dna-and-chromatin-features-in-maize
#20
Rurika Oka, Johan Zicola, Blaise Weber, Sarah N Anderson, Charlie Hodgman, Jonathan I Gent, Jan-Jaap Wesselink, Nathan M Springer, Huub C J Hoefsloot, Franziska Turck, Maike Stam
BACKGROUND: While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling...
July 21, 2017: Genome Biology
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