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Plant dna methylation

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https://www.readbyqxmd.com/read/29224140/whole-genome-bisulfite-sequencing-using-the-ovation%C3%A2-ultralow-methyl-seq-protocol
#1
Christian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, Jörg Tost
The analysis of genome-wide epigenomic alterations including DNA methylation has become a subject of intensive research for many complex diseases. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies can be considered the gold standard for a comprehensive and quantitative analysis of cytosine methylation throughout the genome. Several approaches including tagmentation- and post bisulfite adaptor tagging (PBAT)-based WGBS have been devised. Here, we provide a detailed protocol based on a commercial kit for the preparation of libraries for WGBS from limited amounts of input DNA (50-100 ng) using the classical approach of WGBS by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29214328/5-azacytidine-treatment-and-tapbf-d-over-expression-increases-glutenin-accumulation-within-the-wheat-grain-by-hypomethylating-the-glu-1-promoters
#2
Jiantang Zhu, Linlin Fang, Jiaqi Yu, Ying Zhao, Fanguo Chen, Guangmin Xia
5-azaC treatment and TaPBF - D over-expression decrease C-methylation status of three Glu - 1 gene promoters, and aid in enhancing the expression of the Glu - 1 genes. The wheat glutenins exert a strong influence over dough elasticity, but the regulation of their encoding genes has not been firmly established. Following treatment with 5-azacytidine (5-azaC), both the weight and glutenin content of the developing and mature grains were significantly increased. The abundance of transcript produced by the Glu-1 genes (encoding high-molecular-weight glutenin subunits), as well as those encoding demethylases and transcriptional factors associated with prolamin synthesis was higher than in grain of non-treated plants...
December 6, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29199514/rna-polymerases-iv-and-v-influence-the-3-boundaries-of-polymerase-ii-transcription-units-in-arabidopsis
#3
Anastasia McKinlay, Ram Podicheti, Jered M Wendte, Ross Cocklin, Douglas B Rusch
Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the de novo cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation...
December 4, 2017: RNA Biology
https://www.readbyqxmd.com/read/29197545/potential-cancer-chemopreventive-and-anticancer-constituents-from-the-fruits-of-ficus-hispida-l-f-moraceae
#4
Jie Zhan, Feng Feng, Wei Qu, Cili Wang, Worapong Kitdamrongtham, Aranya Manosroi, Jiradej Manosroi, Harukuni Tokuda, Masahiko Abe, Toshihiro Akihisa
ETHNOPHARMACOLOGICAL RELEVANCE: Ficus hispida L.f. (Moraceae) has been used as alternative for traditional medicine in the treatment of various ailments including cancer-cure. The aim of this study was to evaluate the cancer chemopreventive and anticancer activities of crude extracts of F. hispida, with the objective to screen the inhibition of Epstein-Barr virus early antigen, and cytotoxic active components, and provide foundation for potential applications of this promising medical plant...
November 29, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29196538/parental-dna-methylation-states-are-associated-with-heterosis-in-epigenetic-hybrids
#5
Kathrin Lauss, René Wardenaar, Rurika Oka, Marieke H A van Hulten, Victor Guryev, Joost J B Keurentjes, Maike Stam, Frank Johannes
Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood. Recent studies have implicated changes in DNA methylation and small RNAs in hybrid performance, however, it remains unclear whether epigenetic changes are a cause or consequence of heterosis. Here, we analyze a large panel of over 500 A. thaliana epigenetic hybrid plants (epiHybrids), which we derived from near-isogenic but epigenetically divergent parents...
December 1, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29194997/piecing-together-cis-regulatory-networks-insights-from-epigenomics-studies-in-plants
#6
REVIEW
Shao-Shan Huang, Joseph Ecker
5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell...
November 30, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29191170/the-arabidopsis-elp3-elo3-and-elp4-elo1-genes-enhance-disease-resistance-in-fragaria-vesca-l
#7
Katchen Julliany P Silva, Asha M Brunings, Juliana A Pereira, Natalia A Peres, Kevin M Folta, Zhonglin Mou
BACKGROUND: Plant immune response is associated with a large-scale transcriptional reprogramming, which is regulated by numerous transcription regulators such as the Elongator complex. Elongator is a multitasking protein complex involved in diverse cellular processes, including histone modification, DNA methylation, and tRNA modification. In recent years, Elongator is emerging as a key regulator of plant immune responses. However, characterization of Elongator's function in plant immunity has been conducted only in the model plant Arabidopsis thaliana...
December 1, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29187878/uhrf1-is-an-independent-prognostic-factor-and-a-potential-therapeutic-target-of-esophageal-squamous-cell-carcinoma
#8
Jiecheng Ye, Yong Zhang, Weiye Liang, Jianxian Huang, Lihui Wang, Xueyun Zhong
Purpose: Ubiquitin-like with plant homeodomain and ring-finger domains 1 (UHRF1) plays an essential role in DNA methylation, and the overexpression of UHRF1 is associated with poor prognosis in various cancers. Esophageal squamous cell carcinoma (ESCC) accounts for approximately 90% of esophageal cancer cases in China, but the five-year survival rate for patients is less than 10% due to limited clinical approaches for early diagnosis and treatment. The present research aimed to investigate the expression of UHRF1 in ESCC and its biological role in ESCC development...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/29186299/within-plant-variation-in-seed-size-and-inflorescence-fecundity-is-associated-with-epigenetic-mosaicism-in-the-shrub-lavandula-latifolia-lamiaceae
#9
Conchita Alonso, Ricardo Pérez, Pilar Bazaga, Mónica Medrano, Carlos M Herrera
Background and Aims: Sub-individual variation in traits of homologous structures has multiple ecological consequences for individuals and populations. Assessing the evolutionary significance of such effects requires an improved knowledge of the mechanisms underlying within-plant phenotypic heterogeneity. The hypothesis that continuous within-plant variation in some phenotypic traits can be associated with epigenetic mosaicism was examined. Methods: Fifteen individuals of the long-lived, evergreen Mediterranean shrub Lavandula latifolia were studied...
November 24, 2017: Annals of Botany
https://www.readbyqxmd.com/read/29185505/worldwide-patterns-of-human-epigenetic-variation
#10
Oana Carja, Julia L MacIsaac, Sarah M Mah, Brenna M Henn, Michael S Kobor, Marcus W Feldman, Hunter B Fraser
DNA methylation is an epigenetic modification, influenced by both genetic and environmental variation, that plays a key role in transcriptional regulation and many organismal phenotypes. Although patterns of DNA methylation have been shown to differ between human populations, it remains to be determined how epigenetic diversity relates to the patterns of genetic and gene expression variation at a global scale. Here we measured DNA methylation at 485,000 CpG sites in five diverse human populations, and analysed these data together with genome-wide genotype and gene expression data...
October 2017: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29180596/patterns-and-consequences-of-subgenome-differentiation-provide-insights-into-the-nature-of-paleopolyploidy-in-plants
#11
Meixia Zhao, Biao Zhang, Damon Lisch, Jianxin Ma
Polyploidy is an important feature of plant genomes, but the nature of many polyploidization events remains to be elucidated. Here we demonstrate that the evolutionary fates of the subgenomes in maize (Zea mays) and soybean (Glycine max) have followed different trajectories. One subgenome has been subject to relaxed selection, lower levels of gene expression, higher rates of transposable element accumulation and more small interfering RNAs and DNA methylation around genes, and higher rates of gene loss in maize, whereas none of these features were observed in soybean...
November 27, 2017: Plant Cell
https://www.readbyqxmd.com/read/29175436/3d-chromatin-architecture-of-large-plant-genomes-determined-by-local-a-b-compartments
#12
Pengfei Dong, Xiaoyu Tu, Po-Yu Chu, Peitao Lü, Ning Zhu, Donald Grierson, Baijuan Du, Pinghua Li, Silin Zhong
The spatial organization of the genome plays an important role in the regulation of gene expression. However, the core structural features of animal genomes, such as topologically associated domains (TADs) and chromatin loops, are not prominent in the extremely compact Arabidopsis genome. In this study, we have examined the chromatin architecture, as well as their DNA methylation, histone modifications, accessible chromatin and gene expression, of maize, tomato, sorghum, foxtail millet and rice with genome sizes ranging from 0...
November 21, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29171222/-molecular-regulative-mechanisms-of-aging-and-interventional-effects-of-chinese-herbal-medicine
#13
REVIEW
Bu-Hui Liu, Yi-Huang Gu, Yue Tu, Wei-Ming He, Wei Wu, Ying-Lu Liu, Zi-Yue Wan, Yi-Gang Wan
Aging is a gradual process during the loss of functions in cells,organs and tissues by time. The molecular mechanisms of aging-related theories include the classical ones such as telomere,oxygen radical and nonenzymatic glycosylation,as well as the newly proposed ones such as DNA methylation,mitochondrial DNA (mtDNA)and autophagy. The latest study showed the anti-aging effect of autophagy in hematopoietic stem cells. In recent years,based on the molecular regulative mechanisms of aging,a number of the promising anti-aging drugs have been found,including nicotinamide mononucleotide(NMN)and FOXO4-DRI,a peptide of anti-aging...
August 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29163587/global-dna-methylation-patterns-can-play-a-role-in-defining-terroir-in-grapevine-vitis-vinifera-cv-shiraz
#14
Huahan Xie, Moumouni Konate, Na Sai, Kiflu G Tesfamicael, Timothy Cavagnaro, Matthew Gilliham, James Breen, Andrew Metcalfe, John R Stephen, Roberta De Bei, Cassandra Collins, Carlos M R Lopez
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29161430/methbank-3-0-a-database-of-dna-methylomes-across-a-variety-of-species
#15
Rujiao Li, Fang Liang, Mengwei Li, Dong Zou, Shixiang Sun, Yongbing Zhao, Wenming Zhao, Yiming Bao, Jingfa Xiao, Zhang Zhang
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multiple species and equipping with more enhanced functionalities for data annotation and more friendly web interfaces for data presentation, search and visualization. MethBank 3.0 features large-scale integration of high-quality methylomes, involving 34 consensus reference methylomes derived from a large number of human samples, 336 single-base resolution methylomes from different developmental stages and/or tissues of five plants, and 18 single-base resolution methylomes from gametes and early embryos at multiple stages of two animals...
November 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29149287/genomic-and-epigenomic-immunity-in-common-bean-the-unusual-features-of-nb-lrr-gene-family
#16
Manon M S Richard, Ariane Gratias, Vincent Thareau, Kyung Do Kim, Sandrine Balzergue, Johann Joets, Scott A Jackson, Valérie Geffroy
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu...
November 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149093/evolutionarily-distant-streptophyta-respond-differently-to-genotoxic-stress
#17
Radka Vágnerová, Alena Lukešová, Martin Lukeš, Petra Rožnovská, Marcela Holá, Jana Fulnečková, Jiří Fajkus, Karel J Angelis
Research in algae usually focuses on the description and characterization of morpho-and phenotype as a result of adaptation to a particular habitat and its conditions. To better understand the evolution of lineages we characterized responses of filamentous streptophyte green algae of the genera Klebsormidium and Zygnema, and of a land plant-the moss Physcomitrellapatens-to genotoxic stress that might be relevant to their environment. We studied the induction and repair of DNA double strand breaks (DSBs) elicited by the radiomimetic drug bleomycin, DNA single strand breaks (SSB) as consequence of base modification by the alkylation agent methyl methanesulfonate (MMS) and of ultra violet (UV)-induced photo-dimers, because the mode of action of these three genotoxic agents is well understood...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29140247/ddm1-and-lsh-remodelers-allow-methylation-of-dna-wrapped-in-nucleosomes
#18
David B Lyons, Daniel Zilberman
Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo...
November 15, 2017: ELife
https://www.readbyqxmd.com/read/29118334/temporal-and-spatial-expression-of-genes-involved-in-dna-methylation-during-reproductive-development-of-sexual-and-apomictic-eragrostis-curvula
#19
J P Selva, L Siena, J M Rodrigo, I Garbus, D Zappacosta, J R Romero, J P A Ortiz, S C Pessino, O Leblanc, V Echenique
Recent reports in model plant species have highlighted a role for DNA methylation pathways in the regulation of the somatic-to-reproductive transition in the ovule, suggesting that apomixis (asexual reproduction through seeds) likely relies on RdDM downregulation. Our aim was therefore to explore this hypothesis by characterizing genes involved in DNA methylation in the apomictic grass Eragrostis curvula. We explored floral transcriptomes to identify homologs of three candidate genes, for which mutations in Arabidopsis and maize mimic apomixis (AtAGO9/ZmAGO104, AtCMT3/ZmDMT102/ZmDMT105, and AtDDM1/ZmCHR106), and compared both their spatial and temporal expression patterns during reproduction in sexual and apomictic genotypes...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29115936/analyses-of-methylomes-of-upland-and-lowland-switchgrass-panicum-virgatum-ecotypes-using-medip-seq-and-bs-seq
#20
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
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