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Plant dna methylation

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https://www.readbyqxmd.com/read/28205577/epigenetic-signatures-of-invasive-status-in-populations-of-marine-invertebrates
#1
Alba Ardura, Anastasija Zaiko, Paloma Morán, Serge Planes, Eva Garcia-Vazquez
Epigenetics, as a DNA signature that affects gene expression and enables rapid reaction of an organism to environmental changes, is likely involved in the process of biological invasions. DNA methylation is an epigenetic mechanism common to plants and animals for regulating gene expression. In this study we show, for the first time in any marine species, significant reduction of global methylation levels during the expansive phase of a pygmy mussel (Xenostrobus securis) recent invasion in Europe (two-year old), while in older introductions such epigenetic signature of invasion was progressively reduced...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28204976/variation-in-whole-dna-methylation-in-red-maple-acer-rubrum-populations-from-a-mining-region-association-with-metal-contamination-and-cation-exchange-capacity-cec-in-podzolic-soils
#2
K N Kalubi, M Mehes-Smith, G Spiers, A Omri
Although a number of publications have provided convincing evidence that abiotic stresses such as drought and high salinity are involved in DNA methylation reports on the effects of metal contamination, pH, and cation exchange on DNA modifications are limited. The main objective of the present study is to determine the relationship between metal contamination and Cation exchange capacity (CEC) on whole DNA modifications. Metal analysis confirms that nickel and copper are the main contaminants in sampled sites within the Greater Sudbury Region (Ontario, Canada) and liming has increased soil pH significantly even after 30 years following dolomitic limestone applications...
February 15, 2017: Ecotoxicology
https://www.readbyqxmd.com/read/28203244/pistil-transcriptome-analysis-to-disclose-genes-and-gene-products-related-to-aposporous-apomixis-in-hypericum-perforatum-l
#3
Giulio Galla, Sara Zenoni, Linda Avesani, Lothar Altschmied, Paride Rizzo, Timothy F Sharbel, Gianni Barcaccia
Unlike sexual reproduction, apomixis encompasses a number of reproductive strategies, which permit maternal genome inheritance without genetic recombination and syngamy. The key biological features of apomixis are the circumvention of meiosis (i.e., apomeiosis), the differentiation of unreduced embryo sacs and egg cells, and their autonomous development in functional embryos through parthenogenesis, and the formation of viable endosperm either via fertilization-independent means or following fertilization with a sperm cell...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28193737/exogenous-transposable-elements-circumvent-identity-based-silencing-permitting-the-dissection-of-expression-dependent-silencing
#4
Dalen Fultz, R Keith Slotkin
The propagation of epigenetic marks has received a great deal of attention, yet the initiation of epigenetic silencing of a new transgene, virus, or transposable element (TE) remains enigmatic. The overlapping and simultaneous function of multiple silencing mechanisms has obscured this area of investigation. Here, we have revealed two broad mechanisms that can initiate silencing independently: identity-based and expression-dependent silencing. We found that identity-based silencing is targeted by 21-22 or 24 nucleotide small interfering RNAs (siRNAs) generated from previously silenced regions of the genome...
February 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28186631/dna-methylation-and-gene-expression-regulation-associated-with-vascularization-in-sorghum-bicolor
#5
Gina M Turco, Kaisa Kajala, Govindarajan Kunde-Ramamoorthy, Chew-Yee Ngan, Andrew Olson, Shweta Deshphande, Denis Tolkunov, Barbara Waring, Scott Stelpflug, Patricia Klein, Jeremy Schmutz, Shawn Kaeppler, Doreen Ware, Chia-Lin Wei, J Peter Etchells, Siobhan M Brady
Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues...
February 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/28182313/h3k23me1-is-an-evolutionary-conserved-histone-modification-associated-with-cg-dna-methylation-in-arabidopsis
#6
Minerva S Trejo-Arellano, Walid Mahrez, Miyuki Nakamura, Jordi Moreno-Romero, Paolo Nanni, Claudia Köhler, Lars Hennig
Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a histone modification not previously described in plants. H3K23me1 is an evolutionary conserved mark in diverse flowering plant species. Chromatin immunoprecipitation followed by high-throughput sequencing in Arabidopsis thaliana showed that H3K23me1 was highly enriched in pericentromeric regions and depleted from chromosome arms...
February 9, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28176832/epro-clearsee-a-simple-immunohistochemical-method-that-does-not-require-sectioning-of-plant-samples
#7
Kiyotaka Nagaki, Naoki Yamaji, Minoru Murata
Investigations into the epigenetic status of individual cells within tissues can produce both epigenetic data for different cell types and positional information of the cells. Thus, these investigations are important for understanding the intra- and inter-cellular control systems of developmental and environmental responses in plants. However, a simple method to detect epigenetic modifications of individual cells in plant tissues is not yet available because detection of the modifications requires immunohistochemistry using specific antibodies...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28155665/tea-the-epigenome-platform-for-arabidopsis-methylome-study
#8
Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin Wang, Pao-Yang Chen, Chung-Yen Lin
BACKGROUND: Bisulfite sequencing (BS-seq) has become a standard technology to profile genome-wide DNA methylation at single-base resolution. It allows researchers to conduct genome-wise cytosine methylation analyses on issues about genomic imprinting, transcriptional regulation, cellular development and differentiation. One single data from a BS-Seq experiment is resolved into many features according to the sequence contexts, making methylome data analysis and data visualization a complex task...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28154573/differentially-methylated-epiloci-generated-from-numerous-genotypes-of-contrasting-tolerances-are-associated-with-osmotic-tolerance-in-rice-seedlings
#9
Hui Xia, Weixia Huang, Jie Xiong, Shuaigang Yan, Tao Tao, Jiajia Li, Jinhong Wu, Lijun Luo
DNA methylation plays an essential role in plant responses to environmental stress. Since drought develops into a rising problem in rice cultivation, investigations on genome-wide DNA methylation in responses to drought stress and in-depth explorations of its association with drought-tolerance are required. For this study, 68 rice accessions were used for an evaluation of their osmotic-tolerance related to 20% PEG6000 simulated physiological traits. The tolerant group revealed significantly higher levels of total antioxidant capacity and higher contents of H2O2 in both normal and osmotic-stressed treatments, as well as higher survival ratios...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28149679/the-dna-methylation-level-against-the-background-of-the-genome-size-and-t-heterochromatin-content-in-some-species-of-the-genus-secale-l
#10
Anna Kalinka, Magdalena Achrem, Paulina Poter
Methylation of cytosine in DNA is one of the most important epigenetic modifications in eukaryotes and plays a crucial role in the regulation of gene activity and the maintenance of genomic integrity. DNA methylation and other epigenetic mechanisms affect the development, differentiation or the response of plants to biotic and abiotic stress. This study compared the level of methylation of cytosines on a global (ELISA) and genomic scale (MSAP) between the species of the genus Secale. We analyzed whether the interspecific variation of cytosine methylation was associated with the size of the genome (C-value) and the content of telomeric heterochromatin...
2017: PeerJ
https://www.readbyqxmd.com/read/28125975/embryonic-environment-and-transgenerational-effects-in-quail
#11
Sophie Leroux, David Gourichon, Christine Leterrier, Yann Labrune, Vincent Coustham, Sandrine Rivière, Tatiana Zerjal, Jean-Luc Coville, Mireille Morisson, Francis Minvielle, Frédérique Pitel
BACKGROUND: Environmental exposures, for instance to chemicals, are known to impact plant and animal phenotypes on the long term, sometimes across several generations. Such transgenerational phenotypes were shown to be promoted by epigenetic alterations such as DNA methylation, an epigenetic mark involved in the regulation of gene expression. However, it is yet unknown whether transgenerational epigenetic inheritance of altered phenotypes exists in birds. The purpose of this study was to develop an avian model to investigate whether changes to the embryonic environment had a transgenerational effect that could alter the phenotypes of third-generation offspring...
January 26, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28118754/dna-methylation-and-imprinting-in-plants-machinery-and-mechanisms
#12
P R V Satyaki, Mary Gehring
Imprinting is an epigenetic phenomenon in which genes are expressed selectively from either the maternal or paternal alleles. In plants, imprinted gene expression is found in a tissue called the endosperm. Imprinting is often set by a unique epigenomic configuration in which the maternal chromosomes are less DNA methylated than their paternal counterparts. In this review, we synthesize studies that paint a detailed molecular portrait of the distinctive endosperm methylome. We will also discuss the molecular machinery that shapes and modifies this methylome, and the role of DNA methylation in imprinting...
January 25, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28115468/live-cell-analysis-of-dna-methylation-during-sexual-reproduction-in-arabidopsis-reveals-context-and-sex-specific-dynamics-controlled-by-noncanonical-rddm
#13
Mathieu Ingouff, Benjamin Selles, Caroline Michaud, Thiet M Vu, Frédéric Berger, Andrea J Schorn, Daphné Autran, Matthias Van Durme, Moritz K Nowack, Robert A Martienssen, Daniel Grimanelli
Cytosine methylation is a key epigenetic mark in many organisms, important for both transcriptional control and genome integrity. While relatively stable during somatic growth, DNA methylation is reprogrammed genome-wide during mammalian reproduction. Reprogramming is essential for zygotic totipotency and to prevent transgenerational inheritance of epimutations. However, the extent of DNA methylation reprogramming in plants remains unclear. Here, we developed sensors reporting with single-cell resolution CG and non-CG methylation in Arabidopsis...
January 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28106918/divergent-cytosine-dna-methylation-patterns-in-single-cell-soybean-root-hairs
#14
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/28097691/oilseed-rape-nac56-transcription-factor-modulates-reactive-oxygen-species-accumulation-and-hypersensitive-response-like-cell-death
#15
Qinqin Chen, Fangfang Niu, Jingli Yan, Bisi Chen, Feifei Wu, Xiaohua Guo, Bo Yang, Yuan-Qing Jiang
The NAC (NAM, ATAF1/2, CUC2) transcription factor gene family is plant-specific and plays diverse roles in development and responses to abiotic stresses and pathogen challenge. Oilseed rape (Brassica napus) or canola is an important oil crop worldwide, however, the function of NAC genes in it remains largely elusive. Here, we identified and characterized the NAC56 gene isolated from oilseed rape. Expression of BnaNAC56 was induced by abscisic acid (ABA), jasmonic acid (JA), methyl viologen (MV) and a necrotrophic fungal pathogen Sclerotinia sclerotiorum, but repressed by cold...
January 18, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28089091/characteristics-and-processing-of-pol-iv-dependent-transcripts-in-arabidopsis
#16
Hsuan Yu Kuo, Elise L Jacobsen, Yanping Long, Xinyuan Chen, Jixian Zhai
RNAi is a highly conserved machinery in eukaryotes for transcriptional or post-transcriptional silencing. In plants, RNA-directed DNA Methylation (RdDM) pathway deploys small interfering RNAs (siRNAs) to target DNA methylation. This process is initiated by the plant-specific RNA polymerase IV (Pol IV) to produce RNA precursors that are later processed into siRNAs. Until recently, characterization of Pol IV transcript had been difficult due to its presumed rapid turnover. This review summarizes five recent reports on Pol IV-dependent RNAs that explore the biogenesis and features of Pol IV transcripts, as well as alternative dicer-independent processing of Pol IV products...
January 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28069892/post-translational-regulation-of-the-dicing-activities-of-arabidopsis-dicer-like-3-and-4-by-inorganic-phosphate-and-the-redox-state
#17
Atsushi Seta, Midori Tabara, Yuki Nishibori, Akihiro Hiraguri, Naoko Ohkama-Ohtsu, Tadashi Yokoyama, Satoshi Hara, Keisuke Yoshida, Toru Hisabori, Akihito Fukudome, Hisashi Koiwa, Hiromitsu Moriyama, Nobuhiro Takahashi, Toshiyuki Fukuhara
In Arabidopsis thaliana, small interfering RNAs (siRNAs) generated by two Dicer isoforms, DCL3 and DCL4, function in distinct epigenetic processes, i.e. RNA-directed DNA methylation and post-transcriptional gene silencing, respectively. Plants often respond to their environment by producing a distinct set of small RNAs; however, the mechanism for controlling the production of different siRNAs from the same dsRNA substrate remains unclear. We established a simple biochemical method to visualize the dsRNA-cleaving activities of DCL3 and DCL4 in cell-free extracts prepared from Arabidopsis seedlings...
January 9, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28062591/epigenetic-processes-in-flowering-plant-reproduction
#18
REVIEW
Guifeng Wang, Claudia Köhler
Seeds provide up to 70% of the energy intake of the human population, emphasizing the relevance of understanding the genetic and epigenetic mechanisms controlling seed formation. In flowering plants, seeds are the product of a double fertilization event, leading to the formation of the embryo and the endosperm surrounded by maternal tissues. Analogous to mammals, plants undergo extensive epigenetic reprogramming during both gamete formation and early seed development, a process that is supposed to be required to enforce silencing of transposable elements and thus to maintain genome stability...
January 6, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28057214/chromatin-remodeling-and-plant-immunity
#19
W Chen, Q Zhu, Y Liu, Q Zhang
Chromatin remodeling, an important facet of the regulation of gene expression in eukaryotes, is performed by two major types of multisubunit complexes, covalent histone- or DNA-modifying complexes, and ATP-dependent chromosome remodeling complexes. Snf2 family DNA-dependent ATPases constitute the catalytic subunits of ATP-dependent chromosome remodeling complexes, which accounts for energy supply during chromatin remodeling. Increasing evidence indicates a critical role of chromatin remodeling in the establishment of long-lasting, even transgenerational immune memory in plants, which is supported by the findings that DNA methylation, histone deacetylation, and histone methylation can prime the promoters of immune-related genes required for disease defense...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28051176/transgenerational-epimutations-induced-by-multi-generation-drought-imposition-mediate-rice-plant-s-adaptation-to-drought-condition
#20
Xiaoguo Zheng, Liang Chen, Hui Xia, Haibin Wei, Qiaojun Lou, Mingshou Li, Tiemei Li, Lijun Luo
Epigenetic mechanisms are crucial mediators of appropriate plant reactions to adverse environments, but their involvement in long-term adaptation is less clear. Here, we established two rice epimutation accumulation lines by applying drought conditions to 11 successive generations of two rice varieties. We took advantage of recent technical advances to examine the role of DNA methylation variations on rice adaptation to drought stress. We found that multi-generational drought improved the drought adaptability of offspring in upland fields...
January 4, 2017: Scientific Reports
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