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Plant dna methylation

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https://www.readbyqxmd.com/read/29052200/rna-immunoprecipitation-protocol-to-identify-protein-rna-interactions-in-arabidopsis-thaliana
#1
Benoit Mermaz, Fuquan Liu, Jie Song
The role of RNA-binding proteins in the regulation of epigenetic processes has received increasing attention in the past decades. In particular noncoding RNAs have been shown to play a role in chromatin loop formation, recruitment of chromatin modifiers and RNA-dependent DNA methylation. In plants, the identification of specific RNA-protein interactions is now rising, facilitated by the development of specific approaches for plant tissues. Here, we present a simple one-day RNA immunoprecipitation (RIP) protocol adapted for Arabidopsis, suited for the identification of RNAs that are associated with a protein-of-interest in planta...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052185/identification-of-differentially-methylated-regions-in-the-genome-of-arabidopsis-thaliana
#2
Kamal Kishore, Mattia Pelizzola
DNA methylation profiling in the epigenome of Arabidopsis thaliana (Arabidopsis) has provided great insights in the role of this epigenetic mark for the regulation of transcription in plants, and is often based on high-throughput sequencing. The analysis of these data involves a series of steps including quality checks, filtering, alignment, identification of methyl-cytosines, and the identification of differentially methylated regions. This chapter outlines the computational methodology required to profile genome-wide differential methylation patterns based on publicly available Arabidopsis base-resolution bisulfite sequencing data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29052183/profiling-dna-methylation-using-bisulfite-sequencing-bs-seq
#3
Yun-Ru Chen, Sheng Yu, Silin Zhong
DNA cytosine methylation is one of the most abundant epigenetic marks found in the plant nuclear genome. Bisulfite sequencing (BS-Seq) is the method of choice for profiling DNA cytosine methylation genome-wide at a single nucleotide resolution. The basis of this technique is that the unmethylated cytosine can be deaminated to uracil by sodium bisulfite, while the methylated cytosine is resistant to the treatment. By deep sequencing of the bisulfite converted genomic DNA, the methylation level of each mappable cytosine position in the genome could be measured...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29048607/the-arabidopsis-chromatin-remodeling-factor-chr5-regulates-plant-immune-responses-and-nucleosome-occupancy
#4
Baohong Zou, Qi Sun, Wenli Zhang, Yuan Ding, Dong-Lei Yang, Jian Hua
ATP-dependent chromatin remodeling factors use the energy of ATP hydrolysis to alter the structure of chromatin and are important regulators of eukaryotic gene expression. One such factor CHR5 (Chromatin Remodeling Factor 5) in Arabidopsis (Arabidopsis thaliana) was previously found to be involved in growth and development regulation. Here we show that CHR5 is required for the upregulation of the intracellular immune receptor gene SNC1 (SUPPRESSOR OF npr1-1, CONSTITUTIVE1) and consequently the autoimmunity induced by SNC1 upregulation...
October 17, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29046688/global-analysis-of-small-rna-dynamics-during-seed-development-of-picea-glauca-and-arabidopsis-thaliana-populations-reveals-insights-on-their-evolutionary-trajectories
#5
Yang Liu, Yousry A El-Kassaby
While DNA methylation carries genetic signals and is instrumental in the evolution of organismal complexity, small RNAs (sRNAs), ~18-24 ribonucleotide (nt) sequences, are crucial mediators of methylation as well as gene silencing. However, scant study deals with sRNA evolution via featuring their expression dynamics coupled with species of different evolutionary time. Here we report an atlas of sRNAs and microRNAs (miRNAs, single-stranded sRNAs) produced over time at seed-set of two major spermatophytes represented by populations of Picea glauca and Arabidopsis thaliana with different seed-set duration...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29044868/effects-of-rubiadin-isolated-from-prismatomeris-connata-on-anti-hepatitis-b-virus-activity-in-vitro
#6
Zheng Peng, Gang Fang, Fenghui Peng, Zhiyu Pan, Zhengying Su, Wei Tian, Danrong Li, Huaxin Hou
Prismatomeris connata was a kind of Rubiaceae plant for treatment of hepatitis, hepatic fibrosis and silicosis. Whereas, the effective components of Prismatomeris connata remains unexplored. The aim of this study was to investigate the inhibitory effects and mechanisms of Rubiadin isolated from Prismatomeris connata against HBV using HepG2.2.15 cells. The levels of hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), and hepatitis B core antigen (HBcAg) in the supernatants or cytoplasm were examined using by enzyme-linked immunosorbent assay...
October 18, 2017: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/29039015/whole-genome-dna-methylation-analysis-using-next-generation-sequencing-bs-seq
#7
I-Hsuan Lin
Plant methylation is widely evident and has played crucial roles ranging in defining the epi-genome variations during abiotic and biotic stress. Variations in epi-genomic level has observed not only in the symmetrical as well as the non-symmetrical sequences. Plethora of these epi-genomic variations have been widely also demonstrated at the flowering, tissue-specific, and also at developmental stages revealing a strong association of the observed epi-alleles to the physiological state. In the present chapter, epi-genomic analysis of the s has been described with functional workflow and illustrated methodology...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29038910/analysis-of-somaclonal-variation-in-transgenic-and-regenerated-plants-of-arabidopsis-thaliana-using-methylation-related-metaflp-and-tmd-markers
#8
Carlos J Coronel, Ana I González, María L Ruiz, Carlos Polanco
We provide evidence that nucleotide sequence and methylation status changes occur in the Arabidopsis genome during in vitro tissue culture at a frequency high enough to represent an important source of variation. Somaclonal variation is a general consequence of the tissue culture process that has to be analyzed specifically when regenerated plants are obtained in any plant species. Currently, there are few studies about the variability comprising sequence changes and methylation status at the DNA level, generated by the culture of A...
October 16, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29036466/insights-into-epigenome-evolution-from-animal-and-plant-methylomes
#9
Soojin V Yi
Evolutionary studies of DNA methylation begin to provide insights into the underlying forces governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the contents of repetitive sequences, while the underlying driver of this correlation is less clear in animal genomes...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036316/the-role-of-small-rna-based-epigenetic-silencing-for-purifying-selection-on-transposable-elements-in-capsella-grandiflora
#10
Robert Horvath, Tanja Slotte
To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population...
September 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29034632/-research-progress-and-stress-induced-variation-of-dna-methylation-in-plants
#11
Zhen Yang, Xuanming Peng, Yiyan Zhang, Yuanhai Zhang, Yong Zhang
Chemical modification of DNA bases in recent years has been one of the hot areas of life science research. DNA methylation is a common epigenetic phenomenon and can change the genetic performance without changing the DNA sequence. Various stress factors can induce the variation of DNA methylation in plants, but the response mechanism is still unknown. In this paper, the progress of DNA methylation in plants was reviewed. In combination with the researchconclusions of our own research group, the DNA methylation variation induced by 7Li ion beam and gamma ray was reported to provide a basis for DNA methylation, which may be involved in the phenotypic plasticity of plants...
December 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29032424/not-just-gene-expression-3d-implications-of-chromatin-modifications-during-sexual-plant-reproduction
#12
Stefanie Dukowic-Schulze, Chang Liu, Changbin Chen
DNA methylation and histone modifications are epigenetic changes on a DNA molecule that alter the three-dimensional (3D) structure locally as well as globally, impacting chromatin looping and packaging on a larger scale. Epigenetic marks thus inform higher-order chromosome organization and placement in the nucleus. Conventional epigenetic marks are joined by chromatin modifiers like cohesins, condensins and membrane-anchoring complexes to support particularly 3D chromosome organization. The most popular consequences of epigenetic modifications are gene expression changes, but chromatin modifications have implications beyond this, particularly in actively dividing cells and during sexual reproduction...
October 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29032247/specifications-of-targeting-heterochromatin-modifications-in-plants
#13
REVIEW
Jered M Wendte, Robert J Schmitz
Plants encode a diverse repertoire of DNA methyltransferases that have specialized to target cytosines for methylation in specific sequence contexts. These include the de novo methyltransferase, DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), which methylates cytosines in all sequence contexts through an RNA guided process, the CHROMOMETHYLASES (CMTs), which methylate CHH and CHG cytosines (where H is A, T, or C), and the maintenance methyltransferase, METHYLTRANSFERASE 1 (MET1), which maintains methylation of symmetrical CG contexts...
October 12, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29031162/dna-demethylation-activates-genes-in-seed-maternal-integument-development-in-rice-oryza-sativa-l
#14
Yifeng Wang, Haiyan Lin, Xiaohong Tong, Yuxuan Hou, Yuxiao Chang, Jian Zhang
DNA methylation is an important epigenetic modification that regulates various plant developmental processes. Rice seed integument determines the seed size. However, the role of DNA methylation in its development remains largely unknown. Here, we report the first dynamic DNA methylomic profiling of rice maternal integument before and after pollination by using a whole-genome bisulfite deep sequencing approach. Analysis of DNA methylation patterns identified 4238 differentially methylated regions underpin 4112 differentially methylated genes, including GW2, DEP1, RGB1 and numerous other regulators participated in maternal integument development...
September 27, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29027833/trichostatin-a-and-5-aza-2-deoxycytidine-influence-the-expression-of-cold-induced-genes-in-arabidopsis
#15
Yuan Song, Lijun Liu, Gaopeng Li, Lizhe An, Lining Tian
The expression of cold-induced genes is critical for plants to survive under freezing stress. However, the underlying mechanisms for the decision of when, where, and which genes to express are unclear when a plant meets a sudden temperature drop. Previous studies have demonstrated epigenetics to play a central role in the regulation of gene expression in plant responses to environmental stress. DNA methylation and histone deacetylation are the two most important epigenetic modifications. This study was conducted to investigate the effects of inhibiting DNA methylation and histone deacetylation on gene expression, and to explore the potential role of epigenetics in plant responses to cold stress...
October 13, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/29027325/ecological-plant-epigenetics-evidence-from-model-and-non-model-species-and-the-way-forward
#16
Christina L Richards, Conchita Alonso, Claude Becker, Oliver Bossdorf, Etienne Bucher, Maria Colomé-Tatché, Walter Durka, Jan Engelhardt, Bence Gaspar, Andreas Gogol-Döring, Ivo Grosse, Thomas P van Gurp, Katrin Heer, Ilkka Kronholm, Christian Lampei, Vít Latzel, Marie Mirouze, Lars Opgenoorth, Ovidiu Paun, Sonja J Prohaska, Stefan A Rensing, Peter F Stadler, Emiliano Trucchi, Kristian Ullrich, Koen J F Verhoeven
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation...
October 12, 2017: Ecology Letters
https://www.readbyqxmd.com/read/29026973/active-dna-demethylation-mechanism-and-role-in-plant-development
#17
REVIEW
Yan Li, Suresh Kumar, Weiqiang Qian
Active DNA demethylation (enzymatic removal of methylated cytosine) regulates many plant developmental processes. In Arabidopsis, active DNA demethylation entails the base excision repair pathway initiated by the Repressor of silencing 1/Demeter family of bifunctional DNA glycosylases. In this review, we first present an introduction to the recent advances in our understanding about the mechanisms of active DNA demethylation. We then focus on the role of active DNA demethylation in diverse developmental processes in various plant species, including the regulation of seed development, pollen tube formation, stomatal development, fruit ripening, and nodule development...
October 12, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29025411/maize-rna-poliv-affects-the-expression-of-genes-with-nearby-te-insertions-and-has-a-genome-wide-repressive-impact-on-transcription
#18
Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
BACKGROUND: RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles...
October 12, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29024790/dna-methylation-and-potential-multigenerational-epigenetic-effects-linked-to-uranium-chronic-low-dose-exposure-in-gonads-of-males-and-females-rats
#19
REVIEW
G Elmhiri, C Gloaguen, S Grison, D Kereselidze, C Elie, K Tack, M Benderitter, P Lestaevel, A Legendre, M Souidi
INTRODUCTION: An increased health problem in industrialised countries is the contemporary concern of public and scientific community as well. This has been attributed in part to accumulated environmental pollutants especially radioactive substances and the use of nuclear power plants worldwide. However, the outcome of chronic exposure to low doses of a radionuclide such as uranium remains unknown. Recently, a paradigm shift in the perception of risk of radiotoxicology has emerged through investigating the possibility of transmission of biological effects over generations, in particular by epigenetic pathways...
October 9, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28988043/metabolic-signatures-of-bisphenol-a-and-genistein-in-atlantic-salmon-liver-cells
#20
Pål A Olsvik, Kaja H Skjærven, Liv Søfteland
Screening has revealed that aquafeeds with high inclusion of plant material may contain small amounts of endocrine disrupting agricultural pesticides. In this work, bisphenol A (BPA) and genistein (GEN) were selected as model endocrine disrupting toxicants with impact on DNA methylation in fish. Atlantic salmon hepatocytes were exposed in vitro to four concentrations of BPA and GEN (0.1, 1.0, 10 and 100 μM) for 48 h. Toxicity endpoints included cytotoxicity, global DNA methylation, targeted transcriptomics and metabolomic screening (100 μM)...
September 17, 2017: Chemosphere
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