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Plant dna methylation

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https://www.readbyqxmd.com/read/28340458/toxic-effects-of-environmental-pollutants-comparative-investigation-using-allium-cepa-l-and-lactuca-sativa-l
#1
Graciele Lurdes Silveira, Maria Gabriela Franco Lima, Gabriela Barreto Dos Reis, Marcel José Palmieri, Larissa Fonseca Andrade-Vieria
Studies that help understand the mechanisms of action of environmental pollutants are extremely important in environmental toxicology. In this context, assays using plants as models stand out for their simplicity and low performance cost. Among the plants used for this purpose, Allium cepa L. is the model most commonly applied for cytogenotoxic tests, while Lactuca sativa L., already widely used in phytotoxic investigations, has been gaining prominence in cytotoxic analyses. The present study aimed to compare the responses of A...
March 21, 2017: Chemosphere
https://www.readbyqxmd.com/read/28338020/epigenetic-regulation-of-intronic-transgenes-in-arabidopsis
#2
Kenji Osabe, Yoshiko Harukawa, Saori Miura, Hidetoshi Saze
Defense mechanisms of plant genomes can epigenetically inactivate repetitive sequences and exogenous transgenes. Loss of mutant phenotypes in intronic T-DNA insertion lines by interaction with another T-DNA locus, termed T-DNA suppression, has been observed in Arabidopsis thaliana, although the molecular basis of establishment and maintenance of T-DNA suppression is poorly understood. Here we show that maintenance of T-DNA suppression requires heterochromatinisation of T-DNA sequences and the nuclear proteins, INCREASED IN BONSAI METHYLATION 2 (IBM2) and ENHANCED DOWNY MILDEW 2 (EDM2), which prevent ectopic 3' end processing of mRNA in atypically long introns containing T-DNA sequences...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28333248/the-evolutionary-dynamics-of-orthologs-that-shift-in-gene-body-methylation-between-arabidopsis-species
#3
Shohei Takuno, Danelle K Seymour, Brandon S Gaut
DNA methylation labels a specific subset of genes in plant genomes. Recent work has shown that this gene-body methylation (gbM) is a conserved feature of orthologs, because highly methylated genes in one species tend to be highly methylated in another. In this study, we examined the exceptions to that rule by identifying genes that differ in gbM status between two plant species - Arabidopsis thaliana and Arabidopsis lyrata. Using Capsella grandiflora as an outgroup, we polarized the loss and gain of gbM for orthologs in Arabidopsis lineages...
March 2, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28330159/in-silico-characterization-and-differential-expression-pattern-analysis-of-conserved-hmg-coa-reductase-domain-isolated-from-aconitum-balfourii-stapf
#4
Eti Sharma, Saurabh Pandey, A K Gaur
The 3-hydroxy-3-methyl glutaryl CoA reductase (HMGR) is the key enzyme of mevalonate pathway in plants. A partial genomic DNA fragment encoding HMGR conserved domain (denoted as AbHMGR) is isolated from Aconitum balfourii Stapf. It comprises 871 bp encoding 290 amino acids. In silico analysis reveals that it had extensive similarities to other plant HMGR gene. Domain analysis of AbHMGR showed two highly conserved NADPH and HMG CoA domains. Docking study predicted inhibitor, substrate and cofactor binding sites in the protein...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28317902/a-natural-tandem-array-alleviates-epigenetic-repression-of-ipa1-and-leads-to-superior-yielding-rice
#5
Lin Zhang, Hong Yu, Bin Ma, Guifu Liu, Jianjun Wang, Junmin Wang, Rongcun Gao, Jinjun Li, Jiyun Liu, Jing Xu, Yingying Zhang, Qun Li, Xuehui Huang, Jianlong Xu, Jianming Li, Qian Qian, Bin Han, Zuhua He, Jiayang Li
Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield...
March 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28298479/cyst-nematode-parasitism-induces-dynamic-changes-in-the-root-epigenome
#6
Tarek Hewezi, Thomas Lane, Sarbottam Piya, Aditi Rambani, J Hollis Rice, Meg Staton
A growing body of evidence indicates that epigenetic modifications can provide efficient, dynamic, and reversible cellular responses to a wide range of environmental stimuli. However, the significance of epigenetic modifications in plant-pathogen interactions remains largely unexplored. In this study, we provide a comprehensive analysis of epigenome changes during the compatible interaction between the beet cyst nematode Heterodera schachtii and Arabidopsis (Arabidopsis thaliana). Whole genome bisulfite sequencing was conducted to assess the dynamic changes in the methylome of Arabidopsis roots in response to H schachtii infection...
March 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28295376/both-maternally-and-paternally-imprinted-genes-regulate-seed-development-in-rice
#7
Jingya Yuan, Sushu Chen, Wu Jiao, Longfei Wang, Limei Wang, Wenxue Ye, Jie Lu, Delin Hong, Siliang You, Zhukuan Cheng, Dong-Lei Yang, Z Jeffrey Chen
Genetic imprinting refers to the unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms, including mammals and flowering plants. Although many imprinted genes have been identified in plants, the functions of these imprinted genes have remained largely uninvestigated. We report genome-wide analysis of gene expression, DNA methylation and small RNAs in the rice endosperm and functional tests of five imprinted genes during seed development using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated gene9 (CRISPR/Cas9) gene editing technology...
March 13, 2017: New Phytologist
https://www.readbyqxmd.com/read/28283571/mycofumigation-through-production-of-the-volatile-dna-methylating-agent-n-methyl-n-nitrosoisobutyramide-by-fungi-in-the-genus-muscodor
#8
Michelle L Hutchings, Cambria J Alpha-Cobb, David A Hiller, Julien Berro, Scott A Strobel
Antagonistic microorganisms produce antimicrobials to inhibit the growth of competitors. While water-soluble antimicrobials are limited to proximal interactions via aqueous diffusion, volatile antimicrobials are able to act at a distance and diffuse through heterogenous environments. Here we identify the mechanism of action of Muscodor albus, an endophytic fungus known for its volatile antimicrobial activity towards a wide range of human and plant pathogens and its potential use in mycofumigation. Proposed uses of Muscodor species include protecting crops, produce, and building materials from undesired fungal or bacterial growth...
March 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28280500/post-translational-modifications-in-regulation-of-chloroplast-function-recent-advances
#9
REVIEW
Magda Grabsztunowicz, Minna M Koskela, Paula Mulo
Post-translational modifications (PTMs) of proteins enable fast modulation of protein function in response to metabolic and environmental changes. Phosphorylation is known to play a major role in regulating distribution of light energy between the Photosystems (PS) I and II (state transitions) and in PSII repair cycle. In addition, thioredoxin-mediated redox regulation of Calvin cycle enzymes has been shown to determine the efficiency of carbon assimilation. Besides these well characterized modifications, recent methodological progress has enabled identification of numerous other types of PTMs in various plant compartments, including chloroplasts...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28277978/targeted-dna-demethylation-in-human-cells-by-fusion-of-a-plant-5-methylcytosine-dna-glycosylase-to-a-sequence-specific-dna-binding-domain
#10
Jara Teresa Parrilla-Doblas, Rafael R Ariza, Teresa Roldán-Arjona
DNA methylation is a crucial epigenetic mark associated to gene silencing, and its targeted removal is a major goal of epigenetic editing. In animal cells, DNA demethylation involves iterative 5mC oxidation by TET enzymes followed by replication-dependent dilution and/or replication-independent DNA repair of its oxidized derivatives. In contrast, plants use specific DNA glycosylases that directly excise 5mC and initiate its substitution for unmethylated C in a base excision repair process. In this work, we have fused the catalytic domain of Arabidopsis ROS1 5mC DNA glycosylase (ROS1_CD) to the DNA binding domain of yeast GAL4 (GBD)...
February 23, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28258985/gene-body-dna-methylation-in-plants
#11
REVIEW
Adam J Bewick, Robert J Schmitz
The type, amount, and location of DNA methylation within a gene provides pivotal information on the enzymatic pathway by which it was achieved and its functional consequences. In plants (angiosperms specifically), gene body methylation (gbM) refers to genes with an enrichment of CG DNA methylation within the transcribed regions and depletion at the transcriptional start and termination sites. GbM genes often compose the bulk of methylated genes within angiosperm genomes and are enriched for housekeeping functions...
March 1, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28257158/dna-methylation-of-retrotransposons-dna-transposons-and-genes-in-sugar-beet-beta-vulgaris-l
#12
Falk Zakrzewski, Martin Schmidt, Mieke Van Lijsebettens, Thomas Schmidt
The methylation of cytosines shapes the epigenetic landscape of plant genomes, coordinates transgenerational epigenetic inheritance, represses activity of transposable elements (TEs), affects gene expression, and, hence, can influence the phenotype. Sugar beet (Beta vulgaris ssp. vulgaris), an important crop that accounts for 30% of the worldwide sugar needs, has a relatively small genome size (758 Mbp) consisting of approximately 485 Mbp repetitive DNA (64%) in particular, satellite DNA, retrotransposons, and DNA transposons...
March 3, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28241740/hinokitiol-induces-dna-demethylation-via-dnmt1-and-uhrf1-inhibition-in-colon-cancer-cells
#13
Jung Seon Seo, Young Ha Choi, Ji Wook Moon, Hyeon Soo Kim, Sun-Hwa Park
BACKGROUND: DNA hypermethylation is a key epigenetic mechanism for the silencing of many genes in cancer. Hinokitiol, a tropolone-related natural compound, is known to induce apoptosis and cell cycle arrest and has anti-inflammatory and anti-tumor activities. However, the relationship between hinokitiol and DNA methylation is not clear. The aim of our study was to explore whether hinokitiol has an inhibitory ability on the DNA methylation in colon cancer cells. RESULTS: MTT data showed that hinokitiol had higher sensitivity in colon cancer cells, HCT-116 and SW480, than in normal colon cells, CCD18Co...
February 27, 2017: BMC Cell Biology
https://www.readbyqxmd.com/read/28238081/dna-methyltransferases-contribute-to-the-fungal-development-stress-tolerance-and-virulence-of-the-entomopathogenic-fungus-metarhizium-robertsii
#14
Yulong Wang, Tiantian Wang, Lintao Qiao, Jianyu Zhu, Jinrui Fan, Tingting Zhang, Zhang-Xun Wang, Wanzhen Li, Anhui Chen, Bo Huang
DNA methylation is an important epigenetic mark in mammals, plants, and fungi and depends on multiple genetic pathways involving de novo and maintenance DNA methyltransferases (DNMTases). Metarhizium robertsii, a model system for investigating insect-fungus interactions, has been used as an environmentally friendly alternative to chemical insecticides. However, little is known concerning the molecular basis for DNA methylation. Here, we report on the roles of two DNMTases (MrRID and MrDIM-2) by characterizing ΔMrRID, ΔMrDIM-2, and ΔRID/ΔDIM-2 mutants...
February 25, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28235127/genome-wide-analysis-of-egeve_1-a-transcriptionally-active-endogenous-viral-element-associated-to-small-rnas-in-eucalyptus-genomes
#15
Helena Sanches Marcon, Juliana Costa-Silva, Alan Péricles Rodrigues Lorenzetti, Celso Luis Marino, Douglas Silva Domingues
Endogenous viral elements (EVEs) are the result of heritable horizontal gene transfer from viruses to hosts. In the last years, several EVE integration events were reported in plants by the exponential availability of sequenced genomes. Eucalyptus grandis is a forest tree species with a sequenced genome that is poorly studied in terms of evolution and mobile genetic elements composition. Here we report the characterization of E. grandis endogenous viral element 1 (EgEVE_1), a transcriptionally active EVE with a size of 5,664 bp...
February 23, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28232389/a-complex-of-arabidopsis-drb-proteins-can-impair-dsrna-processing
#16
Marie-Aude Tschopp, Taichiro Iki, Christopher A Brosnan, Pauline E Jullien, Nathan Pumplin
Small RNAs play an important role in regulating gene expression through transcriptional and post-transcriptional gene silencing. Biogenesis of small RNAs from longer double-stranded (ds)RNA requires the activity of DICER-LIKE ribonucleases (DCLs), which in plants are aided by dsRNA binding proteins (DRBs). To gain insight into this pathway in the model plant Arabidopsis, we searched for interactors of DRB4 by immunoprecipitation followed by mass spectrometry-based finger printing and discovered DRB7.1. This interaction, verified by reciprocal co-immunoprecipitation and bimolecular fluorescence complementation, colocalizes with markers of cytoplasmic siRNA bodies and nuclear dicing bodies...
February 23, 2017: RNA
https://www.readbyqxmd.com/read/28231772/rhmkk9-a-rose-map-kinase-kinase-gene-is-involved-in-rehydration-triggered-ethylene-production-in-rose-gynoecia
#17
Jiwei Chen, Qian Zhang, Qigang Wang, Ming Feng, Yang Li, Yonglu Meng, Yi Zhang, Guoqin Liu, Zhimin Ma, Hongzhi Wu, Junping Gao, Nan Ma
BACKGROUND: Flower opening is an important process in the life cycle of flowering plants and is influenced by various endogenous and environmental factors. Our previous work demonstrated that rose (Rosa hybrida) flowers are highly sensitive to dehydration during flower opening and the water recovery process after dehydration induced ethylene production rapidly in flower gynoecia. In addition, this temporal- and spatial-specific ethylene production is attributed to a transient but robust activation of the rose MAP KINASE6-ACC SYNTHASE1 (RhMPK6-RhACS1) cascade in gynoecia...
February 23, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28231765/inter-individual-variation-in-dna-methylation-is-largely-restricted-to-tissue-specific-differentially-methylated-regions-in-maize
#18
Massimiliano Lauria, Rodrigo Antonio Echegoyen-Nava, Dalia Rodríguez-Ríos, Silvio Zaina, Gertrud Lund
BACKGROUND: Variation in DNA methylation across distinct genetic populations, or in response to specific biotic or abiotic stimuli, has typically been studied in leaf DNA from pooled individuals using either reduced representation bisulfite sequencing, whole genome bisulfite sequencing (WGBS) or methylation sensitive amplified polymorphism (MSAP). The latter represents a useful alterative when sample size is large, or when analysing methylation changes in genomes that have yet to be sequenced...
February 23, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28229965/atmbd6-a-methyl-cpg-binding-domain-protein-maintains-gene-silencing-in-arabidopsis-by-interacting-with-rna-binding-proteins
#19
Adwaita Prasad Parida, Amrapali Sharma, Arun Kumar Sharma
DNA methylation, mediated by double-stranded RNA, is a conserved epigenetic phenomenon that protects a genome from transposons, silences unwanted genes and has a paramount function in plant or animal development. Methyl CpG binding domain proteins are members of a class of proteins that bind to methylated DNA. The Arabidopsis thaliana genome encodes 13 methyl CpG binding domain (MBD) proteins, but the molecular/biological functions of most of these proteins are still not clear. In the present study, we identified four proteins that interact with AtMBD6...
March 2017: Journal of Biosciences
https://www.readbyqxmd.com/read/28226269/the-causes-and-consequences-of-dna-methylome-variation-in-plants
#20
REVIEW
Danelle K Seymour, Claude Becker
Epigenetic variation - polymorphisms at the level of DNA methylation or histone modifications - modulates chromatin accessibility, which can perturb transcriptional activity and spur phenotypic variation. Determining the origin, frequency spectrum, and consequences of epigenetic variants is key to understanding the role of this variation in generating stable phenotypic variation in plants. Here we review recent literature on DNA methylation variation in both model and crop plant species with a focus on the link between genotype, epigenotype, and transcription...
February 19, 2017: Current Opinion in Plant Biology
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