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Plant dna methylation

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https://www.readbyqxmd.com/read/28521766/the-histone-h3-variant-h3-3-regulates-gene-body-dna-methylation-in-arabidopsis-thaliana
#1
Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E Jacobsen, Frédéric Berger
BACKGROUND: Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enrichment profiles over gene bodies are correlated and both have a similar dependence on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation. RESULTS: We engineered an H3.3 knockdown in Arabidopsis thaliana and observed transcription reduction that predominantly affects genes responsive to environmental cues...
May 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28513456/aflatoxins-characteristics-and-impact-on-human-health
#2
Anna Kowalska, Katarzyna Walkiewicz, Paweł Kozieł, Małgorzata Muc-Wierzgoń
Some molds commonly occurring in the natural environment produce mycotoxins in the process of secondary metabolism. Aspergillus flavus and A. parasiticus are species of molds, which are responsible for the production of aflatoxins and are crucial in the pathogenesis of human diseases. Aspergillus species present in decaying plants, the soil and their spores are transferred via air currents and insects to crops and food storages. Aflatoxins B1, B2, G1, G2, M1 and M2 are the most common derivatives of aflatoxins...
May 5, 2017: Postȩpy Higieny i Medycyny Doświadczalnej
https://www.readbyqxmd.com/read/28510781/5-azacytidine-mediated-reactivation-of-silenced-transgenes-in-potato-solanum-tuberosum-at-the-whole-plant-level
#3
Dimitrij Tyč, Eva Nocarová, Lenka Sikorová, Lukáš Fischer
Transient 5-azacytidine treatment of leaf explants from potato plants with transcriptionally silenced transgenes allows de novo regeneration of plants with restored transgene expression at the whole plant level. Transgenes introduced into plant genomes frequently become silenced either at the transcriptional or the posttranscriptional level. Transcriptional silencing is usually associated with DNA methylation in the promoter region. Treatments with inhibitors of maintenance DNA methylation were previously shown to allow reactivation of transcriptionally silenced transgenes in single cells or tissues, but not at the whole plant level...
May 16, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28509359/the-dna-translocase-rad5a-acts-independently-of-the-other-main-dna-repair-pathways-and-requires-both-its-atpase-and-ring-domain-for-activity-in-arabidopsis-thaliana
#4
Tobias Klemm, Anja Mannuß, Daniela Kobbe, Alexander Knoll, Oliver Trapp, Annika Dorn, Holger Puchta
Multiple pathways exist to repair DNA damage induced by methylating and cross-linking agents in Arabidopsis thaliana. The SWI2/SNF2 translocase RAD5A, the functional homolog of budding yeast Rad5 that is required for the error-free branch of post replicative repair, plays a surprisingly prominent role in the repair of both kinds of lesions in Arabidopsis. Here we show that both the ATPase domain and the ubiquitination function of the RING domain of the Arabidopsis protein are essential for the cellular response to different forms of DNA damage...
May 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28507144/critical-roles-of-dna-demethylation-in-the-activation-of-ripening-induced-genes-and-inhibition-of-ripening-repressed-genes-in-tomato-fruit
#5
Zhaobo Lang, Yihai Wang, Kai Tang, Dengguo Tang, Tatsiana Datsenka, Jingfei Cheng, Yijing Zhang, Avtar K Handa, Jian-Kang Zhu
DNA methylation is a conserved epigenetic mark important for genome integrity, development, and environmental responses in plants and mammals. Active DNA demethylation in plants is initiated by a family of 5-mC DNA glycosylases/lyases (i.e., DNA demethylases). Recent reports suggested a role of active DNA demethylation in fruit ripening in tomato. In this study, we generated loss-of-function mutant alleles of a tomato gene, SlDML2, which is a close homolog of the Arabidopsis DNA demethylase gene ROS1 In the fruits of the tomato mutants, increased DNA methylation was found in thousands of genes...
May 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28481402/dna-methylation-in-sugarcane-somaclonal-variants-assessed-through-methylation-sensitive-amplified-polymorphism
#6
J H M B Francischini, E L Kemper, J B Costa, J R V Manechini, L R Pinto
Micropropagation is an important tool for large-scale multiplication of plant superior genotypes. However, somaclonal variation is one of the drawbacks of this process. Changes in DNA methylation have been widely reported as one of the main causes of somaclonal variations in plants. In order to investigate the occurrence of changes in the methylation pattern of sugarcane somaclonal variants, the MSAP (methylation-sensitive amplified polymorphism) technique was applied to micro-propagated plantlets sampled at the third subculture phase...
May 4, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28481340/widespread-adenine-n6-methylation-of-active-genes-in-fungi
#7
Stephen J Mondo, Richard O Dannebaum, Rita C Kuo, Katherine B Louie, Adam J Bewick, Kurt LaButti, Sajeet Haridas, Alan Kuo, Asaf Salamov, Steven R Ahrendt, Rebecca Lau, Benjamin P Bowen, Anna Lipzen, William Sullivan, Bill B Andreopoulos, Alicia Clum, Erika Lindquist, Christopher Daum, Trent R Northen, Govindarajan Kunde-Ramamoorthy, Robert J Schmitz, Andrii Gryganskyi, David Culley, Jon Magnuson, Timothy Y James, Michelle A O'Malley, Jason E Stajich, Joseph W Spatafora, Axel Visel, Igor V Grigoriev
N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages. Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi...
May 8, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28475589/long-range-control-of-gene-expression-via-rna-directed-dna-methylation
#8
M Jordan Rowley, M Hafiz Rothi, Gudrun Böhmdorfer, Jan Kuciński, Andrzej T Wierzbicki
RNA-mediated transcriptional silencing, in plants known as RNA-directed DNA methylation (RdDM), is a conserved process where small interfering RNA (siRNA) and long non-coding RNA (lncRNA) help establish repressive chromatin modifications. This process represses transposons and affects the expression of protein-coding genes. We found that in Arabidopsis thaliana AGO4 binding sites are often located distant from genes differentially expressed in ago4. Using Hi-C to compare interactions between genotypes, we show that RdDM-targeted loci have the potential to engage in chromosomal interactions, but these interactions are inhibited in wild-type conditions...
May 5, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28471013/oligonucleotide-addressed-covalent-3-terminal-derivatization-of-small-rna-strands-for-enrichment-and-visualization
#9
Aleksandr Osipenko, Alexandra Plotnikova, Milda Nainytė, Viktoras Masevičius, Saulius Klimašauskas, Giedrius Vilkaitis
The HEN1 RNA 2'-O-methyltransferase plays important roles in the biogenesis of small non-coding RNAs in plants and proved a valuable tool for selective transfer of functional groups from cofactor analogues onto miRNA and siRNA duplexes in vitro. Herein, we demonstrate the versatile HEN1-mediated methylation and alkylation of small RNA strands in heteroduplexes with a range of complementary synthetic DNA oligonucleotides carrying user-defined moieties such as internal or 3'-terminal extensions or chemical reporter groups...
May 4, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28467815/epigenetic-silencing-of-triple-negative-breast-cancer-hallmarks-by-withaferin-a
#10
Katarzyna Szarc Vel Szic, Ken Declerck, René A J Crans, Jolien Diddens, David B Scherf, Clarissa Gerhäuser, Wim Vanden Berghe
Triple negative breast cancer (TNBC) is characterized by poor prognosis and a DNA hypomethylation profile. Withaferin A (WA) is a plant derived steroidal lactone which holds promise as a therapeutic agent for treatment of breast cancer (BC). We determined genome-wide DNA methylation changes in weakly-metastatic and aggressive, metastatic BC cell lines, following 72h treatment to a sub-cytotoxic concentration of WA. In contrast to the DNA demethylating agent 5-aza-2'-deoxycytidine (DAC), WA treatment of MDA-MB-231 cells rather tackles an epigenetic cancer network through gene-specific DNA hypermethylation of tumor promoting genes including ADAM metallopeptidase domain 8 (ADAM8), urokinase-type plasminogen activator (PLAU), tumor necrosis factor (ligand) superfamily, member 12 (TNFSF12), and genes related to detoxification (glutathione S-transferase mu 1, GSTM1), or mitochondrial metabolism (malic enzyme 3, ME3)...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28466841/arabidopsis-proteins-with-a-transposon-related-domain-act-in-gene-silencing
#11
Yoko Ikeda, Thierry Pélissier, Pierre Bourguet, Claude Becker, Marie-Noëlle Pouch-Pélissier, Romain Pogorelcnik, Magdalena Weingartner, Detlef Weigel, Jean-Marc Deragon, Olivier Mathieu
Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein in TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation and short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 and MAIN define an alternative silencing pathway independent of DNA methylation and short interfering RNAs. Mutants for MAIL1 or MAIN exhibit release of silencing and appear to show impaired condensation of pericentromeric heterochromatin...
May 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28457232/the-evolution-of-chromomethylases-and-gene-body-dna-methylation-in-plants
#12
Adam J Bewick, Chad E Niederhuth, Lexiang Ji, Nicholas A Rohr, Patrick T Griffin, Jim Leebens-Mack, Robert J Schmitz
BACKGROUND: The evolution of gene body methylation (gbM), its origins, and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridiplantae, we provide novel insights into the evolution of gbM and its relationship to CHROMOMETHYLASE (CMT) proteins. RESULTS: CMTs are evolutionary conserved DNA methyltransferases in Viridiplantae. Duplication events gave rise to what are now referred to as CMT1, 2 and 3...
May 1, 2017: Genome Biology
https://www.readbyqxmd.com/read/28450872/comparative-analysis-of-ralstonia-solanacearum-methylomes
#13
Ivan Erill, Marina Puigvert, Ludovic Legrand, Rodrigo Guarischi-Sousa, Céline Vandecasteele, João C Setubal, Stephane Genin, Alice Guidot, Marc Valls
Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28450424/tetrahydrofolate-modulates-floral-transition-through-epigenetic-silencing
#14
Lei Wang, Dongdong Kong, Qiang Lv, Guo-Qi Niu, Tingting Han, Xuanchao Zhao, Shulin Meng, Qian Cheng, Shouchun Guo, Jing Du, Zili Wu, Jinzheng Wang, Fang Bao, Yong Hu, Xiaojun Pan, Jinchan Xia, Dong Yuan, Lida Han, Tong Lian, Chunyi Zhang, Haiyang Wang, Xin-Jian He, Yi-Kun He
Folates, termed from tetrahydrofolate (THF) and its derivatives, function as co-enzymes in one-carbon transfer reactions and play a central role in synthesis of nucleotides and amino acids. Dysfunction of cellular folate metabolism leads to serious defects in plant development; however, the molecular mechnisms of folate-mediated cellular modifications and physiological responses in plants are still largely unclear. Here, we reported that THF controls flowering time by adjusting DNA methylation-regulated gene expression in Arabidopsis...
April 27, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28441589/nutrient-stress-induced-chromatin-changes-in-plants
#15
REVIEW
David Secco, James Whelan, Hatem Rouached, Ryan Lister
The ability of plants to appropriately respond to the soil nutrient availability is of primary importance for their development and to complete their life cycle. Deciphering these multifaceted adaptive mechanisms remains a major challenge for scientists to date. Recent technological breakthroughs now enable to assess the dynamism and complexity of these processes at unprecedented resolution. In this review, we present some of the most recent findings on the involvement of histone modifications, histone variants and DNA methylation in response to nutrient stresses as well as discussing the potential roles these chromatin changes could serve as priming or as trans-generational stress memory mechanisms...
April 22, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28439857/assessing-distribution-and-variation-of-genome-wide-dna-methylation-using-short-read-sequencing
#16
Jörg Hagmann, Claude Becker
DNA methylation is one of the most prominent epigenetic marks and is particularly complex in plant genomes. Whole-genome bisulfite sequencing (WGBS) using short reads has become the standard tool to study genome-wide patterns of DNA methylation. The goal of the present protocol is to enable readers to perform WGBS on both the wet lab and the computational side. We briefly outline important steps in bisulfite library preparation, then focus on the different aspects of DNA methylation analysis, from read mapping to identifying biologically relevant differential methylation between different samples...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28438577/genomic-cg-dinucleotide-deficiencies-associated-with-transposable-element-hypermutation-in-basidiomycetes-some-lower-fungi-a-moss-and-a-clubmoss
#17
A John Clutterbuck
Many Basidiomycete genomes include substantial fractions that are deficient in CG dinucleotides, in extreme cases amounting to 70% of the genome. CG deficiency is variable and correlates with genome size and, more closely, with transposable element (TE) content. Many species have limited CG deficiency; it is therefore likely that there are other mechanisms that can control TE proliferation. Examination of TEs confirms that C-to-T transition mutations in CG dinucleotides may comprise a conspicuous proportion of differences between paired elements, however transition/transversion ratios are never as high as those due to RIP in some Ascomycetes, suggesting that repeat-associated CG mutation is not totally pervasive...
April 21, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28431570/a-relative-quantitative-methylation-sensitive-amplified-polymorphism-msap-method-for-the-analysis-of-abiotic-stress
#18
Piotr T Bednarek, Renata Orłowska, Agnieszka Niedziela
BACKGROUND: We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied the technique to analyze aluminum (Al)-tolerant and non-tolerant control and Al-stressed inbred triticale lines. The approach is based on detailed analysis of events affecting HpaII and MspI restriction sites in control and stressed samples, and takes advantage of molecular marker profiles generated by EcoRI/HpaII and EcoRI/MspI MSAP platforms...
April 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28419906/plant-hormone-signaling-in-flowering-an-epigenetic-point-of-view
#19
REVIEW
Gerardo Campos-Rivero, Pedro Osorio-Montalvo, Rafael Sánchez-Borges, Rosa Us-Camas, Fátima Duarte-Aké, Clelia De-la-Peña
Reproduction is one of the most important phases in an organism's lifecycle. In the case of angiosperm plants, flowering provides the major developmental transition from the vegetative to the reproductive stage, and requires genetic and epigenetic reprogramming to ensure the success of seed production. Flowering is regulated by a complex network of genes that integrate multiple environmental cues and endogenous signals so that flowering occurs at the right time; hormone regulation, signaling and homeostasis are very important in this process...
March 31, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28419145/apomixis-frequency-under-stress-conditions-in-weeping-lovegrass-eragrostis-curvula
#20
Juan Manuel Rodrigo, Diego Carlos Zappacosta, Juan Pablo Selva, Ingrid Garbus, Emidio Albertini, Viviana Echenique
To overcome environmental stress, plants develop physiological responses that are triggered by genetic or epigenetic changes, some of which involve DNA methylation. It has been proposed that apomixis, the formation of asexual seeds without meiosis, occurs through the temporal or spatial deregulation of the sexual process mediated by genetic and epigenetic factors influenced by the environment. Here, we explored whether there was a link between the occurrence of apomixis and various factors that generate stress, including drought stress, in vitro culture, and intraspecific hybridization...
2017: PloS One
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