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Plant dna methylation

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https://www.readbyqxmd.com/read/28624556/a-64-bp-sequence-containing-the-gaaga-motif-is-essential-for-camv-35s-promoter-methylation-in-gentian
#1
Asahi Shimada, Azusa Okumura, Satoshi Yamasaki, Yuji Iwata, Nozomu Koizumi, Masahiro Nishihara, Kei-Ichiro Mishiba
This study investigated sequence specificity and perenniality of DNA methylation in the cauliflower mosaic virus (CaMV) 35S promoter of transgenic gentian (Gentiana triflora×G. scabra) plants. Unlike conventional transgene silencing models, 35S promoter hypermethylation in gentian is species-specific and occurs irrespective of the T-DNA copy number and genomic location. Modified 35S promoters were introduced into gentian, and single-copy transgenic lines were selected for methylation analysis. Modified 35S promoter lacking a core (-90) region [35S(Δcore)] in gentian conferred hypermethylation and high levels of de novo methylation of the CpHpH/CpCpG sites in the 35S enhancer regions (-298 to -241 and -148 to -85)...
June 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28621722/comparative-analysis-of-genome-wide-dna-methylation-profiles-for-the-genic-male-sterile-cabbage-line-01-20s-and-its-maintainer-line
#2
Fengqing Han, Xiaoli Zhang, Xing Liu, Henan Su, Congcong Kong, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yumei Liu, Zhansheng Li, Honghao Lv
Methylation modifications play an important role in multiple biological processes. Several studies have reported altered methylation patterns in male sterile plants such as rice and wheat, but little is known about the global methylation profiles and their possible roles in the cabbage (Brassicaoleracea) male sterile line. In this study, single-base-resolution bisulfite sequencing (BS-Seq) was adopted to identify the pattern and degree of cytosine methylation in the male sterile line 01-20S and its near-isogenic fertile line 01-20F...
June 16, 2017: Genes
https://www.readbyqxmd.com/read/28611800/small-rna-sequencing-links-physiological-changes-and-rddm-process-to-vegetative-to-floral-transition-in-apple
#3
Xinwei Guo, Zeyang Ma, Zhonghui Zhang, Lailiang Cheng, Xiuren Zhang, Tianhong Li
Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28608346/computational-analysis-of-genome-wide-argonaute-dependent-dna-methylation-in-plants
#4
Kai Tang, Cheng-Guo Duan, Huiming Zhang, Jian-Kang Zhu
Whole-genome bisulfite sequencing (WGBS) has become a powerful tool to dissect genome-wide methylation profiles at single-base resolution. In this chapter we describe in detail the bioinformatics pipeline used for the analysis of ARGONAUTE-dependent DNA methylation in Arabidopsis thaliana. We provide tools and command lines used for mapping bisulfite sequencing reads, for estimating methylation levels at individual cytosine sites, for identifying differentially methylated regions (DMRs), and for calculating methylation levels of DMRs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28608338/dissecting-the-subnuclear-localization-patterns-of-argonaute-proteins-and-other-components-of-the-rna-directed-dna-methylation-pathway-in-plants
#5
Cheng-Guo Duan, Jian-Kang Zhu
RNA-directed DNA methylation (RdDM) is a nuclear pathway which is comprised of multiple main and accessory protein components, including two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V, and argonaute (AGO) proteins. Regulation in the RdDM pathway can be achieved via multiple mechanisms, including the spatial distribution of different RdDM components. Here we describe a protocol for dissecting the subnuclear localization of AGO proteins and other RdDM components, including nuclei extraction from seedlings, slide preparation, and subsequent immunostaining...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28596013/two-likely-targets-for-the-anti-cancer-effect-of-indole-derivatives-from-cruciferous-vegetables-pi3k-akt-mtor-signalling-pathway-and-the-aryl-hydrocarbon-receptor
#6
REVIEW
Ada Popolo, Aldo Pinto, Maria Daglia, Seyed Fazel Nabavi, Ammad Ahmad Farooqi, Luca Rastrelli
Diets containing high quantities of plant foods are linked with a decreased likelihood of incidence of cancer. Several common plant-based dietary components exert effects on DNA methylation levels, and can positively influence genome stability and the transcription of tumor suppressors and oncogenes. Indole-3-carbinol (I3C) is a substance present in vegetables of the Brassicaeae family, especially broccoli, white cabbage, Brussels sprouts and cauliflower. The in vivo biological effects of I3C are ascribed to a series of oligomeric products (including 3,3'-diindolylmethane), developed under acidic conditions...
June 5, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28575160/dynamic-changes-in-methylome-and-transcriptome-patterns-in-response-to-methyltransferase-inhibitor-5-azacytidine-treatment-in-citrus
#7
Jidi Xu, Xia Wang, Hongbo Cao, Haidan Xu, Qiang Xu, Xiuxin Deng
DNA methylation is known to play an important role in various developmental processes in plants. However, there is a general lack of understanding about the possible functions of DNA methylation in fruit trees. Using callus as a model, methylome, transcriptome and metabolite changes were assessed after treatment with the DNA methyltransferase inhibitor 5-azacytidine (5azaC). Genome-wide methylome analysis revealed the demethylation of a diverse of genes, including many genes encoding transcription factors (TFs), genes involved in biological processes, and the up-regulation of a wide range of transposable elements (TEs)...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28569170/the-developmental-regulator-pkl-is-required-to-maintain-correct-dna-methylation-patterns-at-rna-directed-dna-methylation-loci
#8
Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He, Heng Zhang
BACKGROUND: The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana. RESULTS: Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter...
May 31, 2017: Genome Biology
https://www.readbyqxmd.com/read/28558752/epigenomic-and-functional-analyses-reveal-roles-of-epialleles-in-the-loss-of-photoperiod-sensitivity-during-domestication-of-allotetraploid-cottons
#9
Qingxin Song, Tianzhen Zhang, David M Stelly, Z Jeffrey Chen
BACKGROUND: Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produce meiotically stable epialleles, which are transmissible through selection and breeding. However, the relationship between DNA methylation and polyploid plant domestication remains elusive. RESULTS: We report comprehensive epigenomic and functional analyses, including ~12 million differentially methylated cytosines in domesticated allotetraploid cottons and their tetraploid and diploid relatives...
May 31, 2017: Genome Biology
https://www.readbyqxmd.com/read/28555142/oligodeoxynucleotides-can-transiently-up-and-downregulate-chs-gene-expression-in-flax-by-changing-dna-methylation-in-a-sequence-specific-manner
#10
Magdalena Dzialo, Jan Szopa, Tadeusz Czuj, Magdalena Zuk
Chalcone synthase (CHS) has been recognized as an essential enzyme in the phenylpropanoid biosynthesis pathway. Apart from the leading role in the production of phenolic compounds with many valuable biological activities beneficial to biomedicine, CHS is well appreciated in science. Genetic engineering greatly facilitates expanding knowledge on the function and genetics of CHS in plants. The CHS gene is one of the most intensively studied genes in flax. In our study, we investigated engineering of the CHS gene through genetic and epigenetic approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28542457/genet-specific-dna-methylation-probabilities-detected-in-a-spatial-epigenetic-analysis-of-a-clonal-plant-population
#11
Kiwako S Araki, Takuya Kubo, Hiroshi Kudoh
In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations...
2017: PloS One
https://www.readbyqxmd.com/read/28521766/the-histone-h3-variant-h3-3-regulates-gene-body-dna-methylation-in-arabidopsis-thaliana
#12
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
#13
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
#14
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
#15
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
#16
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 30, 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
#17
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
#18
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...
June 2017: Nature Genetics
https://www.readbyqxmd.com/read/28475589/long-range-control-of-gene-expression-via-rna-directed-dna-methylation
#19
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 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28471013/oligonucleotide-addressed-covalent-3-terminal-derivatization-of-small-rna-strands-for-enrichment-and-visualization
#20
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...
June 1, 2017: Angewandte Chemie
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