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Plant dna methylation

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https://www.readbyqxmd.com/read/27911846/dna-methylome-of-the-20-gigabase-norway-spruce-genome
#1
Israel Ausin, Suhua Feng, Chaowei Yu, Wanlu Liu, Hsuan Yu Kuo, Elise L Jacobsen, Jixian Zhai, Javier Gallego-Bartolome, Lin Wang, Ulrika Egertsdotter, Nathaniel R Street, Steven E Jacobsen, Haifeng Wang
DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27908384/dna-replication-after-mutagenic-treatment-in-hordeum-vulgare
#2
Jolanta Kwasniewska, Arita Kus, Monika Swoboda, Agnieszka Braszewska-Zalewska
The temporal and spatial properties of DNA replication in plants related to DNA damage and mutagenesis is poorly understood. Experiments were carried out to explore the relationships between DNA replication, chromatin structure and DNA damage in nuclei from barley root tips. We quantitavely analysed the topological organisation of replication foci using pulse EdU labelling during the S phase and its relationship with the DNA damage induced by mutagenic treatment with maleic hydrazide (MH), nitroso-N-methyl-urea (MNU) and gamma ray...
December 2016: Mutation Research
https://www.readbyqxmd.com/read/27904456/methylome-analysis-of-two-xanthomonas-spp-using-single-molecule-real-time-sequencing
#3
Hoon Je Seong, Hye-Jee Park, Eunji Hong, Sung Chul Lee, Woo Jun Sul, Sang-Wook Han
Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv...
December 2016: Plant Pathology Journal
https://www.readbyqxmd.com/read/27902305/flavobacterium-cloacae-sp-nov-isolated-from-waste-water
#4
Hongming Liu, Peng Lu, Guoping Zhu
A Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium, named wh15T, was isolated from the waste water of a municipal wastewater treatment plant in Wuhu, China. The taxonomic status of the strain was characterized using a polyphasic taxonomic approach. Growth occurred at 15-45 °C (optimum, 25-40 °C), at pH 5.0-8.0 (optimum, pH 7.0) and with 0-4% NaCl (optimum, 1-2%). Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain wh15T was a member of genus Flavobacterium and shared the highest similarity with F...
November 21, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902260/flavobacterium-luticocti-sp-nov-isolated-from-waste-water
#5
Hongming Liu, Peng Lu, Lei Jin, Guoping Zhu
A Gram-stain-negative, non-spore-forming, rod-shaped and non-motile bacterium, named xz20T, was isolated from the waste water of a municipal wastewater treatment plant in Xuzhou, China. The taxonomic status of strain xz20T was characterized using a polyphasic taxonomic approach. Growth occurred at 15-40°C (optimum, 25-37°C), at pH 6.0-8.5 (optimum, pH 7.0) and with 0-3% NaCl (optimum, 1-2%). 16S rRNA gene sequence analysis revealed that strain xz20T was a member of the genus Flavobacterium and shared the highest similarity with F...
November 3, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27890807/diosmin-induced-senescence-apoptosis-and-autophagy-in-breast-cancer-cells-of-different-p53-status-and-erk-activity
#6
Anna Lewinska, Jagoda Adamczyk-Grochala, Ewa Kwasniewicz, Anna Deregowska, Maciej Wnuk
Relatively low bioavailability of plant-derived nutraceuticals with anticancer properties may limit their usefulness for prevention and therapy of cancer. In the present study, we have screened for nutraceuticals (n=30) that would act at low micromolar range against phenotypically distinct breast cancer cell lines, namely MCF-7 (ER(+), PR(+/-), HER2(-)), MDA-MB-231 (ER(-), PR(-), HER2(-)) and SK-BR-3 (ER(-), PR(-), HER2(+)), and diosmin, a citrus fruit flavonoid belonging to a flavone subclass, was selected...
November 24, 2016: Toxicology Letters
https://www.readbyqxmd.com/read/27885421/role-of-vernalization-mediated-demethylation-in-the-floral-transition-of-brassica-rapa
#7
Weike Duan, Huijun Zhang, Bei Zhang, Xiaoting Wu, Shuaixu Shao, Ying Li, Xilin Hou, Tongkun Liu
Vernalization-mediated demethylation of BrCKA2 (casein kinase II α-subunit) and BrCKB4 (casein kinase II β-subunit) shorten the period of the clock gene BrCCA1 (circadian clock associated 1) in Brassica rapa. Photoperiod and vernalization are two environmental cues involved in the regulation of floral transition, but the ways in which they interact remain unclear. DNA methylation is one of the main mechanisms involved in controlling the functional state of chromatin and gene expression in response to environmental signals...
November 24, 2016: Planta
https://www.readbyqxmd.com/read/27877189/genome-wide-differences-in-dna-methylation-changes-in-two-contrasting-rice-genotypes-in-response-to-drought-conditions
#8
Wensheng Wang, Qiao Qin, Fan Sun, Yinxiao Wang, Dandan Xu, Zhikang Li, Binying Fu
Differences in drought stress tolerance within diverse rice genotypes have been attributed to genetic diversity and epigenetic alterations. DNA methylation is an important epigenetic modification that influences diverse biological processes, but its effects on rice drought stress tolerance are poorly understood. In this study, methylated DNA immunoprecipitation sequencing and an Affymetrix GeneChip rice genome array were used to profile the DNA methylation patterns and transcriptomes of the drought-tolerant introgression line DK151 and its drought-sensitive recurrent parent IR64 under drought and control conditions...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27877178/an-s-adenosyl-methionine-synthetase-sams-gene-from-andropogon-virginicus-l-confers-aluminum-stress-tolerance-and-facilitates-epigenetic-gene-regulation-in-arabidopsis-thaliana
#9
Bunichi Ezaki, Aiko Higashi, Norie Nanba, Takumi Nishiuchi
Candidate clones which conferred Al tolerance to yeast transformants (TFs) were obtained from a cDNA library derived from a highly Al-tolerant poaceae, Andropogon virginicus L. One such clone, AL3A-4, encoded an S-adenosyl methionine synthetase (SAMS) gene. A full-length cDNA was obtained by 5'-RACE, designated AvSAMS1, and introduced into Arabidopsis thaliana to investigate its biological functions under Al stress. Two TF plant lines both showed higher tolerance than the Col-0 ecotype (non-TF) not only for Al stress, but also for Cu, Pb, Zn and diamide stresses, suggesting the AvSAMS1 was a multiple tolerance gene...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27871873/itraq-based-proteomic-analysis-of-defence-responses-triggered-by-the-necrotrophic-pathogen-rhizoctonia-solani-in-cotton
#10
Min Zhang, Shou-Ting Cheng, Hai-Yun Wang, Jia-He Wu, Yuan-Ming Luo, Qian Wang, Fu-Xin Wang, Gui-Xian Xia
: The soil-borne necrotrophic pathogen fungus Rhizoctonia solani is destructive, causing disease in various important crops. To date, little is known about the host defence mechanism in response to invasion of R. solani. Here, an iTRAQ-based proteomic analysis was employed to investigate pathogen-responsive proteins in the disease tolerant/resistant cotton cultivar CRI35. A total of 174 differentially accumulated proteins (DAPs) were identified after inoculation of cotton plants with R...
November 15, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27870873/herbivore-induced-dna-demethylation-changes-floral-signalling-and-attractiveness-to-pollinators-in-brassica-rapa
#11
Roman T Kellenberger, Philipp M Schlüter, Florian P Schiestl
Plants have to fine-tune their signals to optimise the trade-off between herbivore deterrence and pollinator attraction. An important mechanism in mediating plant-insect interactions is the regulation of gene expression via DNA methylation. However, the effect of herbivore-induced DNA methylation changes on pollinator-relevant plant signalling has not been systematically investigated. Here, we assessed the impact of foliar herbivory on DNA methylation and floral traits in the model crop plant Brassica rapa...
2016: PloS One
https://www.readbyqxmd.com/read/27862820/generation-of-marker-free-transgenic-hexaploid-wheat-via-an-agrobacterium-mediated-co-transformation-strategy-in-commercial-chinese-wheat-varieties
#12
Ke Wang, Huiyun Liu, Lipu Du, Xingguo Ye
Genotype-specificity is a big problem lagging the development of efficient hexaploid wheat transformation system. Increasingly, the biosecurity of genetically modified organisms is garnering public attention, so the generation of marker-free transgenic plants is very important to the eventual potential commercial release of transgenic wheat. In this study, 15 commercial Chinese hexaploid wheat varieties were successfully transformed via an Agrobacterium-mediated method, with efficiency of up to 37.7%, as confirmed by the use of Quickstix strips, histochemical staining, PCR analysis, and Southern blotting...
November 10, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27852223/diversity-evolution-and-expression-profiles-of-histone-acetyltransferases-and-deacetylases-in-oomycetes
#13
Xiao-Wen Wang, Li-Yun Guo, Miao Han, Kun Shan
BACKGROUND: Oomycetes are a group of fungus-like eukaryotes with diverse microorganisms living in marine, freshwater and terrestrial environments. Many of them are important pathogens of plants and animals, causing severe economic losses. Based on previous study, gene expression in eukaryotic cells is regulated by epigenetic mechanisms such as DNA methylation and histone modification. However, little is known about epigenetic mechanisms of oomycetes. RESULTS: In this study, we investigated the candidate genes in regulating histone acetylation in oomycetes genomes through bioinformatics approaches and identified a group of diverse histone acetyltransferases (HATs) and histone deacetylases (HDACs), along with three putative novel HATs...
November 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27836324/the-major-arabidopsis-thaliana-apurinic-apyrimidinic-endonuclease-arp-is-involved-in-the-plant-nucleotide-incision-repair-pathway
#14
Zhiger Akishev, Sabira Taipakova, Botagoz Joldybayeva, Caroline Zutterling, Izat Smekenov, Alexander A Ishchenko, Dmitry O Zharkov, Amangeldy K Bissenbaev, Murat Saparbaev
Apurinic/apyrimidinic (AP) endonucleases are important DNA repair enzymes involved in two overlapping pathways: DNA glycosylase-initiated base excision (BER) and AP endonuclease-initiated nucleotide incision repair (NIR). In the BER pathway, AP endonucleases cleave DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases, whereas in NIR, the same AP endonucleases incise DNA 5' to a wide variety of oxidized bases. The flowering plant Arabidopsis thaliana contains three genes encoding homologues of major human AP endonuclease 1 (APE1): Arp, Ape1L and Ape2...
October 29, 2016: DNA Repair
https://www.readbyqxmd.com/read/27833618/depletion-of-key-meiotic-genes-and-transcriptome-wide-abiotic-stress-reprogramming-mark-early-preparatory-events-ahead-of-apomeiotic-transition
#15
Jubin N Shah, Olga Kirioukhova, Pallavi Pawar, Muhammad Tayyab, Juan L Mateo, Amal J Johnston
Molecular dissection of apomixis - an asexual reproductive mode - is anticipated to solve the enigma of loss of meiotic sex, and to help fixing elite agronomic traits. The Brassicaceae genus Boechera comprises of both sexual and apomictic species, permitting comparative analyses of meiotic circumvention (apomeiosis) and parthenogenesis. Whereas previous studies reported local transcriptome changes during these events, it remained unclear whether global changes associated with hybridization, polyploidy and environmental adaptation that arose during evolution of Boechera might serve as (epi)genetic regulators of early development prior apomictic initiation...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27826839/structure-and-mechanism-of-plant-dna-methyltransferases
#16
Jiamu Du
DNA methylation is an important epigenetic mark that functions in eukaryotes from fungi to animals and plants, where it plays a crucial role in the regulation of epigenetic silencing. Once the methylation mark is established by the de novo DNA methyltransferase (MTase), it requires specific regulatory mechanisms to maintain the methylation state during chromatin replication, both during meiosis and mitosis. Plants have distinct DNA methylation patterns that are both established and maintained by unique DNA MTases and are regulated by plant-specific pathways...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27826837/genetic-studies-on-mammalian-dna-methyltransferases
#17
Jiameng Dan, Taiping Chen
Cytosine methylation at the C5-position, generating 5-methylcytosine (5mC), is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80 %) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27821059/recent-and-dynamic-transposable-elements-contribute-to-genomic-divergence-under-asexuality
#18
Julie Ferreira de Carvalho, Victor de Jager, Thomas P van Gurp, Niels C A M Wagemaker, Koen J F Verhoeven
BACKGROUND: Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the common dandelion, Taraxacum officinale and compare it between five accessions from the same apomictic lineage...
November 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27818666/comparative-analysis-of-dna-methyltransferase-gene-family-in-fungi-a-focus-on-basidiomycota
#19
Ruirui Huang, Qiangqiang Ding, Yanan Xiang, Tingting Gu, Yi Li
DNA methylation plays a crucial role in the regulation of gene expression in eukaryotes. Mushrooms belonging to the phylum Basidiomycota are highly valued for both nutritional and pharmaceutical uses. A growing number of studies have demonstrated the significance of DNA methylation in the development of plants and animals. However, our understanding of DNA methylation in mushrooms is limited. In this study, we identified and conducted comprehensive analyses on DNA methyltransferases (DNMtases) in representative species from Basidiomycota and Ascomycota, and obtained new insights into their classification and characterization in fungi...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27813706/global-genome-repair-factors-control-dna-methylation-patterns-in-arabidopsis
#20
Catherine Schalk, Jean Molinier
As obligate photosynthetic organisms plants are particularly exposed to the damaging effects of excess light and ultraviolet wavelengths, which can impact genome and epigenome dynamics by inducing DNA sequence and chromatin alterations. DNA DAMAGE-BINDING PROTEIN 2 (DDB2) is the main factor involved in the recognition of UV-induced DNA lesions during Global Genome Repair (GGR) in mammals and in plants. (1) In a recent study we reported that, in Arabidopsis, loss of DDB2 function alters DNA methylation patterns at many repeat loci and protein coding genes...
November 4, 2016: Plant Signaling & Behavior
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