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Plant dna methylation

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https://www.readbyqxmd.com/read/29423802/methods-for-cpg-methylation-array-profiling-via-bisulfite-conversion
#1
Fatjon Leti, Lorida Llaci, Ivana Malenica, Johanna K DiStefano
DNA methylation is a key factor in epigenetic regulation, and contributes to the pathogenesis of many diseases, including various forms of cancers, and epigenetic events such X inactivation, cellular differentiation and proliferation, and embryonic development. The most conserved epigenetic modification in plants, animals, and fungi is 5-methylcytosine (5mC), which has been well characterized across a diverse range of species. Many technologies have been developed to measure modifications in methylation with respect to biological processes, and the most common method, long considered a gold standard for identifying regions of methylation, is bisulfite conversion...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29411658/antioxidant-properties-and-anti-mutagenic-potential-of-piper-cubeba-fruit-extract-and-molecular-docking-of-certain-bioactive-compounds
#2
Maryam Zahin, Mohammad Shavez Khan, Faizan Abul Qais, Hussein Hasan Abulreesh, Iqbal Ahmad
Spices and herbs are recognized as sources of natural antioxidants and thus play an important role in the chemoprevention of diseases and aging. Piper cubeba is one among them and known for its medicinal properties for decades. Various biological activities are associated with its extract and phytocompounds. However, the anti-mutagenic activity of antioxidant rich extract is less explored. In this study, we performed the fraction-based antioxidant activity of P. cubeba using four different assays and evaluated the anti-mutagenic activity of most potent antioxidant fraction using Salmonella typhimurium tester strains against four mutagens (methyl methanesulfonate [MMS], sodium azide [SA], benzo(a)pyrene, and 2-aminoflourene) respectively...
February 7, 2018: Drug and Chemical Toxicology
https://www.readbyqxmd.com/read/29396421/conserved-noncoding-sequences-conserve-biological-networks-and-influence-genome-evolution
#3
Jianbo Xie, Kecheng Qian, Jingna Si, Liang Xiao, Dong Ci, Deqiang Zhang
Comparative genomics approaches have identified numerous conserved cis-regulatory sequences near genes in plant genomes. Despite the identification of these conserved noncoding sequences (CNSs), our knowledge of their functional importance and selection remains limited. Here, we used a combination of DNA methylome analysis, microarray expression analyses, and functional annotation to study these sequences in the model tree Populus trichocarpa. Methylation in CG contexts and non-CG contexts was lower in CNSs, particularly CNSs in the 5'-upstream regions of genes, compared with other sites in the genome...
February 3, 2018: Heredity
https://www.readbyqxmd.com/read/29395786/an-intramolecular-interaction-of-uhrf1-reveals-dual-control-for-its-histone-association
#4
Linfeng Gao, Xiao-Feng Tan, Shen Zhang, Tianchen Wu, Zhi-Min Zhang, Hui-Wang Ai, Jikui Song
UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) is one of the essential components of mammalian DNA methylation machinery. Chromatin association of UHRF1 is controlled via an interplay between its intramolecular interaction and dual recognition of histone H3 trimethylated at lysine 9 (H3K9me3) and hemimethylated DNA. Here, we report the crystal structure of the N-terminal tandem Tudor domain (TTD) of UHRF1 in complex with the C-terminal polybasic region (PBR). Structural analysis reveals that PBR binding leads to displacement of the TTD-plant homeodomain (PHD) linker, as well as blockage of the H3K9me3-engaging cage, both of which contribute to a chromatin-occluded UHRF1 conformation...
January 18, 2018: Structure
https://www.readbyqxmd.com/read/29393726/otu5-tunes-environmental-responses-by-sustaining-chromatin-structure
#5
Der-Fen Suen, Wolfgang Schmidt
Phenotypic plasticity is dependent on the correct interpretation of environmental cues. We recently showed that the deubiquitinase OTU5 is required for orchestrating internal and external signals, tuning the morphogenesis of epidermal cells to the prevailing conditions. Homozygous otu5 mutants developed long and dense root hairs, resembling phosphate-deficient plants. The phenotype of otu5 plants was similar to that of arp6 plants, which carries a mutation that compromises the deposition of H2A.Z. Homozygous otu5 arp6 double mutants exhibited a synergistic phenotype, suggesting that the two mutations are functionally related...
February 2, 2018: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/29392401/ddm1-guards-against-telomere-truncation-in-arabidopsis
#6
Xiaoyuan Xie, Dorothy E Shippen
Prolonged hypomethylation of DNA leads to telomere truncation correlated with increased telomere recombination, transposon mobilization and stem cell death. Epigenetic pathways, including DNA methylation, are crucial for telomere maintenance. Deficient in DNA Methylation 1 (DDM1) encodes a nucleosome remodeling protein, required to maintain DNA methylation in Arabidopsis thaliana. Plants lacking DDM1 can be self-propagated, but in the sixth generation (G6) hypomethylation leads to rampant transposon activation and infertility...
February 1, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29382649/control-of-maize-vegetative-and-reproductive-development-fertility-and-rrnas-silencing-by-histone-deacetylase-108
#7
Cristian Forestan, Silvia Farinati, Jacques Rouster, Hervé Lassagne, Massimiliano Lauria, Nicola Dal Ferro, Serena Varotto
Histone deacetylases (HDACs) catalyze the removal of acetyl groups from acetylated histone tails that consequently interact more closely with DNA, leading to chromatin state refractory to transcription. Zea mays HDA108 belongs to the Rpd3/HDA1 HDAC family and is ubiquitously expressed during development. The newly isolated hda108/hda108 insertional mutant exhibited many developmental defects: significant reduction in plant height, alterations of shoot and leaf development, alterations of inflorescence patterning and fertility...
January 30, 2018: Genetics
https://www.readbyqxmd.com/read/29379150/rna-directed-dna-methylation-involves-co-transcriptional-small-rna-guided-slicing-of-polymerase-v-transcripts-in-arabidopsis
#8
Wanlu Liu, Sascha H Duttke, Jonathan Hetzel, Martin Groth, Suhua Feng, Javier Gallego-Bartolome, Zhenhui Zhong, Hsuan Yu Kuo, Zonghua Wang, Jixian Zhai, Joanne Chory, Steven E Jacobsen
Small RNAs regulate chromatin modifications such as DNA methylation and gene silencing across eukaryotic genomes. In plants, RNA-directed DNA methylation (RdDM) requires 24-nucleotide small interfering RNAs (siRNAs) that bind to ARGONAUTE 4 (AGO4) and target genomic regions for silencing. RdDM also requires non-coding RNAs transcribed by RNA polymerase V (Pol V) that probably serve as scaffolds for binding of AGO4-siRNA complexes. Here, we used a modified global nuclear run-on protocol followed by deep sequencing to capture Pol V nascent transcripts genome-wide...
January 29, 2018: Nature Plants
https://www.readbyqxmd.com/read/29372509/early-flowering-in-short-days-efs-regulates-the-seed-size-in-arabidopsis
#9
Lingling Cheng, Sarfraz Shafiq, Wei Xu, Qianwen Sun
Post-transcriptional modifications, including histone modifications and DNA methylation, alter the chromatin landscape to regulate gene expression, thus control various cellular processes in plants. EARLY FLOWERING IN SHORT DAYS (EFS) is the major contributor for H3K36 methylation in Arabidopsis and is important for plant development. Here, we find that EFS is expressed in different stages of embryo morphogenesis, and the efs mutant produces larger embryo that results in enlarged seeds. Further analysis reveals that an imprinted gene MOP9...
January 9, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29368664/extensive-epigenetic-reprogramming-during-the-life-cycle-of-marchantia-polymorpha
#10
Marc W Schmid, Alejandro Giraldo-Fonseca, Moritz Rövekamp, Dmitry Smetanin, John L Bowman, Ueli Grossniklaus
BACKGROUND: In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles...
January 25, 2018: Genome Biology
https://www.readbyqxmd.com/read/29366935/glycine-betaine-rather-than-acting-only-as-an-osmolyte-also-plays-a-role-as-regulator-in-cellular-metabolism
#11
REVIEW
Ciria G Figueroa-Soto, Elisa M Valenzuela-Soto
For many years, glycine betaine (GB) has been widely studied as an osmolyte in plants and bacteria. In animal cells, GB is an osmolyte mainly in the kidneys, but in humans many studies have shown its role as a methyl donor in homocysteine metabolism in the liver. GB is also a protein stabilizer, and thus, it became known as an osmoprotector. In many organisms GB is synthesized from choline and can also be obtained from some foods. Over the last twenty years GB has gone from being considered simply as an osmolyte to being known as a cytoprotector involved in cell metabolism and as a chemical chaperone...
January 20, 2018: Biochimie
https://www.readbyqxmd.com/read/29361906/genome-wide-dna-methylation-analysis-in-response-to-salinity-in-the-model-plant-caliph-medic-medicago-truncatula
#12
Mahmoud W Yaish, Abbas Al-Lawati, Ibtisam Al-Harrasi, Himanshu Vishwas Patankar
BACKGROUND: DNA methylation has a potential role in controlling gene expression and may, therefore, contribute to salinity adaptation in plants. Caliph medic (Medicago truncatula) is a model legume of moderate salinity tolerance capacity; however, a base-resolution DNA methylome map is not yet available for this plant. RESULTS: In this report, a differential whole-genome bisulfite sequencing (WGBS) was carried out using DNA samples extracted from root tissues exposed to either control or saline conditions...
January 24, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29361035/wox11-recruits-a-histone-h3k27me3-demethylase-to-promote-gene-expression-during-shoot-development-in-rice
#13
Saifeng Cheng, Feng Tan, Yue Lu, Xiaoyun Liu, Tiantian Li, Wenjia Yuan, Yu Zhao, Dao-Xiu Zhou
WUSCHEL-related homeobox (WOX) genes are key regulators of meristem activity and plant development, the chromatin mechanism of which to reprogram gene expression remains unclear. Histone H3K27me3 is a chromatin mark of developmentally repressed genes. How the repressive mark is removed from specific genes during plant development is largely unknown. Here, we show that WOX11 interacts with the H3K27me3 demethylase JMJ705 to activate gene expression during shoot development in rice. Genetic analysis indicates that WOX11 and JMJ705 cooperatively control shoot growth and commonly regulate the expression of a set of genes involved in meristem identity, chloroplast biogenesis, and energy metabolism in the shoot apex...
January 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29356846/epigenetics-and-epigenomics-of-plants
#14
Chandra Bhan Yadav, Garima Pandey, Mehanathan Muthamilarasan, Manoj Prasad
The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels...
January 23, 2018: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29352281/differential-dna-methylation-and-transcription-profiles-in-date-palm-roots-exposed-to-salinity
#15
Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation...
2018: PloS One
https://www.readbyqxmd.com/read/29352065/a-role-for-miniyo-and-quatre-quart-2-in-the-assembly-of-rna-polymerases-ii-iv-and-v-in-arabidopsis
#16
Yaoxi Li, Yuxiang Yuan, Xiaofeng Fang, Xiuli Lu, Bi Lian, Gaozhan Zhao, Yijun Qi
RNA polymerases IV and V (Pol IV and Pol V) are required for the generation of noncoding RNAs in RNA-directed DNA methylation (RdDM). Their subunit compositions resemble that of Pol II. The mechanism and accessory factors involved in their assembly remain largely unknown. In this study, we identified mutant alleles of MINIYO (IYO), QUATRE-QUART 2 (QQT2) and NUCLEAR RNA POLYMERASE B11/D11/E11 (NRPB/D/E11) that cause defects in RdDM in Arabidopsis. We found that Pol IV-dependent small interfering RNAs (siRNAs) and Pol V-dependent transcripts were greatly reduced in the mutants...
January 18, 2018: Plant Cell
https://www.readbyqxmd.com/read/29342280/epigenetic-differentiation-of-natural-populations-of-lilium-bosniacum-associated-with-contrasting-habitat-conditions
#17
V Zoldoš, I Biruš, E Muratovic, Z Šatovic, A Vojta, O Robin, F Pustahija, F Bogunic, V Vicic Bockor, S Siljak-Yakovlev
Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses revealed that the three populations did not differentiate genetically, but were clearly separated in the three distinct clusters according to DNA methylation profiles...
January 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29335548/paternal-easirnas-regulate-parental-genome-dosage-in-arabidopsis
#18
German Martinez, Philip Wolff, Zhenxing Wang, Jordi Moreno-Romero, Juan Santos-González, Lei Liu Conze, Christopher DeFraia, R Keith Slotkin, Claudia Köhler
The regulation of parental genome dosage is of fundamental importance in animals and plants, as exemplified by X-chromosome inactivation and dosage compensation. The 'triploid block' is a classic example of dosage regulation in plants that establishes a reproductive barrier between species differing in chromosome number1,2. This barrier acts in the embryo-nourishing endosperm tissue and induces the abortion of hybrid seeds through a yet unknown mechanism 3 . Here we show that depletion of paternal epigenetically activated small interfering RNAs (easiRNAs) bypasses the triploid block in response to increased paternal ploidy in Arabidopsis thaliana...
January 15, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29321305/arabidopsis-rna-polymerase-v-mediates-enhanced-compaction-and-silencing-of-geminivirus-and-transposon-chromatin-during-host-recovery-from-infection
#19
Tami Coursey, Elizabeth Regedanz, David M Bisaro
Plants employ RNA-directed DNA methylation (RdDM) and dimethylation of histone 3 lysine 9 (H3K9me2) to silence geminiviruses and transposable elements (TEs). We previously showed that canonical RdDM (Pol IV-RdDM) involving RNA polymerases IV and V (Pol IV and Pol V) is required for Arabidopsis thaliana to recover from infection with Beet curly top virus lacking a suppressor protein that inhibits methylation (BCTV L2-). Recovery, which is characterized by reduced viral DNA levels and symptom remission, allows normal floral development...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29296019/extreme-haplotype-variation-in-the-desiccation-tolerant-clubmoss-selaginella-lepidophylla
#20
Robert VanBuren, Ching Man Wai, Shujun Ou, Jeremy Pardo, Doug Bryant, Ning Jiang, Todd C Mockler, Patrick Edger, Todd P Michael
Plant genome size varies by four orders of magnitude, and most of this variation stems from dynamic changes in repetitive DNA content. Here we report the small 109 Mb genome of Selaginella lepidophylla, a clubmoss with extreme desiccation tolerance. Single-molecule sequencing enables accurate haplotype assembly of a single heterozygous S. lepidophylla plant, revealing extensive structural variation. We observe numerous haplotype-specific deletions consisting of largely repetitive and heavily methylated sequences, with enrichment in young Gypsy LTR retrotransposons...
January 2, 2018: Nature Communications
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