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Plant dna methylation

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https://www.readbyqxmd.com/read/29659948/mir156-spls-module-regulates-somatic-embryogenesis-induction-in-citrus-callus
#1
Jian-Mei Long, Chao-Yang Liu, Meng-Qi Feng, Yun Liu, Xiao-Meng Wu, Wen-Wu Guo
As a highly conserved plant miRNA, miR156 has been intensively investigated for its versatile roles in plant development. Herein we report a novel role of miR156 in regulating somatic embryogenesis (SE) of citrus, one of the most widely cultivated fruit crops in the world. SE is an important way of regeneration, but SE potential of the preserved citrus embryogenic callus always declined during long-term sub-culturing, becoming a key obstacle for citrus biotechnology. In our study, either overexpression of csi-miR156a or individual knock-down of the two target genes CsSPL3 and CsSPL14 significantly enhanced SE competence of citrus callus, indicating that the effect of miR156-SPLs module was established for the initial phases of SE induction...
April 5, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29656930/dna-n-6-adenine-methylation-in-arabidopsis-thaliana
#2
Zhe Liang, Lisha Shen, Xuean Cui, Shengjie Bao, Yuke Geng, Guoliang Yu, Fan Liang, Shang Xie, Tiegang Lu, Xiaofeng Gu, Hao Yu
DNA methylation on N6 -adenine (6mA) has recently been found to be a potentially epigenetic mark in several unicellular and multicellular eukaryotes. However, its distribution patterns and potential functions in land plants, which are primary producers for most ecosystems, remain largely unknown. Here we report global profiling of 6mA sites at single-nucleotide resolution in the genome of Arabidopsis thaliana at different developmental stages using single-molecule real-time sequencing. 6mA sites are widely distributed across the Arabidopsis genome and enriched over the pericentromeric heterochromatin regions...
April 12, 2018: Developmental Cell
https://www.readbyqxmd.com/read/29656392/epigenetic-modifications-preserve-the-hyperaccumulator-noccaea-caerulescens-from-ni-geno-toxicity
#3
Mariolina Gullì, Laura Marchi, Rosaria Fragni, Annamaria Buschini, Giovanna Visioli
The Ni hyperaccumulator Noccaea caerulescens has adapted to live in a naturally stressed environment, evolving a complex pattern of traits to cope with adverse conditions. Evidence is accumulating regarding the important role of epigenetic modifications in regulating plant responses to stress. In this study, we present data from the natural "open-field" adaptation of the Ni hyperaccumulator N. caerulescens to serpentine soil and provide the first evidence of the involvement of epigenetic changes in response to the high Ni content present in plant leaves...
April 15, 2018: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/29624160/tabrizicola-fusiformis-sp-nov-isolated-from-an-industrial-wastewater-treatment-plant
#4
Dong-Jin Ko, Ji-Sun Kim, Doo-Sang Park, Dae-Hee Lee, Sun-Yeon Heo, Jeong-Woo Seo, Chul Ho Kim, Baek-Rock Oh
The translucent white-coloured, Gram-stain-negative, aerobic, non-motile, fusiform-shaped bacterium (designated strain SY72T ) was isolated from waste-activated sludge. Optimal growth occurred at 30-37 °C and pH 6.0-7.0. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the novel isolate belonged to the family Rhodobacteraceae of the class Alphaproteobacteria. Strain SY72T is closely related to Tabrizicola aquatica KCTC 23724T (97.8 % 16S rRNA gene sequence similarity) and Pseudorhodobacter aquaticus DC2N1-10T (96...
April 6, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29618467/subtle-perturbations-of-the-maize-methylome-reveal-genes-and-transposons-silenced-by-chromomethylase-or-rna-directed-dna-methylation-pathways
#5
Sarah N Anderson, Greg Zynda, Jawon Song, Zhaoxue Han, Matthew Vaughn, Qing Li, Nathan M Springer
DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes...
April 4, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29616225/toxicological-effects-of-berberine-and-sanguinarine
#6
REVIEW
Nitika Singh, Bechan Sharma
Berberine and Sanguinarine alkaloids belong to a group of naturally occurring chemical compounds that mostly contain basic nitrogen atoms. This group also includes some related compounds with neutral or weakly acidic properties. Alkaloids are produced by a large number of organisms including bacteria, fungi, plants, and animals. Berberine and Sanguinarine both are isoquinoline derivatives and belong to protoberberine and benzophenanthridines, respectively. Tyrosine or phenylalanine is common precursor for the biosynthesis of both...
2018: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29616066/modify-the-histone-to-win-the-battle-chromatin-dynamics-in-plant-pathogen-interactions
#7
REVIEW
Juan S Ramirez-Prado, Sophie J M Piquerez, Abdelhafid Bendahmane, Heribert Hirt, Cécile Raynaud, Moussa Benhamed
Relying on an immune system comes with a high energetic cost for plants. Defense responses in these organisms are therefore highly regulated and fine-tuned, permitting them to respond pertinently to the attack of a microbial pathogen. In recent years, the importance of the physical modification of chromatin, a highly organized structure composed of genomic DNA and its interacting proteins, has become evident in the research field of plant-pathogen interactions. Several processes, including DNA methylation, changes in histone density and variants, and various histone modifications, have been described as regulators of various developmental and defense responses...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29608716/modeling-interactions-between-transposable-elements-and-the-plant-epigenetic-response-a-surprising-reliance-on-element-retention
#8
Kyria Roessler, Alexandros Bousios, Esteban Meca, Brandon S Gaut
Transposable elements (TEs) compose the majority of angiosperm DNA. Plants counteract TE activity by silencing them epigenetically. One form of epigenetic silencing requires 21-22 nt small interfering RNAs that act to degrade TE mRNA and may also trigger DNA methylation. DNA methylation is reinforced by a second mechanism, the RNA-dependent DNA methylation (RdDM) pathway. RdDM relies on 24 nt small interfering RNAs and ultimately establishes TEs in a quiescent state. These host factors interact at a systems level, but there have been no system level analyses of their interactions...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29600844/click-chemical-ligation-initiated-on-bead-dna-polymerization-for-the-sensitive-flow-cytometric-detection-of-3%C3%A2-terminal-2%C3%A2-o-methylated-plant-microrna
#9
Wenjiao Fan, Yan Qi, Liying Qiu, Pan He, Chenghui Liu, Zhengping Li
A versatile flow cytometric strategy is developed for the sensitive detection of plant microRNA (miRNA) by coupling the target-templated click nucleic acid ligation (CNAL) with on-bead terminal enzymatic DNA polymerization (TEP). Unlike ligase-catalyzed ligation reaction, the plant miRNA-templated enzyme-free CNAL between two single-stranded DNA (ssDNA) probes respectively modified with Aza-dibenzocyclooctyne (Aza-DBCO) and N3, can not only simplify the operation but also achieve a much higher ligation efficiency...
March 30, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29594496/pdhs-elm-computational-predictor-for-plant-dnase-i-hypersensitive-sites-based-on-extreme-learning-machines
#10
Shanxin Zhang, Minjun Chang, Zhiping Zhou, Xiaofeng Dai, Zhenghong Xu
DNase I hypersensitive sites (DHSs) are hallmarks of chromatin zones containing transcriptional regulatory elements, making them critical in understanding the regulatory mechanisms of gene expression. Although large amounts of DHSs in the plant genome have been identified by high-throughput techniques, current DHSs obtained from experimental methods cover only a fraction of plant species and cell processes. Furthermore, these experimental methods are both time-consuming and expensive. Hence, it is urgent to develop automated computational means to efficiently and accurately predict DHSs in the plant genome...
March 29, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29588388/sumoylome-profiling-reveals-a-diverse-array-of-nuclear-targets-modified-by-the-sumo-ligase-siz1-during-heat-stress
#11
Therese C Rytz, Marcus J Miller, Fionn McLoughlin, Robert C Augustine, Richard S Marshall, Yu-Ting Juan, Yee-Yung Charng, Mark Scalf, Lloyd M Smith, Richard D Vierstra
The post-translational addition of Small Ubiquitin-Like Modifier (SUMO) is an essential protein modification in plants that provides protection against numerous environmental challenges. Ligation is accomplished by a small set of SUMO ligases, with the SAP-MIZ domain-containing SIZ1 and METHYL METHANESULFONATE-SENSITIVE 21 (MMS21) ligases having critical roles in stress protection and DNA endoreduplication/repair, respectively. To help identify their corresponding targets in Arabidopsis thaliana, we used siz1 and mms21 mutants for proteomic analyses of SUMOylated proteins enriched via an engineered SUMO1 isoform suitable for mass spectrometric studies...
March 27, 2018: Plant Cell
https://www.readbyqxmd.com/read/29582638/extraction-and-characterization-of-chick-pea-cicer-arietinum-extract-with-immunostimulant-activity-in-balb-c-mice
#12
Bindhu Jayaprakash, Arunava Das
Traditional plant medicines are used for a range of cancer conditions. The chickpea is highly proteinaceous and consumed as a staple in many parts of the world. An evaluation of chemoprotective and immunomodulatory activities of Cicer arietinum (CE) in cisplatin-induced immunosuppressed mice was here performed. Cisplatin was given at 100mg/kg, intraperitoneally, and after induction of immunosuppression mice were treated with Cicer arietinum (0.5 mg/dose/animal/IP) for a period of 10-day. The influence of the extract on lymphoid organ weight, bone marrow cellularity, alpha esterase activity and on enzyme levels such as (SGOT,SGPT, Urea, Creatinine was assessed to identify any chemoprotective influence...
March 27, 2018: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29579641/expression-of-heterologous-lycopene-%C3%AE-cyclase-gene-in-flax-can-cause-silencing-of-its-endogenous-counterpart-by-changes-in-gene-body-methylation-and-in-aba-homeostasis-mechanism
#13
Aleksandra Boba, Kamil Kostyn, Marta Preisner, Wioleta Wojtasik, Jan Szopa, Anna Kulma
Previously we described flax plants with expression of Arabidopsis lycopene β-cyclase (lcb) gene in which decreased expression of the endogenous lcb and increased resistance to fungal pathogen was observed. We suggested that co-suppression was responsible for the change. In this study we investigated the molecular basis of the observed effect in detail. We found that methylation changes in the Lulcb gene body might be responsible for repression of the gene. Treatment with azacitidine (DNA methylation inhibitor) confirmed the results...
March 21, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29576081/selenoprotein-o-is-a-chloroplast-protein-involved-in-ros-scavenging-and-its-absence-increases-dehydration-tolerance-in-arabidopsis-thaliana
#14
Yosef Fichman, Zsuzsa Koncz, Noam Reznik, Gad Miller, László Szabados, Katharina Kramer, Hirofumi Nakagami, Hillel Fromm, Csaba Koncz, Aviah Zilberstein
The evolutionary conserved family of Selenoproteins performs redox-regulatory functions in bacteria, archaea and eukaryotes. Among them, members of the SELENOPROTEIN O (SELO) subfamily are located in mammalian and yeast mitochondria, but their functions are thus far enigmatic. Screening of T-DNA knockout mutants for resistance to the proline analogue thioproline (T4C), identified mutant alleles of the plant SELO homologue in Arabidopsis thaliana. Absence of SELO resulted in a stress-induced transcriptional activation instead of silencing of mitochondrial proline dehydrogenase, and also high elevation of Δ(1)-pyrroline-5-carboxylate dehydrogenase involved in degradation of proline, thereby alleviating T4C inhibition and lessening drought-induced proline accumulation...
May 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29575326/the-crispr-cas-revolution-reaches-the-rna-world-cas13-a-new-swiss-army-knife-for-plant-biologists
#15
Felix Wolter, Holger Puchta
Application of the bacterial CRISPR/Cas systems to eukaryotes is revolutionizing biology. Cas9 and Cas12 (previously called Cpf1) are widely used as DNA nucleases for inducing site specific DNA breaks for different kinds of genome engineering applications, and in their mutated forms as DNA binding proteins to modify gene expression. Moreover, histone modifications, as well as cytosine methylation or base editing, were achieved with these systems in plants. Recently, with the discovery of the nuclease Cas13a (previously called C2c2), molecular biologists have obtained a system that enables sequence specific cleavage of single stranded RNA molecules...
March 25, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29573427/transgenerational-phenotype-aggravation-in-caf-1-mutants-reveals-parent-of-origin-specific-epigenetic-inheritance
#16
Iva Mozgova, Thomas Wildhaber, Minerva S Trejo-Arellano, Jiri Fajkus, Pawel Roszak, Claudia Köhler, Lars Hennig
Chromatin is assembled by histone chaperones such as chromatin assembly factor CAF-1. We had noticed that vigor of Arabidopsis thaliana CAF-1 mutants decreased over several generations. Because changes in mutant phenotype severity over generations are unusual, we asked how repeated selfing of Arabidopsis CAF-1 mutants affects phenotype severity. CAF-1 mutant plants of various generations were grown, and developmental phenotypes, transcriptomes and DNA cytosine-methylation profiles were compared quantitatively...
March 24, 2018: New Phytologist
https://www.readbyqxmd.com/read/29572390/methionine-adenosyltransferase-4-mediates-dna-and-histone-methylation
#17
Jingjing Meng, Lishuan Wang, Jingyi Wang, Xiaowen Zhao, Jinkui Cheng, Wenxiang Yu, Dan Jin, Qing Li, Zhizhong Gong
DNA and histone methylation co-regulate heterochromatin formation and gene silencing in animals and plants. To identify factors involved in maintaining gene silencing, we conducted a forward genetic screen for mutants that release the silenced transgene Pro35S::NEOMYCIN PHOSPHOTRANSFERASE II in the transgenic Arabidopsis thaliana line L119. We identified MAT4/SAMS3/MTO3/AT3G17390, which encodes methionine adenosyltransferase 4 (MAT4)/S-adenosyl-methionine synthetase 3 that catalyzes the synthesis of S-adenosyl-methionine (SAM) in the one-carbon metabolism cycle...
March 23, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29569777/maternal-components-of-rna-directed-dna-methylation-are-required-for-seed-development-in-brassica-rapa
#18
Jeffrey W Grover, Timmy Kendall, Abdul Baten, Diane Burgess, Michael Freeling, Graham J King, Rebecca A Mosher
Small RNAs trigger repressive DNA methylation at thousands of transposable elements in a process called RNA-directed DNA Methylation (RdDM). The molecular mechanism of RdDM is well-characterized in Arabidopsis, yet the biological function remains unclear, since loss of RdDM in Arabidopsis causes no overt defects, even after generations of inbreeding. 24 nucleotide Pol IV-dependent siRNAs, the hallmark of RdDM, are abundant in flowers and developing seeds, indicating that RdDM might be important during reproduction...
March 23, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29566130/unravelling-the-epigenomic-interactions-between-parental-inbreds-resulting-in-an-altered-hybrid-methylome-in-pigeonpea
#19
Alim Junaid, Himanshu Kumar, A R Rao, A N Patil, N K Singh, Kishor Gaikwad
DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation...
March 16, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29563767/in-silico-modeling-of-epigenetic-induced-changes-in-photoreceptor-cis-regulatory-elements
#20
Reafa A Hossain, Nicholas R Dunham, Raymond A Enke, Christopher E Berndsen
Purpose: DNA methylation is a well-characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of transcription is controlled by proteins that regulate recruitment and activity of RNA polymerase by binding to specific cis-regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell-specific gene expression...
2018: Molecular Vision
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