epigenetic in plant development
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epigenetic in plant development
acetylation, methylation, phosphorylation and ubiquitinylation
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Rescooped by tianxing84 from Plant Pathogenomics
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PLOS Genetics: Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans (2014)

PLOS Genetics: Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans (2014) | epigenetic in plant development | Scoop.it

Plant pathogens secrete an arsenal of small secreted proteins (SSPs) acting as effectors that modulate host immunity to facilitate infection. SSP-encoding genes are often located in particular genomic environments and show waves of concerted expression at diverse stages of plant infection. To date, little is known about the regulation of their expression. The genome of the Ascomycete Leptosphaeria maculans comprises alternating gene-rich GC-isochores and gene-poor AT-isochores. The AT-isochores harbor mosaics of transposable elements, encompassing one-third of the genome, and are enriched in putative effector genes that present similar expression patterns, namely no expression or low-level expression during axenic cultures compared to strong induction of expression during primary infection of oilseed rape (Brassica napus). Here, we investigated the involvement of one specific histone modification, histone H3 lysine 9 methylation (H3K9me3), in epigenetic regulation of concerted effector gene expression in L. maculans. For this purpose, we silenced the expression of two key players in heterochromatin assembly and maintenance, HP1 and DIM-5 by RNAi. By using HP1-GFP as a heterochromatin marker, we observed that almost no chromatin condensation is visible in strains in which LmDIM5 was silenced by RNAi. By whole genome oligoarrays we observed overexpression of 369 or 390 genes, respectively, in the silenced-LmHP1 and -LmDIM5 transformants during growth in axenic culture, clearly favouring expression of SSP-encoding genes within AT-isochores. The ectopic integration of four effector genes in GC-isochores led to their overexpression during growth in axenic culture. These data strongly suggest that epigenetic control, mediated by HP1 and DIM-5, represses the expression of at least part of the effector genes located in AT-isochores during growth in axenic culture. Our hypothesis is that changes of lifestyle and a switch toward pathogenesis lift chromatin-mediated repression, allowing a rapid response to new environmental conditions.


Via Kamoun Lab @ TSL
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Arabidopsis MSI1 connects LHP1 to PRC2 complexes : Abstract : The EMBO Journal

Arabidopsis MSI1 connects LHP1 to PRC2 complexes : Abstract : The EMBO Journal | epigenetic in plant development | Scoop.it
The EMBO Journal encourages and publishes articles that report novel findings of wide biological significance in the areas of development, immunology, neuroscience, plant biology, structural biology, genomic & computational biology, genome...

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PMG's curator insight, July 24, 2013 9:36 PM

MSI1 was required for the functions of the EMBRYONIC FLOWER and the VERNALIZATION PRC2 complexes including trimethylation of histone H3 Lys27 (H3K27) at the target chromatin, as well as gene repression and establishment of competence to flower. We found that MSI1 serves to link PRC2 to LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), a protein that binds H3K27me3 in vitro and in vivo and is required for a functional plant PcG system. The LHP1–MSI1 interaction forms a positive feedback loop to recruit PRC2 to chromatin that carries H3K27me3. Consequently, this can provide a mechanism for the faithful inheritance of local epigenetic information through replication.

Rescooped by tianxing84 from Plant-microbe interaction
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Advanced Proteomic Analyses Yield a Deep Catalog of Ubiquitylation Targets in Arabidopsis

Advanced Proteomic Analyses Yield a Deep Catalog of Ubiquitylation Targets in Arabidopsis | epigenetic in plant development | Scoop.it

The posttranslational addition of ubiquitin (Ub) profoundly controls the half-life, interactions, and/or trafficking of numerous intracellular proteins. Using stringent two-step affinity methods to purify Ub-protein conjugates followed by high-sensitivity mass spectrometry, we identified almost 950 ubiquitylation substrates in whole Arabidopsis thaliana seedlings. The list
includes key factors regulating a wide range of biological processes, including metabolism, cellular transport, signal transduction, transcription, RNA biology, translation, and proteolysis. The ubiquitylation state of more than half of the targets increased after treating seedlings with the proteasome inhibitor MG132 (carbobenzoxy-Leu-Leu-Leu-al), strongly suggesting that Ub addition commits many to degradation by the 26S proteasome. Ub-attachment sites were resolved for a number of
targets, including six of the seven Lys residues on Ub itself with a Lys-48>Lys-63>Lys-11>>>Lys-33/Lys-29/Lys-6 preference. However, little sequence consensus was detected among conjugation sites, indicating that the local environment has little influence on global ubiquitylation. Intriguingly, the level of Lys-11–linked Ub polymers increased substantially upon MG132 treatment, revealing that they might be important signals for proteasomal breakdown. Taken together, this proteomic analysis illustrates the breadth of plant processes affected by ubiquitylation and provides a deep data set of individual targets from which to explore the roles of Ub in various physiological and developmental pathways.


Via Suayib Üstün
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PLOS Genetics: ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1-Regulated Genes

PLOS Genetics: ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1-Regulated Genes | epigenetic in plant development | Scoop.it

We provide a definitive answer to the question regarding the role of histone H3 lysine 4 tri-methylation marks in the transcription of two ATX1-regulated genes. Despite the proven correlation between the gene transcriptional activity and the level of H3K4me3 modification on the nucleosomes, whether H3K4me3 contributes to, or simply “registers,” active transcription has remained unclear. Another broader-relevance question is whether histone-modifying proteins are required for recruitment of the general transcription machinery, thus playing roles beyond their catalytic activity. Using a combination of gene deletion and specific point mutation analyses, we untangle overlapping effects and reveal that H3K4me3 is not required for TBP/Pol II recruitment to promoters but is critical as an activating mark for transcription elongation. The existing hitherto ambiguity about the role of H3K4me3 as an activating mark has been largely due to the unknown duality of the ATX1/AtCOMPASS functions: facilitating PIC assembly and producing H3K4me3 as an activating mark for transcription elongation.


Via Guogen Yang
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Rescooped by tianxing84 from Plants and Microbes
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PLOS Biology: Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants (2007)

PLOS Biology: Autoimmune Response as a Mechanism for a Dobzhansky-Muller-Type Incompatibility Syndrome in Plants (2007) | epigenetic in plant development | Scoop.it

Epistatic interactions between genes are a major factor in evolution. Hybrid necrosis is an example of a deleterious phenotype caused by epistatic interactions that is observed in many intra- and interspecific plant hybrids. A large number of hybrid necrosis cases share phenotypic similarities, suggesting a common underlying mechanism across a wide range of plant species. Here, we report that approximately 2% of intraspecific crosses in Arabidopsis thaliana yield F1 progeny that express necrosis when grown under conditions typical of their natural habitats. We show that several independent cases result from epistatic interactions that trigger autoimmune-like responses. In at least one case, an allele of an NB-LRR disease resistance gene homolog is both necessary and sufficient for the induction of hybrid necrosis, when combined with a specific allele at a second locus. The A. thaliana cases provide insights into the molecular causes of hybrid necrosis, and serve as a model for further investigation of intra- and interspecific incompatibilities caused by a simple epistatic interaction. Moreover, our finding that plant immune-system genes are involved in hybrid necrosis suggests that selective pressures related to host–pathogen conflict might cause the evolution of gene flow barriers in plants.


Via Kamoun Lab @ TSL
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Fungal Genetics and Biology: Origin of pisatin demethylase (PDA) in the genus Fusarium (2012)

Fungal Genetics and Biology: Origin of pisatin demethylase (PDA) in the genus Fusarium (2012) | epigenetic in plant development | Scoop.it
Host specificity of plant pathogens can be dictated by genes that enable pathogens to circumvent host defenses. Upon recognition of a pathogen, plants initiate defense responses that can include the production of antimicrobial compounds such as phytoalexins. The pea pathogen Nectria haematococca mating population VI (MPVI) is a filamentous ascomycete that contains a cluster of genes known as the pea pathogenicity (PEP) cluster in which the pisatin demethylase (PDA) gene resides. The PDA gene product is responsible for the detoxification of the phytoalexin pisatin, which is produced by the pea plant (Pisum sativum L.). This detoxification activity allows the pathogen to evade the phytoalexin defense mechanism. It has been proposed that the evolution of PDA and the PEP cluster reflects horizontal gene transfer (HGT). Previous observations consistent with this hypothesis include the location of the PEP cluster and PDA gene on a dispensable portion of the genome (a supernumerary chromosome), a phylogenetically discontinuous distribution of the cluster among closely related species, and a bias in G + C content and codon usage compared to other regions of the genome. In this study we compared the phylogenetic history of PDA, beta-tubulin, and translation elongation factor 1-alpha in three closely related fungi (Nectria haematococca, Fusarium oxysporum, and Neocosmospora species) to formally evaluate hypotheses regarding the origin and evolution of PDA. Our results, coupled with previous work, robustly demonstrate discordance between the gene genealogy of PDA and the organismal phylogeny of these species, and illustrate how HGT of pathogenicity genes can contribute to the expansion of host specificity in plant-pathogenic fungi.
Via Kamoun Lab @ TSL
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BAT1, a Putative Acyltransferase, Modulates Brassinosteroid Levels in Arabidopsis

BAT1, a Putative Acyltransferase, Modulates Brassinosteroid Levels in Arabidopsis | epigenetic in plant development | Scoop.it

Summary

Brassinosteroids (BRs) are essential for various aspects of plant development. Cellular BR homeostasis is critical for proper growth and development of plants; however, its regulatory mechanism remains largely unknown. BAT1 (BR-related AcylTransferase1), a gene encoding a putative acyltransferase, was found to be involved in vascular bundle development in our full-length cDNA overexpressor (FOX) screen. Overexpression of BAT1 rendered typical BR-deficient phenotypes, which could be rescued by exogenously applied castasterone and brassinolide. Analyses of BR profiles demonstrated that BAT1 alters levels of several brassinolide biosynthetic intermediates including 6-deoxotyphasterol, typhasterol, and 6-deoxocastasterone. BAT1 is mainly localized in the endoplasmic reticulum. BAT1 is highly expressed in young tissues and vascular bundles, and its expression is induced by auxin. These data suggest that BAT1 is involved in BR homeostasis, probably by conversion of brassinolide intermediates into acylated-BR conjugates.

 

© 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd


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Rescooped by tianxing84 from Viruses and Bioinformatics from Virology.uvic.ca
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History of parvovirus B19 infection is associated with a DNA methylation signature in childhood acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) likely has a multistep etiology, with initial genetic aberrations occurring early in life. An abnormal immune response to common infections has emerged as a plausible candidate for triggering the proliferation of pre-leukemic clones and the fixation of secondary genetic mutations and epigenetic alterations. We investigated whether evidence of infection with a specific common myelotropic childhood virus, parvovirus B19 (PVB19), relates to patterns of gene promoter DNA methylation in ALL patients. ...


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PLoS ONE: DNA Methylation Profiles of the Brain-Derived Neurotrophic Factor (BDNF) Gene as a Potent Diagnostic Biomarker in Major Depression

PLoS ONE: DNA Methylation Profiles of the Brain-Derived Neurotrophic Factor (BDNF) Gene as a Potent Diagnostic Biomarker in Major Depression | epigenetic in plant development | Scoop.it
PLoS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.

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Rescooped by tianxing84 from Lung Cancer Research Digest
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Glutathione S-transferase PI (GST-PI) expression and DNA methylation involved in NSCLC pathogenesis and prognosis

High levels of GST–PI DNA methylation in tumor tissue of NSCLC patients have a potential as a biomarker identifying subpopulations with a more aggressive tumor biology. Quantitation of GST–PI DNA methylation may be a useful method to identify patients with a poor prognosis after curative resection and who will benefit from intensive adjuvant therapy.


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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

Abstract

DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification and cancer development. Here, we describe an R package, methylKit, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNA methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylKit is available at http://code.google.com/p/methylkit webcite.


Via Biswapriya Biswavas Misra
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Rescooped by tianxing84 from Plant Genomics
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RNA-Directed DNA Methylation and Chromatin Modification

RNA-Directed DNA Methylation and Chromatin Modification | epigenetic in plant development | Scoop.it

RNA-directed DNA Methylation (RdDM) was discovered in plants as a first example of a RNA-directed Chromatin Modification mechanism. Initially, it was suggested to be an exceptional plant de novo DNA methylation mechanism. However, within the past 10 years, it became clear that RdDM is a key process for the introduction of methylated cytosines into genomic DNA frequently triggering chromatin modification processes. Thus, RNA can have a direct effect on the epigenetic status of an organism. RdDM in plants is closely related to RNA interference (RNAi) and may be considered as nuclear RNAi. Both mechanisms employ members of identical enzyme classes Several chromatin remodeling and RNA-binding proteins were found to be associated with RdDM.
Despite the fact that fantastic work has been published in the field of de novo DNA methylation, so far, we are far away from understanding the RdDM mechanism in detail. It is still elusive which type of RNA directs the methylation machinery to its targets. Proteins guiding the RNA to a target have not been identified. It is unclear if only one or both DNA strands are targeted. In addition, developmental and spatial triggers of RdDM are not characterized. Little information about RdDM in stress response is available.
Finally, only few reports indicated that RdDM may also function in non-plants, e. g. mammalian systems have been published. And beyond that, RNA-directed Chromatin Modification is not dependent on DNA methylation. In fission yeast, which does not methylate its DNA at all, RNA-induced transcriptional gene silencing leading to heterochromatin formation shares many features with RdDM in plants. And similar mechanisms are operating in many other eukaryotes.


Via Biswapriya Biswavas Misra
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Cellectis study: Overcoming TALE DNA Binding Domain Sensitivity to Cytosine Methylation - JBC

(via Tom Schreiber [again! ... keep going])

Valton et al 2012, JBC, Cellectis, France

 

Within the past two years, TAL DNA binding domains have emerged as the new generation of engineerable platform for production of custom DNA binding domains. However, their recently described sensitivity to cytosine methylation represents a major bottleneck for genome engineering applications. Using a combination of biochemical, structural and cellular approaches, we were able to identify the molecular basis of such sensitivity and propose a simple, drug-free and universal method to overcome it.

 

Background: TALE-based technologies are poised to revolutionize the field of biotechnology however, their sensitivity to cytosine methylation may drastically restrict the range of their
applications.


Results: TALE repeat N* is able to proficiently bind to 5-methylated cytosine.

 

Conclusion: Sensitivity of TALE DNA binding domains to cytosine methylation can be overcome by using TALE repeat N*.

Significance: Utilization of TALE repeat N* enables broadening the scope of TALE-based technologies.


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Rescooped by tianxing84 from Plant Pathogenomics
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Trends in Microbiology: Epigenetics and the evolution of virulence (2013)

Trends in Microbiology: Epigenetics and the evolution of virulence (2013) | epigenetic in plant development | Scoop.it
Pathogens must evolve rapidly in response to host or environmental challenges.Clonal and invasive species adapt quickly despite a lack of genetic diversity.Evasion of host immunity can result from silencing of relevant effectors.Epigenetic reprogramming of gene expression can aid in pathogen adaptation.

 

A feature of pathogenic and invasive organisms is their adaptability when confronted with host and environmental challenges. Recent studies have demonstrated that plant pathogens rely on epigenetic processes for this purpose. Epiallelic variation of effector genes that results in evasion of host immunity is one emerging phenomenon. Another is the epigenetically induced reprogramming and diversification of transcriptional patterns by de-repression of transposable elements. These observations indicate that epigenetic control of gene expression provides a versatile means of generating phenotypic diversity that is adaptable and heritable across generations.


Via Kamoun Lab @ TSL
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Rescooped by tianxing84 from Plants and Microbes
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Plant Phys: Regulation of transcription of NB-LRR-encoding genes SNC1 and RPP4 via H3K4 tri-methylation (2013)

Plant Phys: Regulation of transcription of NB-LRR-encoding genes SNC1 and RPP4 via H3K4 tri-methylation (2013) | epigenetic in plant development | Scoop.it

Plant nucleotide-binding leucine-rich repeat (NB-LRR) proteins serve as intracellular sensors to detect pathogen effectors and trigger immune responses. Transcription of the NB-LRR-encoding Resistance (R) genes needs to be tightly controlled to avoid inappropriate defense activation. How the expression of the NB-LRR R genes is regulated is poorly understood. The Arabidopsis snc1 mutant carries a gain-of-function mutation in a TIR-NB-LRR-encoding gene, resulting in the constitutive activation of plant defence responses. A snc1 suppressor screen identified modifier of snc1, 9 (mos9), which partially suppresses the autoimmune phenotypes of snc1. Positional cloning revealed that MOS9 encodes a plant-specific protein of unknown function. Expression analysis showed that MOS9 is required for the full expression of TIR-NB-LRR protein-encoding RPP4 and SNC1, both of which reside in the RPP4 cluster. Co-immunoprecipitation and mass spectrometry analyses revealed that MOS9 associates with the Set1 class H3K4 methyl transferase ATXR7. Like MOS9, ATXR7 is also required for the full expression of SNC1 and the autoimmune phenotypes in the snc1 mutant. In atxr7 mutant plants, the expression of RPP4 is similarly reduced and resistance against Hyaloperonospora arabidopsidis Emwa1 is compromised. Consistent with the attenuated expression of SNC1 and RPP4, H3K4me3 marks are reduced around the promoters of SNC1 and RPP4 in mos9 plants. Our data suggest that MOS9 functions together with ATXR7 to regulate the expression of SNC1 and RPP4 through H3K4 methylation, which plays an important role in fine-tuning their transcription levels and functions in plant defence.


Via Kamoun Lab @ TSL
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Rescooped by tianxing84 from Plant Biology Teaching Resources (Higher Education)
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PlantCell: PIF3 Associates with the Histone Deacetylase HDA15 in .. Etiolated Arabidopsis Seedlings

PlantCell: PIF3 Associates with the Histone Deacetylase HDA15 in .. Etiolated Arabidopsis Seedlings | epigenetic in plant development | Scoop.it

"PHYTOCHROME INTERACTING FACTOR3 (PIF3) is a key basic helix-loop-helix transcription factor of Arabidopsis thaliana that negatively regulates light responses, repressing chlorophyll biosynthesis, photosynthesis, and photomorphogenesis in the dark. However, the mechanism for the PIF3-mediated transcription regulation remains largely unknown. In this study, we found that the REDUCED POTASSIUM DEPENDENCY3/HISTONE DEACETYLASE1-type histone deacetylase HDA15 directly interacted with PIF3 in vivo and in vitro."


Via Mary Williams
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Mary Williams's curator insight, April 3, 2013 6:43 AM

A while ago, one of the world's top plant scientists tipped me off to the emerging recognition of the role of the PIF family of transcription factors in coordinating growth with environmental inputs. Here's a good review from 2011 on the role of PIFs as "Pivotal components in a cellular signaling hub" (http://www.cell.com/trends/plant-science/retrieve/pii/S1360138510001627).

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The Arabidopsis Elongator Complex Subunit2 Epigenetically Regulates Plant Immune Responses

This work identifies a role for the Arabidopsis Elongator complex subunit ELP2 in somatic DNA demethylation/methylation and suggests that ELP2-mediated epigenetic regulation plays a vital function in plant immune responses.

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PLOS Genetics: ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1-Regulated Genes

PLOS Genetics: ATX1-Generated H3K4me3 Is Required for Efficient Elongation of Transcription, Not Initiation, at ATX1-Regulated Genes | epigenetic in plant development | Scoop.it

We provide a definitive answer to the question regarding the role of histone H3 lysine 4 tri-methylation marks in the transcription of two ATX1-regulated genes. Despite the proven correlation between the gene transcriptional activity and the level of H3K4me3 modification on the nucleosomes, whether H3K4me3 contributes to, or simply “registers,” active transcription has remained unclear. Another broader-relevance question is whether histone-modifying proteins are required for recruitment of the general transcription machinery, thus playing roles beyond their catalytic activity. Using a combination of gene deletion and specific point mutation analyses, we untangle overlapping effects and reveal that H3K4me3 is not required for TBP/Pol II recruitment to promoters but is critical as an activating mark for transcription elongation. The existing hitherto ambiguity about the role of H3K4me3 as an activating mark has been largely due to the unknown duality of the ATX1/AtCOMPASS functions: facilitating PIC assembly and producing H3K4me3 as an activating mark for transcription elongation.


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Plant J- C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with Beet severe curly top virus - Yan...

Plant J- C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with Beet severe curly top virus - Yan... | epigenetic in plant development | Scoop.it

Cytosine methylation is one form of epigenetic information marked on the DNA sequence. In plants, small interfering RNAs (siRNAs) target homologous genomic DNA sequences for cytosine methylation. This process, known as RNA-directed DNA methylation (RdDM), plays an important role in transposon control, regulation of gene expression and virus resistance. In this study, we demonstrated that the C2 protein, encoded by a geminivirus, Beet severe curly top virus (BSCTV), mediated decreases in DNA methylation of the repeat regions in the promoters of ACD6, an upstream regulator of the salicylic acid defense pathway, and GSTF14, an endogenous gene in the glutathione S-transferase (GST) superfamily that is implicated in numerous stress responses. Relatively, C2-mediated decreases in DNA methylation reduced the accumulation of the siRNAs derived from the promoter repeats and enhanced the steady-state expression of both ACD6 and GSTF14 transcripts. Reduced accumulation of BSCTV-derived siRNAs was detected in BSCTV-infected plants, but not in plants infected with C2-deficient BSCTV (c2-BSCTV). C2 protein exhibited no siRNA-binding activity. Instead, our results revealed that C2-protein-mediated decreases in DNA methylation appeared to tamper with the production of siRNAs that are required for targeting and reinforcing RdDM, a process that inevitably activated expression of defense-related genes that are normally dampened by these siRNAs in the host plants. However, C2-dependent reduction in virus-derived siRNAs also benefits the viruses by breaking the positive feedback loop reinforcing DNA-methylation-mediated antiviral silencing.

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C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with Beet severe curly top virus - Yang - The P...

C2-mediated decrease in DNA methylation, accumulation of siRNAs, and increase in expression for genes involved in defense pathways in plants infected with Beet severe curly top virus - Yang - The P... | epigenetic in plant development | Scoop.it

Cytosine methylation is one form of epigenetic information marked on the DNA sequence. In plants, small interfering RNAs (siRNAs) target homologous genomic DNA sequences for cytosine methylation. This process, known as RNA-directed DNA methylation (RdDM), plays an important role in transposon control, regulation of gene expression and virus resistance. In this study, we demonstrated that the C2 protein, encoded by a geminivirus, Beet severe curly top virus (BSCTV), mediated decreases in DNA methylation of the repeat regions in the promoters of ACD6, an upstream regulator of the salicylic acid defense pathway, and GSTF14, an endogenous gene in the glutathione S-transferase (GST) superfamily that is implicated in numerous stress responses. Relatively, C2-mediated decreases in DNA methylation reduced the accumulation of the siRNAs derived from the promoter repeats and enhanced the steady-state expression of both ACD6 and GSTF14 transcripts. Reduced accumulation of BSCTV-derived siRNAs was detected in BSCTV-infected plants, but not in plants infected with C2-deficient BSCTV (c2-BSCTV). C2 protein exhibited no siRNA-binding activity. Instead, our results revealed that C2-protein-mediated decreases in DNA methylation appeared to tamper with the production of siRNAs that are required for targeting and reinforcing RdDM, a process that inevitably activated expression of defense-related genes that are normally dampened by these siRNAs in the host plants. However, C2-dependent reduction in virus-derived siRNAs also benefits the viruses by breaking the positive feedback loop reinforcing DNA-methylation-mediated antiviral silencing.

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Rescooped by tianxing84 from Viruses and Bioinformatics from Virology.uvic.ca
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PLoS ONE: Parvovirus B19 DNA CpG Dinucleotide Methylation and Epigenetic Regulation of Viral Expression

PLoS ONE: Parvovirus B19 DNA CpG Dinucleotide Methylation and Epigenetic Regulation of Viral Expression | epigenetic in plant development | Scoop.it

CpG DNA methylation is one of the main epigenetic modifications playing a role in the control of gene expression. For DNA viruses whose genome has the ability to integrate in the host genome or to maintain as a latent episome, a correlation has been found between the extent of DNA methylation and viral quiescence. No information is available for Parvovirus B19, a human pathogenic virus, which is capable of both lytic and persistent infections. Within Parvovirus B19 genome, the inverted terminal regions display all the characteristic signatures of a genomic CpG island; therefore we hypothesised a role of CpG dinucleotide methylation in the regulation of viral genome expression.


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Rescooped by tianxing84 from Hereditary Genetics
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Advances in Bioinformatics Tools for High-Throughput Sequencing Data of DNA Methylation

Advances in Bioinformatics Tools for High-Throughput Sequencing Data of DNA Methylation | epigenetic in plant development | Scoop.it

DNA methylation plays crucial roles in regulating gene expression during cellular development and differentiation. Recently, Next-generation sequencing (NGS) technologies spurred a revolution in investigating global DNA methylation profiles. Analysis of DNA methylation patterns on a genome-wide scale is essential to understanding the underlying mechanisms of DNA methylation. Here, we reviewed several next-generation sequencing techniques coupled with different pretreatment methods (endonuclease digestion, affinity enrichment and bisulfite conversion) and summarized the relative bioinformatics tools and resources for further analysis of DNA methylation.(Read more Interesting)


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Epigenetic reprogramming of cancer cells via targeted DNA methylation.

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Epigenetic reprogramming of cancer cells via targeted DNA methylation.
Epigenetics.

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The effects of DNA methylation and epigenetic ... [J Ovarian Res. 2012] - PubMed - NCBI

PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

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Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

Abstract

Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. mRRBS achieves similar CpG coverage to the original RRBS protocol, while the higher throughput and lower cost make it better suited for large-scale DNA methylation mapping studies, including cohorts of cancer samples.


Via Biswapriya Biswavas Misra
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