Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE76651 | GEO | 2016/08/17
SECONDARY ACCESSION(S): PRJNA308230
REPOSITORIES: GEO
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Project description:We report the methylome analysis of Arabidopsis plants deficient for the expression of 2 factors involved in global genome repair using whole genome bisulfite sequencing technology
2016-08-17 | GSE76648 | GEO
Project description:We report the small RNA analysis of Arabidopsis plants deficient for the expression DDB2 involved in global genome repair using small RNA sequencing. In addition we performed RNA immunoprecipitation (RIP) of DDB2.
2016-08-17 | GSE76649 | GEO
Project description:Global Genome Repair factors are essential for shaping the DNA methylation landscape in Arabidopsis
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Project description:The universal nature of networks' structural and physical properties across diverse systems offers a better prospect to elucidate the interplay between a system and its environment. In the last decade, several large-scale transcriptome and interactome studies were conducted to understand the complex and dynamic nature of interactions between Arabidopsis and its bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. We took advantage of these publicly available datasets and performed "-omics"-based integrative, and network topology analyses to decipher the transcriptional and protein-protein interaction activities of effector targets. We demonstrated that effector targets exhibit shorter distance to differentially expressed genes (DEGs) and possess increased information centrality. Intriguingly, effector targets are differentially expressed in a sequential manner and make for 1% of the total DEGs at any time point of infection with virulent or defense-inducing DC3000 strains. We revealed that DC3000 significantly alters the expression levels of 71% effector targets and their downstream physical interacting proteins in Arabidopsis interactome. Our integrative "-omics"--based analyses identified dynamic complexes associated with MTI and disease susceptibility. Finally, we discovered five novel plant defense players using a systems biology-fueled top-to-bottom approach and demonstrated immune-related functions for them, further validating the power and resolution of our network analyses.
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Project description:During sexual reproduction, one-half of the genetic material is deposited in gametes, and a complete set of chromosomes is restored upon fertilization. Reduction of the genetic information before gametogenesis occurs in meiosis, when cross-overs (COs) between homologous chromosomes secure an exchange of their genetic information. COs are not evenly distributed along chromosomes and are suppressed in chromosomal regions encompassing compact, hypermethylated centromeric and pericentromeric DNA. Therefore, it was postulated that DNA hypermethylation is inhibitory to COs. Here, when analyzing meiotic recombination in mutant plants with hypomethylated DNA, we observed unexpected and counterintuitive effects of DNA methylation losses on CO distribution. Recombination was further promoted in the hypomethylated chromosome arms while it was inhibited in heterochromatic regions encompassing pericentromeric DNA. Importantly, the total number of COs was not affected, implying that loss of DNA methylation led to a global redistribution of COs along chromosomes. To determine by which mechanisms altered levels of DNA methylation influence recombination--whether directly in cis or indirectly in trans by changing expression of genes encoding recombination components--we analyzed CO distribution in wild-type lines with randomly scattered and well-mapped hypomethylated chromosomal segments. The results of these experiments, supported by expression profiling data, suggest that DNA methylation affects meiotic recombination in cis. Because DNA methylation exhibits significant variation even within a single species, our results imply that it may influence the evolution of plant genomes through the control of meiotic recombination.
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Project description:DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however, its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 preferentially binds histone H3 Lys9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small-RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the landscapes of histone modification and small noncoding RNA.
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Project description:Habitat loss and fragmentation causes a decline in insect populations. Odonata (both dragonflies and damselflies) are especially threatened by the destruction of both aquatic and terrestrial environment. Moreover, effects of large-scale habitat heterogeneity on Odonata assemblages are poorly studied. In a two years study along East-European lowland watercourses both aquatic and terrestrial environment were studied to reveal the importance of local (e.g. water depth, macrovegetation cover, etc.) and landscape-scale (e.g. farmland patch size, forest patch proportion, etc.) variables to Odonata (as well as to dragonflies and damselflies separately) through increasing spatial sampling scales. The specimens were sampled using 500?m long transects from May to September. Results, both on local and landscape scales emphasized the importance of terrestrial environment on Odonata. Local variables influence damselflies, while dragonflies are more sensitive to landscape variables. Damselfly's diversity decreased with increasing macrovegetation cover, while dragonfly's diversity decreased with the increasing degree of land use intensification, but increased with the length of watercourses. It is thus vital to stress the importance of partial watercourse clearing, and moderate maintenance of traditional farm management based on small parcel farming near watercourses to maintain diverse and healthy Odonata assemblages.
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Project description:BackgroundIt is challenging to determine the effect of DNA methylation on the epigenetic landscape and the function in higher organisms due to the lack of DNA methylation-free mutants.ResultsHere, the analysis of a recently generated Arabidopsis mutant completely devoid of DNA methylation reveals that DNA methylation underpins the genome-wide landscape of histone modifications. Complete loss of DNA methylation causes an upheaval of the histone modification landscape, including complete loss of H3K9me2 and widespread redistribution of active and H3K27me3 histone marks, mostly owing to the role of DNA methylation in initiating H3K9me2 deposition and excluding active marks and repressive mark H3K27me3; CG and non-CG methylation can act independently at some genomic regions while they act cooperatively at many other regions. The transcriptional reprogramming upon loss of all DNA methylation correlates with the extensive redistribution or switches of the examined histone modifications. Histone modifications retained or gained in the DNA methylation-free mutant serve as DNA methylation-independent transcriptional regulatory signals: active marks promote genome transcription, whereas the repressive mark H3K27me3 compensates for the lack of DNA hypermethylation/H3K9me2 at multiple transposon families.ConclusionsOur results show that an intact DNA methylome constitutes the scaffolding of the epigenomic landscape in Arabidopsis and is critical for controlled genome transcription and ultimately for proper growth and development.
| S-EPMC9487137 | biostudies-literature
Project description:Background: Preterm birth, defined as infants born before 37 weeks of gestation, is the largest contributor to child mortality. Despite new evidence highlighting the global burden of prematurity, policymakers have failed to adequately prioritize preterm birth despite the magnitude of its health impacts. Given current levels of political attention and investment, it is unlikely that the global community will be adequately mobilized to meet the 2012 Born Too Soon report goal of reducing the preterm birth rate by 50% by 2025. Methods: This study adapts the Shiffman and Smith framework for political priority to examine four components contributing to policy action in global health: actor power, ideas, political context, and issue characteristics. We conducted key informant interviews with 18 experts in prematurity and reproductive, maternal, newborn, and child health (RMNCH) and reviewed key literature on preterm birth. We aimed to identify the factors that shape the global political priority of preterm birth and to describe policy opportunities to increase its priority moving forward. Results: The global preterm birth community (academic researchers, multilateral organizations, government agencies, and civil society organizations) lacks evidence about the causes of and solutions to preterm birth; and country-level data quality is poor with gaps in the understanding required for implementing effective interventions. Limited funding compounds these challenges, creating divisions among experts on what policy actions to recommend. These factors contribute to the lack of priority and underrepresentation of preterm birth within the larger RMNCH agenda. Conclusion: Increasing the political priority of prematurity is essential to reduce preventable newborn and child mortality, a key target of the 2030 Sustainable Development Goal for health (target 3.2). This study identifies three policy recommendations for the preterm birth community: address data and evidence gaps, clarify and invest in viable solutions, and bring visibility to prematurity within the larger RMNCH agendas.
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Project description:We conducted whole-genome bisulfite sequencing (WGBS) of Arabidopsis thaliana mutation accumulation (MA) lines under different temperature treatments over sucessive generations, and then we identified the global methylation in each MA line. Our result showed taht DNA methylation was observed more frequently at DNA mutation sites, indicating its contribution to the mutation process at elevated temperatures.
2021-05-01 | GSE173660 | GEO