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Genome-wide bisulfite sequencing of methylation from seedings of of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

ABSTRACT: Genome-wide bisulfite sequencing of methylation from seedings of of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

PROVIDER: PRJNA488622 | ENA |

REPOSITORIES: ENA

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Genome-wide bisulfite sequencing of methylation from seedings of of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

Project description:The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 Signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 Signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. Results: We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function mutants of the COP9 Signalosome. Our results indicate that the COP9 Signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. In addition, our analyses suggest that COP9 Signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 Signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 Signalosome conservation among eukaryotes may also suggest that COP9 Signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. We report the application of Bisulfite-sequencing to compare methylation of two CSN mutants with their corresponding wild types: a non-lethal csn5a-1 mutant, vs. columbia ecotype, and a lethal, csn8 mutant, vs. Wassilewskija ecotype

2020-07-28 | GSE119259 | GEO

Expression data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

Project description:Expression data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

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Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids

Project description:This SuperSeries is composed of the following subset Series: GSE34655: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - mRNA-seq GSE34656: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - small RNA-seq GSE34657: Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq Refer to individual Series

2011-12-22 | E-GEOD-34658 | biostudies-arrayexpress

Expression and methylation data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes.

Project description:Expression and methylation data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes.

| PRJNA488899 | ENA

Expression data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes

Project description:The COP9 signalosome (CSN) is a highly conserved complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. Mutations in each of the CSN subunits exhibits diverse pleiotropic phenotypes We used microarrays to compare gene expression of two CSN mutants with their corresponding wild types: a non-lethal csn5a-1 mutant, vs. columbia ecotype, and a lethal, csn8 mutant, vs. Wassilewskija ecotype

2020-07-28 | GSE108376 | GEO

Arabidopsis thaliana ecotypes Rodasen-47 (Sweden) and Castelnuovo-12 (Italy) grown in high light and/or cold

Project description:Illumina HiSeq RNAseq data from the youngest fully developed leaf collected from two ecotypes of Arabidopsis thaliana, Rodasen-47 (Sweden) and Castelnuovo-12 (Italy), adapted to contrasting local climates, grown at different temperatures and/or light levels. Plants were all vegatively growing in one gallon pots to prevent root bounding. Plants were sampled at the 40th day of growth.

2020-07-14 | GSE154349 | GEO

Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids - Bisulfite-seq

Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of DNA methylation by Bisulfite sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.

2011-12-22 | E-GEOD-34657 | biostudies-arrayexpress

Expression and methylation data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes.

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-07-28 | GSE119363 | GEO

arabidopsis ecotypes-Transcriptionnal response to potyviruses infection in Arabidopsis

Project description:ra06-05_potyvirus-ecotypes - arabidopsis ecotypes - Common and specific genes deregulated in response to various potyviruses in different Arabidopsis genetic backgrounds. - Four different Arabidopsis ecotypes were inoculated with one Potyviruse. About 4 weeks after sowing, the 6 expanded leaves plants were inoculated with the different viruses or were mock-inoculated. Seven days after inoculation, inoculated leaves were collected, RNA was extracted and virus infection controlled. RNA fron infected plants was then used for microarrays hybridization. Three biological repeat have been done and two dye-swap. Keywords: normal vs disease comparison

2008-10-20 | GSE10711 | GEO

sRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids

Project description:We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis. The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles. The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents. Examination of sRNA populations from two-week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal hybrids.

2011-01-12 | E-GEOD-25022 | biostudies-arrayexpress

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