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Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight. [Bisulfite-Seq]

ABSTRACT: Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight. [Bisulfite-Seq]

PROVIDER: PRJNA485775 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7689240_1.fastq.gz	Fastqsanger.gz
	SRR7689240_2.fastq.gz	Fastqsanger.gz
	SRR7689250_1.fastq.gz	Fastqsanger.gz
	SRR7689250_2.fastq.gz	Fastqsanger.gz
	SRR7689260_1.fastq.gz	Fastqsanger.gz

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Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight. [Bisulfite-Seq]

Project description:Epigenetic changes in the DNA methylome are increasingly shown to play an integral role in regulating gene expression necessary for plants’ adaption to environmental stressors. Plants subjected to the novel environment of spaceflight onboard the International Space Station (ISS), show stress-related transcriptomic changes most notably associated with pathogen stress response. Here, we investigate how known terrestrial stress associated epigenetic modulations might play a role in spaceflight adaptation. To examine the role of 5mCyt in spaceflight adaptation, the APEX04-EPEX experiment conducted onboard the ISS evaluated the spaceflight altered genome wide methylation profiles of two methylation regulating gene mutants (methyltransferase 1 (met1-7) and elongator complex subunit 2 (elp2-5)) that are involved in pathogen defense response, along with a wild type Col-0 control. MethylSeq and RNAseq analyses were performed on both spaceflight grown samples and ground grown controls. In addition, the epigenetics effects that may contribute to the differential gene expression patterns observed between leaf and root tissues were also investigated in an organ-specific manner.

2021-08-13 | GSE118483 | GEO

Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight. [RNA-Seq]

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Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight.

Project description:Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight.

| PRJNA486536 | ENA

Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight. [RNA-Seq]

Project description:Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight. [RNA-Seq]

| PRJNA486575 | ENA

Genomics Analysis of met1-derived epiRILs [BiSulfite-seq]

Project description:Genomics Analysis of met1-derived epiRILs [BiSulfite-seq]

| PRJNA1074416 | ENA

Expression data in Arabidopsis axe1-5 and met1-3 mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants.

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Bisulfite Methylation Profiling (BiMP) analysis of met1-3 epigenetic Recombinant Inbred Lines (epiRILs)

Project description:Epigenomic mapping of DNA methylation polymorphisms segregating within an epigenetic Recombinant Inbred Line population resultant from crossing the wild-type Col-0 and DNA maintenance methyltransferase mutant, met1-3, parental lines. Each line within the epiRIL population was self-fertilized for 7 generations, 10 individual F7 plants were then bulk harvested to create the F8 generation. Here, data files for three DNA methylation profiled epiRIL lines (epi01, epi12, epi28) are deposited. The DNA methylation polymorphisms were determined using the BiMP method with the Affymetrix Arabidopsis Tiling 1.0R array. The main objective for these samples was to create an epigenomic map to analyze the inheritance of DNA methylation polymorphisms within these three epiRIL entries. Keywords: Bisulfite Methylation Profiling (BiMP) by genome tiling array

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Deubiquitinases that digest Met1 chains in Rice

Project description:Met1 type ubiquitination and deubiquitination are involved in the regulation of many fundamental processes such as inflammation and innate immunity, and their interference by pathogens can suppress immune responses in human cells. However, few plant-derived deubiquitinases (DUBs) against Met1 ubiquitin chains has been reported, and the selection mechanism for linkage-type of ubiquitin chains remains elusive, which greatly limits our understanding of the functions of plant-derived DUBs. Using a dehydroalanine (DHA)-bearing Met1 diubiquitin (Met1-diUb) suicide probe, synthesized in one-pot, we captured OTUB1 from Oryza sativa (OsOTUB1) and uncovered its ability to hydrolyze Met1 ubiquitin chains (Met1 activity). Further, by resolving the apo structure of OsOTUB1 and its complex with Met1-diUb, we found that Met1-specific motifs (N-handle motif and C-handle motif) in the S1’ pocket of OsOTUB1 confers its Met1 activity. Through large-scale sequence alignment and hydrolysis experiments, Met1-specific motifs in the S1' pocket of the OTUB subfamily (OTUBs) were found to determine the Met1 ability of OTUBs, regardless of species. Furthermore, by analyzing the species distribution of OTUBs capable of hydrolyzing Met1 ubiquitin chains, we found that whereas this activity does not exist in metazoans, it is conserved in green plants (Viridiplantae). This discovery may inform studies of the differentiation between primitive plants and animals.

2022-10-15 | PXD032822 | Pride

Characterizing Epigenetic Changes in Methylation Mutants (elp2-5 and met1-7) in Response to Spaceflight.

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

2021-08-13 | GSE118503 | GEO

Genomics Analysis of met1-derived epiRILs [BiSulfite-seq]

Project description:Epigenetic recombinant inbred lines (epiRILs) are a set of Arabidopsis line obtained by crossing the Arabidopsis mutant in the main DNA METHYLTRANSFERASE 1 (MET1) with the wild-type Col-0 background. A wild-type selection of F2 plants have been then propagated by single-seed descent. In this dataset, we provide a complete genomic analysis of these lines, including the DNA methylation profile at single cytosine resolution (WGBS) for 68 epiRILs, and expression profile (RNAseq) for 37 lines. A genomic DNA resequencing for the same epiRILs is provided in GSE120571 (Catoni et al. 2018).

2026-02-25 | GSE255302 | GEO

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