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

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

PROVIDER: PRJNA486575 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7694680_1.fastq.gz	Fastqsanger.gz
	SRR7694680_2.fastq.gz	Fastqsanger.gz
	SRR7694690_1.fastq.gz	Fastqsanger.gz
	SRR7694690_2.fastq.gz	Fastqsanger.gz
	SRR7694700_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. [Bisulfite-Seq]

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

| PRJNA485775 | 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.

2011-05-16 | GSE23950 | GEO

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

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. Fifteen-day-old Arabidopsis plants grown on the agar plates were harvested. The total RNA was prepared from 15-day-old Arabidopsis plants (axe1-5 (hda6 mutant), DR5 (parental line of axe1-5), met1-3 and Col) and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

2011-05-15 | E-GEOD-23950 | biostudies-arrayexpress

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.

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Drosophila melanogaster gene expression changes after spaceflight.

Project description:Gene expression levels were determined in 3rd instar and adult Drosophila melanogaster reared during spaceflight, to elucidate the genetic and molecular mechanisms underpinning the effects of microgravity on the immune system. The goal was to validate the Drosophila model for understanding alterations of innate immune responses in humans due to spaceflight. Five containers of flies, with ten female and five male fruit flies in each container, were housed and bred on the space shuttle (average orbit altitude of 330.35 km) for 12 days and 18.5 hours, with a new generation reared in microgravity. RNA was extracted on the day of shuttle landing from whole body animals (3rd instar larvae and adults), hybridized to Drosophila 2.0 Affymetrix genome arrays, and the expression level of all genes was normalized against the gene expression level from the corresponding developmental stage animals raised on ground. Spaceflight altered the expression of larval genes involved in the maturation of plasmatocytes (macrophages) and their phagocytic response, as well as the level of constitutive expression of pattern recognition receptors and opsonins that specifically recognize bacteria, and of lysozymes, antimicrobial peptide pathway and immune stress genes, hallmarks of humoral immunity. Larval microarrays (FL 6 samples) are based on RNA extracted from 6 independent sets of 50 mid 3rd instar larvae reared in microgravity and collected on the day of landing after 12 days and 18.5 hours on the space shuttle and the same number of control larvae raised on ground (GL 6 samples). Adults microarrays (F1 3 samples) are based on RNA from 3 sets of 20 adult females each, that emerged during spaceflight and within 4 hours of landing and the same number of adult females from the corresponding ground control containers (G1 3 samples).

2011-08-31 | E-GEOD-23880 | biostudies-arrayexpress

CDCA7 facilitates MET1 mediated CG methylation maintenance at pericentromeric and centromeric chromatin [RNA-seq]

Project description:DNA methylation is a conserved epigenetic modification critical for transposable element (TE) silencing and genome stability. However, how methyltransferases maintain CG methylation within compact heterochromatin remains unclear. In humans, CDCA7 is required for DNA methylation inheritance at juxta-centromeres, and mutations impairing its binding to heterochromatic nucleosomes lead to satellite DNA hypomethylation and ICF syndrome. In Arabidopsis thaliana, we identified two CDCA7 orthologs, CDCA7A and CDCA7B, as key regulators of DNA methylation. Loss of both causes CG hypomethylation specifically at pericentromeric and centromeric regions. Machine learning analysis revealed that nucleosome density, H1 enrichment, the H2A.W variant, and H3K9me2 levels predict methylation loss in cdca7a cdca7b mutants. Notably, H1 depletion restores methylation in these mutants, indicating that CDCA7A and CDCA7B enable MET1 access to H1-containing nucleosomes and are particularly required for methylation maintenance in compact chromatin. Additionally, in h1.1 h1.2 mutants, CG methylation increases modestly at pericentromeric regions but significantly at centromeric sites, revealing an inhibitory role for H1 in centromeric methylation. This hypermethylation is abolished in h1.1 h1.2 cdca7a cdca7b quadruple mutants, demonstrating that CDCA7A and CDCA7B promote MET1 activity at heterochromatic nucleosomes independently of H1. Together, these results establish CDCA7A and CDCA7B as conserved and versatile chromatin remodelers that facilitate MET1 activity within heterochromatin.

2025-11-27 | GSE308805 | GEO

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