Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression in Arabidopsis ddm1 mutants with high levels of Transposable Element activity

ABSTRACT: Background: Transposable elements are known to influence the regulation of some genes. We aimed to determine which genes show altered gene expression when transposable elements are epigenetically activated. Results: We find over 2000 genes with altered steady-state expression levels in ddm1 mutants. Some of these genes are influenced by neighboring transposable element fragments, while other genes are targeted by transposable element derived 21 nucleotide siRNAs. Conclusion: The regulation of the genic portion of the Arabidopsis genome is heavily influenced by the epigenetic regulation of transposable elements. The regulation of genes by transposable elements can occur through multiple mechanisms.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE46050 | GEO | 2014/04/07

SECONDARY ACCESSION(S): PRJNA197304

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression in Arabidopsis ddm1 mutants with high levels of Transposable Element activity

Project description:Background: Transposable elements are known to influence the regulation of some genes. We aimed to determine which genes show altered gene expression when transposable elements are epigenetically activated. Results: We find over 2000 genes with altered steady-state expression levels in ddm1 mutants. Some of these genes are influenced by neighboring transposable element fragments, while other genes are targeted by transposable element derived 21 nucleotide siRNAs. Conclusion: The regulation of the genic portion of the Arabidopsis genome is heavily influenced by the epigenetic regulation of transposable elements. The regulation of genes by transposable elements can occur through multiple mechanisms. Three biological replicates for two genotypes

2014-04-07 | E-GEOD-46050 | biostudies-arrayexpress

Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes

Project description:Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-silenced and Transposable Element-active epigenome backgrounds. Results: We found that Transposable Elements generate large amounts of 21-22nt siRNAs only when they are transcriptionally active. These 21-22nt siRNAs are incorporated into the AGO6 protein. Conclusion: Ago6 is the key protein that bridges the post-transcriptional degradation of Transposable Element mRNAs and the establishment of DNA methylation. Examination of flower bud small RNAs from wild type and 5 single or double mutant combinations, many of which have biological replicates. In addition, IP purification of the AGO6 protein (and mock no-antigen controls) followed by sequencing of the incorporated small RNAs. Replicate A for Col and ddm1 are submitted in GSE41755

2014-11-14 | E-GEOD-57191 | biostudies-arrayexpress

Incorporation of transposable element small RNAs into the Arabidopsis AGO1 protein

Project description:Background: Transposable element 24 nucleotide small RNAs are not efficiently incorporated into the AGO1 protein, which is involved in endogenous RNAi and gene regulation through the microRNA and tasiRNA pathways. Results: The AGO1 protein incorporates large quantities of transposable element siRNAs when transposable elements are epigenetically activated and transcribed. The incorporation of transposable element siRNAs is at the expense of the most abundant microRNAs. These transposable element siRNAs can act as tasiRNAs, regulating genes that they have partial complementarity to. Conclusion: Transposable element small RNAs are more dynamic than previously thought. They can be incorporated into AGO1 and regulate genes. Three biological replicates of small RNA sequencing from two genotypes

2014-04-07 | E-GEOD-45990 | biostudies-arrayexpress

Incorporation of transposable element small RNAs into the Arabidopsis AGO1 protein

2014-04-07 | GSE45990 | GEO

Small RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes

2014-11-14 | GSE57191 | GEO

DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis

Project description:Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from the most heterochromatic transposons to euchromatic genes determines the requirement of DDM1 for methylation maintenance in all sequence contexts. We also show that small RNA-directed DNA methylation (RdDM) is inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. DDM1 and RdDM independently mediate nearly all transposon methylation, which is catalyzed by the methyltransferases MET1 (CG), CMT3 (CHG), DRM2 (CHH) and CMT2 (CHH), and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that the Arabidopsis genome is defined by a heterochromatic continuum that governs the access of DNA methyltransferases and potentially all DNA binding proteins. Examination of DNA methylation, transcription and nucleosomes in Arabidopsis wild-type and/or ddm1, RdDM and DNA methylase mutants.

2013-04-17 | E-GEOD-41302 | biostudies-arrayexpress

Detection of Active Transposable Elements using Mobilome-seq on Poplar WT and ddm1 meristems in water stress conditions

Project description:Long time considered as « junk DNA », the evolutive force of transposable elements (TEs) is now well established and TEs contribute strongly to eukaryote genome plasticity. However, it is difficult to fully characterize the mobile part of a genome, or active mobilome, and tracking TE activity remains challenging. He we have applied the detection of extrachromosomal circular DNA (mobilome-seq) as a diagnostic for plant TE activity on Poplar mersitems from WT and ddm1 RNAi plants grown in normal or hydric stress conditions.

2023-03-22 | GSE147934 | GEO

Pathogenic tau-induced piRNA depletion promotes neuronal death through transposable element dysregulation in neurodegenerative tauopathies

Project description:Transposable elements, known colloquially as “jumping genes,” constitute approximately 45% of the human genome. Cells utilize epigenetic defenses to limit transposable element jumping, including formation of silencing heterochromatin and generation of piwi-interacting RNAs (piRNAs), small RNAs that facilitate clearance of transposable element transcripts. Here we identify transposable element activation as a key mediator of neuronal death in tauopathies, a group of neurodegenerative disorders, including Alzheimer’s disease, that are pathologically characterized by deposits of tau protein in the brain. Mechanistically, we find that heterochromatin decondensation and reduction of piwi/piRNAs drive transposable element activation in tauopathy. Using genetic and pharmacological approaches in a Drosophila melanogaster model of tauopathy, we provide evidence for a causal relationship between pathogenic tau-induced heterochromatin decondensation, piwi/piRNA depletion, active transposable element obilization, and neurodegeneration. We further report a significant increase in transcripts of the endogenous retrovirus class of transposable elements in human Alzheimer’s disease and progressive supranuclear palsy, suggesting that transposable element dysregulation is conserved in human tauopathy. Taken together, our data identify heterochromatin decondensation, piwi/piRNA depletion and consequent transposable element activation as a novel, pharmacologically targetable, mechanistic driver of neurodegeneration in tauopathy.

2018-07-04 | GSE115606 | GEO

DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis

2013-04-17 | GSE41302 | GEO

DDM1 represses noncoding RNA expression and RNA-directed DNA methylation in heterochromatin

Project description:In this work, we studied function of rice DDM1 in coordinating DNA methylation, expression of small (sRNA) and long noncoding (lncRNA) RNAs, and nucleosome positioning by high throughput approaches.We show that the ddm1a/1b mutation resulted in ectopic CHH methylation of transposable elements (TE) and repeats. The ectopicCHH methylationwas dependent on DRM2, a DNA methyltransferase involved in sRNA-dependent DNA-methylation (RdDM). The ddm1a/1b mutation resulted in increases of heterochromatic sRNA but decreases of euchromatic sRNA production,induced expression of a set of developmentally regulated heterochromatic lncRNA , and increased nucleosome occupancy of TE-related or silent genes including heterochromatic lncRNA loci. In particular,DDM1-mediated repression ofCentromericRetrotransposons of Rice1 (CRR1) was essential for centromere function.

2018-06-06 | GSE108527 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data