Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

WGBS of Arabidopsis thaliana tho2-8 mutant

ABSTRACT: The mechanistic connection between the THO/TREX complex and RdDM remains poorly understood. To address this, we performed EMS mutagenesis in a transgenic Col-0 background harboring pro2×35S::LUC and pro2×35S::NPTII reporters and homozygous for rdr6, and identified a low-fluorescence mutant, tho2-8. Unlike null alleles, tho2-8 is a viable homozygous allele, offering a unique opportunity to explore THO2 function in DNA methylation. Here, we report that THO2 is required for proper siRNA accumulation and RdDM activity, revealing a previously uncharacterized role for the THO/TREX complex in epigenetic gene silencing. This study expands our understanding of the molecular coordination between RNA metabolism and epigenetic regulation in plants.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE304222 | GEO | 2025/09/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

sRNA-Seq of Arabidopsis thaliana tho2-8 mutant

Project description:The mechanistic connection between the THO/TREX complex and RdDM remains poorly understood. To address this, we performed EMS mutagenesis in a transgenic Col-0 background harboring pro2×35S::LUC and pro2×35S::NPTII reporters and homozygous for rdr6, and identified a low-fluorescence mutant, tho2-8. Unlike null alleles, tho2-8 is a viable homozygous allele, offering a unique opportunity to explore THO2 function in DNA methylation. Here, we report that THO2 is required for proper siRNA accumulation and RdDM activity, revealing a previously uncharacterized role for the THO/TREX complex in epigenetic gene silencing. This study expands our understanding of the molecular coordination between RNA metabolism and epigenetic regulation in plants.

2025-09-07 | GSE304227 | GEO

mRNA-Seq of Arabidopsis thaliana tho2-8 mutant

2025-09-07 | GSE304225 | GEO

Tho2-mediated escort of Nrd1 regulates gene expression for lifespan maintenance

Project description:The relationship between aging and RNA biogenesis and trafficking is attracting growing interest, yet the precise mechanisms are unknown. The THO complex is crucial for mRNA cotranscriptional maturation and export. Herein, we report that the THO complex is closely linked to maintaining a normal lifespan. Deficiencies in Hpr1 and Tho2, components of the THO complex, reduced replicative lifespan (RLS) and are linked to a novel Sir2-independent RLS control pathway. Although transcript sequestration in hpr1Δ or tho2Δ mutants was countered by exosome component Rrp6, loss of this failed to mitigate RLS defects in hpr1Δ. However, RLS impairment in tho2Δ was counteracted by Nrd1-specific mutants that interacted with Rrp6. This effect relied on the interaction of Nrd1, a transcriptional regulator of aging-related genes, including ribosome biogenesis or RNA metabolism genes, with RNA polymerase II. Nrd1 overexpression reduced RLS in a Tho2-dependent pathway. Intriguingly, THO2 deletion mirrored Nrd1 overexpression effects by inducing arbitrary Nrd1 chromatin binding. Taken together, these findings underscore the importance of Tho2-mediated Nrd1 escorting in maintaining a normal lifespan by transcriptional regulation of aging-related genes.

2024-08-21 | GSE261087 | GEO

Tho2-mediated escort of Nrd1 regulates gene expression for lifespan maintenance

2024-08-21 | GSE262156 | GEO

Tho2 participates in yeast nuclear mRNP quality control by recruiting the 3'-5' exoribonuclease Rrp6

Project description:In order to dissect the nuclear RNA quality control (QC) mechanisms, we used a powerful assay based on global perturbation of mRNP biogenesis in yeast Saccharomyces cerevisiae by the bacterial Rho helicase. We have monitored the recruitment of THO complex subunit upon Rho activation, which revealed that Tho2 was over-recruited in opposition to its counterparts. We then tracked the recruitment of Rrp6 upon Rho induction in WT strain and in strains lacking either Mft1 or Tho2, showing the implication of Tho2 in Rrp6 recruitment over Rho induction. Finally, we measured the recruitment of Rrp6 upon partial deletion of Tho2 C-terminal domain responsible for its RNA interaction ability, proving that Tho2 presence on the chromatin is required for the Rho-induced Rrp6 recruitment..

2023-04-30 | E-MTAB-12378 | biostudies-arrayexpress

Accumulation of the coumarin scopolin under abiotic stress conditions is mediated by the Arabidopsis thaliana THO/TREX complex

Project description:Secondary metabolites are involved in the plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that in Arabidopsis thaliana, scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low temperature stress. A genetic screen for altered scopolin levels in Arabidopsis thaliana identified a mutant compromised for scopolin accumulation in response to stress; the lesion was present in a homologue of THO1, the product of which contributes to the THO/TREX complex. The THO/TREX complex contributes to RNA silencing, supposedly by trafficking precursors of small RNAs. Mutants carrying defective THO and RDR6 genes were impaired with respect to scopolin accumulation in response to stress, suggesting a mechanism based on RNA silencing like the transacting small interfering RNA pathway which requires THO/TREX and RDR6 function.

2018-02-05 | MTBLS389 | MetaboLights

Expression data from Saccharomyces cerevisiae strains deleted for different subunits of the THO/TREX complex

Project description:THO/TREX is a conserved nuclear complex that functions in mRNP biogenesis at the interface of transcription-RNA export with a key role in preventing transcription-associated genome instability. We used microarrays to analyze the impact of different THO/TREX mutations on gene expression and found that THO-Sub2 deletions have a high functional impact on highly expressed, long and G+C-rich genes regardless of gene function.

2011-06-29 | GSE24802 | GEO

Expression data from Saccharomyces cerevisiae strains deleted for different subunits of the THO/TREX complex

2011-06-28 | E-GEOD-24802 | biostudies-arrayexpress

Expression profile of TAP tagged Tho2 strain

Project description:Tho2 protein was tagged with a TAP tag and the gene expression profile was compared to an untagged wildtype strain of the same background using DNA microarrays

2013-09-24 | E-MTAB-1892 | biostudies-arrayexpress

Arabidopsis small RNAs associated with RDR6-dependent RNA-directed DNA Methylation

Project description:Background: The majority of plant transposable elements (TEs) are found in a silenced state that is epigenetically propagated by the maintenance of symmetrical DNA methylation. TE methylation is established and reinforced by a mechanism of RNA-dependent DNA methylation, which is dependent on transcription of the PolIV RNA polymerase. Recently, a pathway has been described that initiates de novo DNA methylation dependent on components of the RNAi post-transcriptional silencing pathway, independent of PolIV. To define the function of this new pathway, we have focused on the RDR6 protein, which plays a central role in the pathway we refer to as RDR6-dependent RNA-directed DNA Methylation (RDR6-RdDM). Methods: We have sequenced total small RNAs from wild-type and three mutant genotypes: ddm1, ddm1/rdr6, and rdr6. Conclusions: We demonstrate that RDR6-RdDM utilizes 21 and 22 nucleotide siRNAs to de novo methylate actively transcribing TEs. In addition, we find that the RDR6-RdDM pathway functions in the efficient initiation and re-establishment of TE transcriptional silencing, while it is not necessary to maintain trans-generational epigenetic silencing.

2013-04-11 | GSE41755 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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