Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RIP-seq of the Arabidopsis mRNA export mutant aly1 and associated controls.

ABSTRACT: RNA-directed DNA methylation (RdDM) is a set of mechanisms by which transcriptionally-repressive DNA methylation and histone modifications are targeted de novo to transposable element and transgene regions of the genome. We identified a mutant in which all forms of RdDM are deficient, leading to the transcriptional activation of some transposable elements and the complete inability to initiate transgene silencing. The mutated gene, ALY1, encodes an RNA-binding nuclear export protein belonging to a family of four ALY proteins in Arabidopsis. ALY proteins function together to export a large number of mRNAs from the nucleus for translation, but we found that ALY1 is unique in its ability to enable RdDM. We sequenced methylomes (via MethylC-seq) to identify the genome-wide loss of CHH methylation targeted by RdDM in aly1 mutants. We sequenced small RNAs and determined that ALY1 functions in RdDM downstream of small RNA production and export. We sequenced total, nuclear and cytoplasmic mRNAs to determine that ALY1 functions in the nuclear export directly or indirectly on 2,612 mRNAs. Additionally, we sequenced RNAs bound to the ALY1 protein using RNA-immunoprecipitation followed by high throughput sequencing.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE123648 | GEO | 2019/05/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome of the Arabidopsis mRNA export mutant aly1 and associated controls

Project description:RNA-directed DNA methylation (RdDM) is a set of mechanisms by which transcriptionally-repressive DNA methylation and histone modifications are targeted de novo to transposable element and transgene regions of the genome. We identified a mutant in which all forms of RdDM are deficient, leading to the transcriptional activation of some transposable elements and the complete inability to initiate transgene silencing. The mutated gene, ALY1, encodes an RNA-binding nuclear export protein belonging to a family of four ALY proteins in Arabidopsis. ALY proteins function together to export a large number of mRNAs from the nucleus for translation, but we found that ALY1 is unique in its ability to enable RdDM. We sequenced methylomes (via MethylC-seq) to identify the genome-wide loss of CHH methylation targeted by RdDM in aly1 mutants. We sequenced small RNAs and determined that ALY1 functions in RdDM downstream of small RNA production and export. We sequenced total, nuclear and cytoplasmic mRNAs to determine that ALY1 functions in the nuclear export directly or indirectly on 2,612 mRNAs. Additionally, we sequenced RNAs bound to the ALY1 protein using RNA-immunoprecipitation followed by high throughput sequencing.

2019-05-15 | GSE118708 | GEO

Methylome of the Arabidopsis mRNA export mutant aly1 and associated controls

2019-05-15 | GSE118695 | GEO

Small RNA-seq of the Arabidopsis mRNA export mutant aly1 and associated controls

2019-05-15 | GSE118705 | GEO

Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation

Project description:The Microrchidia (MORC) family of ATPases are required for transposable element (TE) silencing and heterochromatin condensation in plants and animals, and C. elegans MORC-1 has been shown to topologically entrap and condense DNA. In Arabidopsis thaliana, mutation of MORCs has been shown to reactivate silent methylated genes and transposons and to decondense heterochromatic chromocenters, despite only minor changes in the maintenance of DNA methylation. Here we provide the first evidence localizing Arabidopsis MORC proteins to specific regions of chromatin and find that MORC4 and MORC7 are closely co-localized with sites of RNA directed DNA methylation (RdDM). We further show that MORC7, when tethered to DNA by an artificial zinc finger, can facilitate the establishment of RdDM. Finally, we show that MORCs are required for the efficient RdDM mediated establishment of DNA methylation and silencing of a newly integrated FWA transgene, even though morc mutations have no effect on the maintenance of preexisting methylation at the endogenous FWA gene. We propose that MORCs function as a molecular tether in RdDM complexes to reinforce RdDM activity for methylation establishment. These findings have implications for MORC protein function in a variety of other eukaryotic organisms.

2021-07-02 | PXD026674 | Pride

Human inositol polyphosphate multikinase regulates transcript-selective nuclear mRNA export to preserve genome integrity

Project description:Messenger (m)RNA export from the nucleus is essential for eukaryotic gene expression. Here, we identify a transcript-selective nuclear export mechanism affecting certain human transcripts, enriched for functions in genome duplication and repair, controlled by inositol polyphosphate multikinase (IPMK), an enzyme catalyzing inositol polyphosphate and phosphoinositide turnover. We studied transcripts encoding RAD51, a protein essential for DNA repair by homologous recombination (HR), to characterize the mechanism underlying IPMK-regulated mRNA export. IPMK depletion or catalytic inactivation selectively decreases the nuclear export of RAD51 mRNA, and RAD51 protein abundance, thereby impairing HR. Recognition of a sequence motif in the untranslated region of RAD51 transcripts by the mRNA export factor ALY requires IPMK. Phosphatidylinositol (3,4,5)-trisphosphate (PIP3), an IPMK product, restores ALY recognition in IPMK-depleted cell extracts, suggesting a mechanism underlying transcript selection. Our findings implicate IPMK in a transcript-selective mRNA export pathway controlled by phosphoinositide turnover that preserves genome integrity in humans. We used gene expression profiling to compare the abundance of cytoplasmic RNAs after IPMK depletion

2013-09-27 | E-GEOD-49658 | biostudies-arrayexpress

Exogenous Transposable Elements Circumvent Homology Permitting the Dissection of Expression Dependent Silencing

Project description:The propagation of epigenetic marks has received a great deal of attention, yet the initiation of epigenetic silencing on a new transgene, virus, or transposable element remains incompletely characterized. The overlapping function of multiple silencing mechanisms has obscured this area of investigation. Here, we have revealed two broad mechanisms that are both able to initiate silencing independently: homology-based silencing and expression-dependent silencing. By transforming exogenous transposable elements into Arabidopsis, we circumvented homology-based silencing allowing us to isolate and investigate the molecular mechanism of expression-dependent silencing. We found that several small RNA-generating mechanisms all trigger de novo expression-dependent RNA-directed DNA methylation (RdDM) through RNA Polymerase V. In addition, the silencing of transposable elements fragments stalls at the RdDM phase, while full-length elements quickly progress through RdDM to maintenance methylation and heterochromatin formation. We found that there is a narrow window of time for the transition to a fully silenced state. Transformation into a mutant genotype followed by introgression into wild-type does not result in the same level of silencing as direct transformation into wild-type. This demonstrates that the genotype of transposable element insertion or transgene transformation is key for establishing the transgenerational extent of epigenetic silencing.

2017-08-25 | GSE86787 | GEO

Human inositol polyphosphate multikinase regulates transcript-selective nuclear mRNA export to preserve genome integrity

2013-09-27 | GSE49658 | GEO

DNA Topoisomerase 1a Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis [RNA-Seq]

Project description:RNA-directed DNA methylation (RdDM) is a transcriptional silencing mechanism mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1a (TOP1a) was able to de-repress LUCL by reducing its DNA methylation and H3K9 dimethylation (H3K9me2) levels. Further studies with Arabidopsis top1a mutants showed that TOP1a promotes RdDM by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at transposable elements (TEs). 5 small RNA libraries were sequenced

2014-07-08 | E-GEOD-50719 | biostudies-arrayexpress

Comparing the targets of distinct RNA Directed DNA Methylation mechanisms in Arabidopsis thaliana

Project description:The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wt Col ecotype of Arabidopsis thaliana. In plants mutant for the SWI/SNF2 histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Activated TEs go through additional non-canonical forms of RdDM. However, the global targets of the non-canonical RdDM pathway are unidentified. In an attempt to identify and contrast the targets of canonical and non-canonical RdDM, we sequenced small RNAs from several RdDM mutants in either the TE-silent or the TE-active (ddm1) contexts.

2016-07-22 | GSE79780 | GEO

DNA Topoisomerase 1M-NM-1 Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis [Bisulfite-Seq]

Project description:RNA-directed DNA methylation (RdDM) is a transcriptional silencing mechanism mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1M-NM-1 (TOP1M-NM-1) was able to de-repress LUCL by reducing its DNA methylation and H3K9 dimethylation (H3K9me2) levels. Further studies with Arabidopsis top1M-NM-1 mutants showed that TOP1M-NM-1 promotes RdDM by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at transposable elements (TEs). ten bisufite libraries were sequenced

2014-07-07 | E-GEOD-50691 | biostudies-arrayexpress

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