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The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production [small RNA-seq]

ABSTRACT: The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production [small RNA-seq]

PROVIDER: PRJNA624172 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11521540.fastq.gz	Fastqsanger.gz
	SRR11521541.fastq.gz	Fastqsanger.gz
	SRR11521542.fastq.gz	Fastqsanger.gz
	SRR11521543.fastq.gz	Fastqsanger.gz
	SRR11521544.fastq.gz	Fastqsanger.gz

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Similar Datasets

The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production [Bisulfite-seq]

Project description:Small interfering RNAs (siRNAs) are required for establishment and maintenance of DNA methylation through RNA-directed DNA methylation (RdDM) pathway in plants. While the siRNA biogenesis is well known, relatively little is known about how the process is regulated. By a forward genetic screen in Arabidopsis thaliana, we identified a mutant defective in NOT1 and demonstrated that NOT1 is required for transcriptional silencing at RdDM target genomic loci. Furthermore, we revealed that NOT1 is required for Pol IV-dependent siRNA accumulation and DNA methylation at a subset of RdDM target loci. By immunoprecipitation combined with mass spectrometry, we showed that NOT1 is a constituent of a multi-subunit CCR4-NOT deadenylase complex. We demonstrated that the CCR4-NOT components can function as a whole to mediate chromatin silencing. Our work thus establishes that the CCR4-NOT complex regulates the production of Pol IV-dependent siRNAs and thereby facilitates DNA methylation and transcriptional silencing in Arabidopsis.

2020-05-15 | GSE148428 | GEO

The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production [small RNA-seq]

2020-05-15 | GSE148429 | GEO

The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production

Project description:The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production

| PRJNA624170 | ENA

The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production [Bisulfite-seq]

Project description:The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production [Bisulfite-seq]

| PRJNA624173 | ENA

Transcription profiling of S. cerevisiae wild type reference strain, two simple mutants (not1-2 and spt3) and one double mutant (not1-2 spt3) reveals a SAGA-Independent function of SPT3 mediates transcriptional deregulation in a mutant of the Ccr4-Not Complex

Project description:The conserved multi-subunit Ccr4-Not complex regulates gene expression in diverse ways. In this work, we characterize the suppression of temperature sensitivity associated with a mutation in the gene encoding the scaffold subunit of the Ccr4-Not complex, NOT1, by the deletion of SPT3. We determine that the deletion of SPT3, but not the deletion of genes encoding other subunits of the SAGA complex, globally suppresses transcriptional defects of not1-2. We find that transcriptional activation in not1-2 is associated with increased binding of TFIID and SAGA at promoters of upregulated genes, and this is suppressed by the deletion of SPT3. Interestingly, Spt3p-dependent activation of transcription occurs in not1-2 even if the SAGA complex is disrupted by the deletion of SPT7 that encodes a subunit of SAGA required for its integrity. Consistent with a SAGA-independent function of Spt3p, the deletion of SPT3 displays synthetic phenotypes when combined with a deletion of SPT7. Taken together, our results provide a new view of the Spt3 protein by identifying a SAGA-independent function of this protein that is functionally linked to the Ccr4-Not complex. Experiment Overall Design: 4 strains were analyzed: the wild type reference strain, two simple mutants (not1-2 and spt3) and one double mutant (not1-2 spt3). All strains were in duplicate.

2008-06-16 | E-GEOD-9432 | biostudies-arrayexpress

RNAi knock-down of CAF1-CCR4-NOT1 deadenylase complex or AGO1 in D. melanogaster S2 cells

Project description:miRNAs silence gene expression by repressing translation and/or by promoting mRNA decay. AGO1 is a key protein required for miRNA-mediated gene silencing. In animal cells, mRNA degradation of partially complementary miRNA targets occurs via deadenylation by the CAF1-CCR4-NOT1 deadenylase complex, followed by decapping and subsequent exonucleolytic digestion. To determine how generally miRNAs trigger deadenylation, we compared mRNA expression profiles in D. melanogaster cells depleted of AGO1, CAF1 or NOT1. We show that approximately 45% of AGO1-targets are regulated by both CAF1 and NOT1, indicating deadenylation is a widespread effect of miRNA regulation.<br><br>We employed RNA interference using long double-stranded RNAs to deplete cultured S2 cells of AGO1 (CG6671, 2 independent samples), CAF1 (CG5684, 2 independent samples), or NOT1 (CG1884, 3 independent samples). Further, we used Affymetrix oligonucleotide microarrays to analyze expression profiles in these samples. We included the following controls: mock RNAi treatment and GFP dsRNA treatment (3 and 2 independent samples, respectively).<br>

2008-12-03 | E-MEXP-1713 | biostudies-arrayexpress

The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production

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

2020-05-15 | GSE148430 | GEO

Transcriptome analysis of Arabidopsis mature pollen grains from wild type and heterozygous NOT1 mutants

Project description:In flowering plants, pollen development is under a dynamic and well-orchestrated transcriptional control, characterized by an early phase with high transcript diversity and a late post-mitotic phase skewed to a cell-type specific-transcriptome. Such transcriptional changes require a balance between synthesis and degradation of mRNA transcripts, the latter being initiated by deadenylation. The CCR4-NOT complex is the main evolutionary conserved deadenylase complex in eukaryotes, and its function is essential during germline specification in animals. We hypothesised that the CCR4-NOT complex might play a central role in mRNA turnover during microgametogenesis in Arabidopsis. Disruption of NOT1 gene, which encodes the scaffold protein of the CCR4-NOT complex, showed abnormal seed set. Genetic analysis failed to recover homozygous progeny and reciprocal crosses confirmed reduced transmission through the male and female gametophytes. Concordantly not1 embryo sacs showed delayed development and defects in embryogenesis. not1 pollen grains exhibited abnormal male germ unit configurations and failed to germinate. Transcriptome analysis of pollen from not1/+ mutants revealed that lack of NOT1 leads to an extensive transcriptional deregulation during microgametogenesis. Therefore, our work establishes NOT1 as an important player during gametophyte development in Arabidopsis.

2020-04-24 | GSE133490 | GEO

A SAGA-Independent Function of SPT3 Mediates Transcriptional Deregulation in a Mutant of the Ccr4-Not Complex

2007-10-26 | GSE9432 | GEO

Identification of acetylation-regulated interactors of the human CCR4-NOT complex

Project description:The evolutionarily conserved CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon histone deacetylase (HDAC) inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified ring finger protein 219 (RNF219) as an acetylation-regulated cofactor. We provide evidence that RNF219 is an active RING-type E3 ubiquitin ligase which stably associates with the CCR4-NOT complex via the NOT9 module through a short linear motif located in the C-terminal low-complexity region of RNF219. Using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 acts as an inhibitor of deadenylation. Accordingly, our transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, independently of its E3 ligase activity. Our results establish RNF219 as a negative regulator of CCR4-NOT-mediated mRNA deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.

2021-12-15 | PXD027237 | Pride

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