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Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay

ABSTRACT: Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay

PROVIDER: PRJNA414048 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6163601_1.fastq.gz	Fastqsanger.gz
	SRR6163601_2.fastq.gz	Fastqsanger.gz
	SRR6163602_1.fastq.gz	Fastqsanger.gz
	SRR6163602_2.fastq.gz	Fastqsanger.gz
	SRR6163603_1.fastq.gz	Fastqsanger.gz

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Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay

Project description:APUM9 is a conserved PUF RNA-binding protein (RBP) and the expression of this protein is under complex epigenetic regulation. A transposable element (TE)-mediates this epigenetic regulation and thereby restricts its expression in Arabidopsis. Currently, little is known about the molecular function of the APUM protein family and the biological relevance of the TE-mediated epigenetic control of APUM9 in plant development and stress responses. By combining a range of transient assays, we show here that APUM9 binding to target transcripts can trigger their rapid decay via its conserved C-terminal RNA-binding domain. APUM9 directly interacts with DCP2, the catalytic subunits of the decapping complex suggesting that APUM9-mediated mRNA decay predominantly occurs via the decapping-dependent exonucleolytic pathway. APUM9 negatively regulates the expression of ABA signaling genes during seed imbibition, and thereby might contribute to the switch from dormant stage to seed germination. By contrast, strong TE-mediated repression of APUM9 is important for normal plant growth in the later developmental stages. Finally, APUM9 overexpression plants show slightly enhanced heat tolerance suggesting that TE-mediated epigenetic control of plant APUM9, might have a role not only in embryonic development, but also in plant adaptation to heat stress conditions.

2019-10-11 | GSE104860 | GEO

Chlamydomonas pumilio var pumilio COI

Project description:Chlamydomonas pumilio var pumilio Cytochromome oxydase 1 (COI)

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affy_sunflower_2010_13-ROS and hormones in sunflower seed dormancy.

Project description:affy_sunflower_2010_13 - affy_sunflower_2010_13 - It concerns the interaction between ROS and hormones in dormancy release in sunflower seeds. ABA is responsible for dormancy maintenance, while GA and ethylene promote seed germination. Based on our results, ROS could represent good candidate to shift from a hormone signalling to another determining the dormancy state in sunflower seeds.-We aim to understand the mechanisms controlling sunflower seed dormancy at the transcriptomic level, by the application of treatments which maintain dormancy as ABA, or alleviate dormancy as ROS and ethylene. Transcripts comparison will be performed between dormant and non-dormant sunflower embryo imbibed 24h on water, on ABA, on methylviologen, a pro-oxidant compound or on ethylene.

2013-08-01 | GSE44165 | GEO

affy_sunflower_2010_13-ROS and hormones in sunflower seed dormancy.

2013-08-01 | E-GEOD-44165 | biostudies-arrayexpress

Oophaga pumilio

Project description:Oophaga pumilio overview

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Rhabdomys pumilio

Project description:Rhabdomys pumilio overview

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Rhabdomys pumilio

Project description:Rhabdomys pumilio Genome sequencing

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Gene expression profiles in NORAD knockout and PUMILIO overexpressing cells

Project description:Purpose: PUMILIO proteins are known to repress target genes by specifically binding to PUMILIO response elements (PREs) in target mRNAs. NORAD is a noncoding RNA that negatively regulates PUMILIO activity. The goal of this study was to determine the gene expression changes that result from knockout of NORAD or overexpression of PUMILIO and to test whether NORAD knockout causes PUMILIO hyperactivity. Methods: RNA-seq libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat Sample Preparation kit (Illumina) and sequenced using the 100 bp paired-end protocol on an Illumina HiSeq 2000. For comparing NORAD+/+ and NORAD-/- HCT116 cells, 3 biological replicates per genotype were sequenced. For PUM overexpression experiments, 3 replicates of GFP-expressing HCT116 cells (negative control) and 2 independent PUM1- or PUM2-overexpressing clones (2 replicates each) were sequenced. Results: Gene expression profiles show that PUMILIO target genes are downregulated in both NORAD knockout cells and PUMILIO overexpressing cells. Conclusions: These data indicate that NORAD sequesters PUMILIO, preventing excessive repression of PUMILIO target genes that are important for maintaining genomic stability.

2015-12-03 | GSE75440 | GEO

Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome

Project description:Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that are essential for vertebrate development and neurological functions. PUM1&2 function to negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism and impact of human PUM1&2 on the transcriptome. We identified subunits of the CCR4-NOT (CNOT) deadenylase complex required for stable interaction with PUM1&2 and to elicit CNOT-dependent repression. Isoform-level RNA sequencing revealed broad co-regulation of target mRNAs through the PUM-CNOT repression mechanism. Functional dissection of the domains of PUM1&2 identified a conserved N-terminal region that confers the predominant repressive activity via direct interaction with CNOT. In addition, we show that the DCP2 mRNA decapping enzyme has an important role in repression by PUM1&2 N-terminal regions. Our results support a molecular model of repression by human PUM1&2 via direct recruitment of CNOT deadenylation machinery in a decapping-dependent pathway.

2021-09-09 | GSE159510 | GEO

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