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Identification of total and subcellular gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

ABSTRACT: Identification of total and subcellular gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

PROVIDER: PRJNA639357 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12010300_1.fastq.gz	Fastqsanger.gz
	SRR12010300_2.fastq.gz	Fastqsanger.gz
	SRR12010301_1.fastq.gz	Fastqsanger.gz
	SRR12010301_2.fastq.gz	Fastqsanger.gz
	SRR12010302_1.fastq.gz	Fastqsanger.gz

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Identification of subcellular gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

Project description:Identification of subcellular gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

| PRJNA639359 | ENA

Identification of subcellular gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

Project description:Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the Endoplasmic Reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Here, we show that NBAS fulfils an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 co-regulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER protective function by ensuring quality control of ER-translated mRNAs.

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Identification of total gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

2020-06-15 | GSE152435 | GEO

Identification of total gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

Project description:Identification of total gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

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Ribosome footprinting in the cytosol and endoplasmic reticulum

Project description:In eukaryotic cells, the spatial regulation of protein expression is frequently conferred through the coupling of mRNA localization and the local control of translation. mRNA localization to the endoplasmic reticulum (ER) is a prominent example of such regulation and serves a ubiquitous role in segregating the synthesis of secretory and integral membrane proteins to the ER. Recent genomic and biochemical studies have now expanded this view to suggest a role for the ER in global protein synthesis. We have utilized cell fractionation and ribosome profiling to obtain a genomic survey of the subcellular organization of mRNA translation and report that ribosomal loading of mRNAs, a proxy for mRNA translation, is biased to the ER. Notably, ER-associated mRNAs encoding both cytosolic and topogenic signal-encoding proteins display similar ribosome loading densities, suggesting that ER-associated ribosomes serve a global role in mRNA translation. We propose that the partitioning of mRNAs and their translation between the cytosol and ER compartments may represent a novel mechanism for the post-transcriptional regulation of gene expression. HEK293 cells were fractionated between the cytosol and endoplasmic reticulum. Within each fraction, ribosome footprints were generated and sequenced. In parallel, total mRNA was sequenced.

2011-12-20 | E-GEOD-31539 | biostudies-arrayexpress

Identification of total and subcellular gene expression changes due to a Nonsense-Mediated Decay pathway at the Endoplasmic Reticulum

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

2020-06-15 | GSE152437 | GEO

Tunicamycin-induced Endoplasmic Reticulum-Quality Control Pathway and Endoplasmic Reticulum-Associated Degradation Mechanism in the diatom Phaeodactylum tricornutum

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EMD37 triggers endoplasmic reticulum stress in cancer cells

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Phosphorylation-Regulated Cleavage of ETHYLENE INSENSITIVE2 Mediates Hormone Signaling from the Endoplasmic Reticulum to the Nucleus

Project description:Ethylene gas is essential for many developmental processes and stress responses in plants. ETHYLENE INSENSITIVE2 (EIN2), an NRAMP-homologous integral membrane protein, plays an essential role in ethylene signaling but its function remains enigmatic. Here we report that phosphorylation-regulated proteolytic processing of EIN2 triggers its endoplasmic reticulum (ER)-nucleus translocation, which is essential for hormone signaling and response in Arabidopsis. Without ethylene, or in hormone receptors mutants, ER-tethered EIN2 shows CTR1 kinase-dependent phosphorylation. Ethylene exposure triggers dephosphorylation and proteolytic cleavage, resulting in rapid nuclear translocation of a carboxyl-terminal EIN2 fragment (C’). Plants containing mutations that mimic EIN2 dephosphorylation, or inactivate CTR1, show constitutive cleavage and nuclear localization of EIN2-C’, and EIN3/EIL1-dependent activation of ethylene responses. These findings uncover a mechanism of subcellular communication whereby ethylene gas stimulates rapid phosphorylation-dependent cleavage and nuclear movement of the EIN2-C’ peptide, thus linking hormone perception and signaling components located in the ER with nuclear-localized transcriptional regulators.

2012-10-22 | E-MTAB-4360 | biostudies-arrayexpress

The SND proteins constitute an alternative targeting route to the endoplasmic reticulum

Project description:In eukaryotes, up to one-third of cellular proteins are targeted to the endoplasmic reticulum, where they undergo folding, processing, sorting and trafficking to subsequent endomembrane compartments. Targeting to the endoplasmic reticulum has been shown to occur co-translationally by the signal recognition particle (SRP) pathway or post-translationally by the mammalian transmembrane recognition complex of 40 kDa (TRC40) and homologous yeast guided entry of tail-anchored proteins (GET) pathways. Despite the range of proteins that can be catered for by these two pathways, many proteins are still known to be independent of both SRP and GET, so there seems to be a critical need for an additional dedicated pathway for endoplasmic reticulum relay. We set out to uncover additional targeting proteins using unbiased high-content screening approaches. To this end, we performed a systematic visual screen using the yeast Saccharomyces cerevisiae, and uncovered three uncharacterized proteins whose loss affected targeting. We suggest that these proteins work together and demonstrate that they function in parallel with SRP and GET to target a broad range of substrates to the endoplasmic reticulum. The three proteins, which we name Snd1, Snd2 and Snd3 (for SRP-independent targeting), can synthetically compensate for the loss of both the SRP and GET pathways, and act as a backup targeting system. This explains why it has previously been difficult to demonstrate complete loss of targeting for some substrates. Our discovery thus puts in place an essential piece of the endoplasmic reticulum targeting puzzle, highlighting how the targeting apparatus of the eukaryotic cell is robust, interlinked and flexible.

2016-11-30 | GSE85686 | GEO

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