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Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis

ABSTRACT: Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis

PROVIDER: PRJNA323733 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3606100.fastq.gz	Fastqsanger.gz
	SRR3606110.fastq.gz	Fastqsanger.gz
	SRR3606160.fastq.gz	Fastqsanger.gz
	SRR3606101.fastq.gz	Fastqsanger.gz
	SRR3606111.fastq.gz	Fastqsanger.gz

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Endoplasmic reticulum as a hub organizing microRNAs and a subset of endogenous siRNAs in Arabidopsis [Ribo-Seq and RNA-Seq]

Project description:Endoplasmic reticulum (ER) was implicated as the site of microRNA (miRNA)-mediated translational repression in plants. Here, we examined the ER- and rough ER- associated small RNAome, transcriptome and translatome. We found that nearly all cellular transcripts were present on membrane-bound polysomes (MBPs), and miRNAs and a small set of endogenous siRNAs were particularly enriched on MBPs. The MBP- enriched miRNAs and siRNAs associated with, and were recruited to membranes by, their effector protein ARGONAUTE1 (AGO1). AGO1 associated with ER in a partly RNA-independent manner. Reduced membrane association of 22-nt miRNAs, which trigger the biogenesis of phased, secondary siRNAs (phasiRNAs) from their target transcripts, was accompanied by decreased production or loss of phasing of phasiRNAs. The phasiRNA precursor transcripts, previously thought to be noncoding, were associated with MBPs in a manner that supported phasiRNA production. These findings point to the ER as a hub that hosts and organizes endogenous small RNAs in plants.

2016-12-27 | GSE92922 | GEO

Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis [RNA-Seq]

Project description:The endoplasmic reticulum (ER) was implicated as the site of microRNA (miRNA)-mediated translation repression in plants. Here, we examined the ER- and rough ER-associated small RNAome, transcriptome and translatome. We found that almost all cellular transcripts were present on membrane-bound polysomes (MBPs), and miRNAs were enriched in membranes and on MBPs. miRNAs were recruited to membranes by their effector protein AGO1, whereas AGO1 associated with membranes and, partly ribosomes, in an RNA-independent manner. Most strikingly, 22 ntmiRNA isoformsand a set of 22 ntsiRNAs, were enriched in the membrane fraction and onMBPs, where they trigger phasedsecondary siRNAproduction from target transcripts. Loss of membrane association of the 22 nt small RNAs resulted in the loss of phasing in secondary siRNA production.These findings point to the ER as a hub that hosts and organizes endogenous small RNAs in plants.

2016-12-23 | GSE82040 | GEO

Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis [ncRNA-Seq]

2016-12-23 | GSE82039 | GEO

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

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

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

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Endoplasmic reticulum as a hub organizing the activities of microRNAs and a subset of endogenous siRNAs in Arabidopsis

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

2016-12-23 | GSE82041 | GEO

EMD37 triggers endoplasmic reticulum stress in cancer cells

Project description:EMD37 triggers endoplasmic reticulum stress in cancer cells

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Tmem45b Modulates itch via Endoplasmic Reticulum Calcium Regulation

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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

Mutant p53 promotes tumor progression by the endoplasmic reticulum UDPase ENTPD5

Project description:Mutations in the p53 tumor suppressor gene are the most frequent genetic alteration in cancer and often associated with progression from benign to invasive, metastatic stages. Mutations inactivate tumor suppression by p53 and endow the protein with novel gain-of-function (GOF) activities that actively promote tumor progression, metastasis and therapy resistance. By comparative gene expression profiling of p53-mutated and p53-depleted cancer cells we identified ectonucleoside triphosphate diphosphohydrolase 5 (ENTPD5) as a mutant p53 (mutp53) target gene. A comprehensive pan-cancer analysis revealed a highly significant correlation between GOF p53 mutations and elevated expression of ENTPD5. Mechanistically, regulation of ENTPD5 by mutp53 is mediated by the histone H3 lysine 4 (H3K4) methyltransferase COMPASS complex. ENTPD5 has been shown to function in the endoplasmic reticulum as a UDPase to promote the N-glycosylation and folding of membrane proteins such as growth factor receptors and integrins. We show ENTPD5 to be a mediator of mutp53 GOF activity in clonogenic growth, architectural tissue remodeling, migration, invasion, and lung colonization in an experimental metastasis mouse model. Our study reveals N-glycosylation in the endoplasmic reticulum as a novel mechanism underlying the progression of tumors with mutp53 that could provide new possibilities for treating cancers driven by GOF p53 mutations.

2016-11-29 | E-MTAB-4672 | biostudies-arrayexpress

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