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The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (smRNA-seq dataset)

ABSTRACT: The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (smRNA-seq dataset)

PROVIDER: PRJNA566009 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10134600.fastq.gz	Fastqsanger.gz
	SRR10134601.fastq.gz	Fastqsanger.gz
	SRR10134602.fastq.gz	Fastqsanger.gz
	SRR10134603.fastq.gz	Fastqsanger.gz
	SRR10134604.fastq.gz	Fastqsanger.gz

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The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (smRNA-seq dataset)

Project description:We employed small non-coding RNA sequecing to profile the small RNAs in extracellular vesicles (EVs) from WT cells and cells deficient for the LC3 conjugation machinery

2019-12-26 | GSE137617 | GEO

The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (lrgRNA-seq dataset)

Project description:We employed RNA sequecing to profile large RNAs (mRNAs and lincRNAs) packaged into extracellular vesicles (EVs) from WT cells and cells deficient for the LC3 conjugation machinery

2019-12-26 | GSE137616 | GEO

The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles

Project description:The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles

| PRJNA566007 | ENA

The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (lrgRNA-seq dataset)

Project description:The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (lrgRNA-seq dataset)

| PRJNA566010 | ENA

The LC3-conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles.

Project description:Traditionally viewed as an autodigestive pathway, autophagy also facilitates cellular secretion; however, the mechanisms underlying these processes remain unclear. Here, we demonstrate that components of the autophagy machinery specify secretion within extracellular vesicles (EVs). Using a proximity-dependent biotinylation proteomics strategy, we identify 200 putative targets of LC3-dependent secretion. This secretome consists of a highly interconnected network enriched in RNA-binding proteins (RBPs) and EV cargoes. Proteomic and RNA profiling of EVs identifies diverse RBPs and small non-coding RNAs requiring the LC3-conjugation machinery for packaging and secretion. Focusing on two RBPs, heterogeneous nuclear ribonucleoprotein K (HNRNPK) and scaffold-attachment factor B (SAFB), we demonstrate that these proteins interact with LC3 and are secreted within EVs enriched with lipidated LC3. Furthermore, their secretion requires the LC3-conjugation machinery, neutral sphingomyelinase 2 (nSMase2) and LC3-dependent recruitment of factor associated with nSMase2 activity (FAN). Hence, the LC3-conjugation pathway controls EV cargo loading and secretion.

| S-EPMC7007875 | biostudies-literature

The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles

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

2019-12-22 | GSE137618 | GEO

Secretory autophagy mediates mitochondria clearance in the absence of the mATG8-conjugation machinery

Project description:PINK1-Parkin mediated mitophagy, a selective form of autophagy, represents an important mechanism in mitochondrial quality control (MQC) via clearance of damaged mitochondria. Although it is well known that the conjugation of mammalian ATG8s to phosphatidylethanolamine (PE) is a key step in autophagy, its role in mitophagy remains controversial. In this study, we attempted to clarify the role of the mATG8-conjugation system in mitophagy by generating knockouts of the mATG8-conjugation machinery. Unexpectedly, we show that mitochondria could still be cleared in the absence of mATG8 lipidation, in a process that was found to be independent of lysosomal degradation. Instead, mitochondria were found to be cleared via a secretory autophagy pathway, resulting in the extracellular release of mitochondria, in a process we defined as autophagic secretion of mitochondria (ASM). Functionally, increased ASM promoted the activation of the innate immune cGAS-STING pathway in recipient cells. Overall, data from this study reveal ASM as a novel mechanism in MQC, especially when the cellular mATG8-conjugation machinery is dysfunctional.

2022-06-03 | PXD025356 | Pride

Treatment with Cefotaxime Affects Expression of Conjugation Associated Proteins and Conjugation Transfer Frequency of an IncI1 Plasmid in Escherichia coli

Project description:Horizontal gene transfer (HGT) is the major mechanism responsible for spread of antibiotic resistance. Antibiotic treatment has been suggested to promote HGT, either by directly affecting the conjugation process itself or by selecting for conjugations subsequent to DNA transfer. However, recent research suggests that the effect of antibiotic treatment on plasmid conjugation frequencies, and hence the spread of resistance plasmids, may have been overestimated. We addressed the question by quantifying transfer proteins and conjugation frequencies of a blaCTX-M-1 encoding IncI1 resistance plasmid in Escherichia coli MG1655 in the presence and absence of therapeutically relevant concentrations of cefotaxime (CTX). Analysis of the proteome by iTRAQ labeling and liquid chromatography tandem mass spectrometry revealed that Tra proteins were significantly up regulated in the presence of CTX. The up-regulation of the transfer machinery was confirmed at the transcriptional level for five selected genes. The CTX treatment did not cause induction of the SOS39 response as revealed by absence of significantly regulated SOS associated proteins in the proteome and no significant up-regulation of recA and sfiA genes. The frequency of plasmid conjugation, measured in an antibiotic free environment, increased significantly when the donor was pre-grown in broth containing CTX compared to growth without this drug, regardless of whether blaCTX-M-1 was located on the plasmid or in trans on the chromosome. The results shows that antibiotic treatment can affect expression of a plasmid conjugation machinery and subsequent DNA transfer.

2017-11-21 | PXD006679 | Pride

Receptor-mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy

Project description:Autophagosome formation requires multiple autophagy-related (ATG) factors. However, we find that a subset of autophagy substrates remains robustly targeted to the lysosome in the absence of several core ATGs, including the LC3 lipidation machinery. To address this unexpected result, we performed genome-wide CRISPR screens identifying genes required for NBR1 flux in ATG7KO cells. We find that ATG7-independent autophagy still requires canonical ATG factors including FIP200. However, in the absence of LC3 lipidation, additional factors are required including TAX1BP1 and TBK1. TAX1BP1's ability to cluster FIP200 around NBR1 cargo and induce local autophagosome formation enforces cargo specificity and replaces the requirement for lipidated LC3. In support of this model, we define a ubiquitin-independent mode of TAX1BP1 recruitment to NBR1 puncta, highlighting that TAX1BP1 recruitment and clustering, rather than ubiquitin binding per se, is critical for function. Collectively, our data provide a mechanistic basis for reports of selective autophagy in cells lacking the lipidation machinery, wherein receptor-mediated clustering of upstream autophagy factors drives continued autophagosome formation.

| MSV000086106 | MassIVE

Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin

Project description:This SuperSeries is composed of the following subset Series: GSE32348: Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin (mRNA) GSE32349: Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin (ChIP-Seq) Refer to individual Series

2011-10-06 | E-GEOD-32350 | biostudies-arrayexpress

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