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Enzyme-mediated proximity labeling identifies small RNAs in the endoplasmic reticulum lumen

ABSTRACT: Enzyme-mediated proximity labeling identifies small RNAs in the endoplasmic reticulum lumen

PROVIDER: PRJNA944259 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23851072_1.fastq.gz	Fastqsanger.gz
	SRR23851072_2.fastq.gz	Fastqsanger.gz
	SRR23851073_1.fastq.gz	Fastqsanger.gz
	SRR23851073_2.fastq.gz	Fastqsanger.gz
	SRR23851074_1.fastq.gz	Fastqsanger.gz

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Enzyme-mediated proximity labeling identifies small RNAs in the endoplasmic reticulum lumen

Project description:In eukaryotic cells, the subcellular targeting of RNA controls many fundamental aspects of cellular physiology. RNA molecules are broadly distributed throughout the nucleoplasm and cytoplasm, but are conventionally believed to be excluded from the secretory pathway compartments, including the endoplasmic reticulum (ER). Recent discovery of RNA N-glycan modification (glycoRNAs) has challenged this view, but direct evidence of RNA localization in the ER lumen has been lacking. In this study, we applied enzyme-mediated proximity labeling to profile the ER lumen-localized RNAs in human embryonic kidney 293T cells and rat cortical neurons. Our dataset revealed the presence of small non-coding RNAs in the ER lumen, including U RNAs, sco/sca RNAs and Y RNAs, which partially overlap with glycoRNAs. These findings shed light on novel RNA targeting mechanism and raise interesting questions regarding the biological functions of ER lumenal RNAs.

2024-03-10 | GSE227266 | GEO

Meta-organization of Translation Centers Revealed by Proximity Mapping of Endoplasmic Reticulum Ribosome Interactors

Project description:We report a method to use BioID proximity labeling to map the sub-organization of translating mRNAs on the endoplasmic reticulum. This method first isolates membrane bound polysomes using a Sephacryl 400 resin-based enrichment followed by isolation of biotin labeled polysomes by streptavidin beads and high-throughput sequencing of the bound polysomes. We find that, for the two pools of polysomes labeled by either LRRC59 or Sec61beta BioID reporters, there is an interesting divergence in specific mRNAs that are entering into the secretory pathway such that secreted proteins are much more enriched towards the LRRC59 reporter with Sec61beta serving a more varied role in mRNA translation.

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Project description:Meta-organization of Translation Centers Revealed by Proximity Mapping of Endoplasmic Reticulum Ribosome Interactors

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mRNA transcription profiling by array of adult flies expressing a artificial construct designed to bring mitochondria and the endoplasmic reticulum in close proximity

Project description:Global analysis of transcriptional changes in adult flies genetically modified to express an artificial linker that brings the mitochondria and endoplasmic reticulum together. Whole flies were analysed in this study. RNA was prepared from 3-day-old and thirty-day-old flies.

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Profiling stress-triggered RNA condensation with photocatalytic proximity labeling

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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.

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In vivo proximity labeling and sequencing (IPL-seq) for SNRPN70 in 293T-Rex

Project description:This proof-of-principle experiment was designed to demonstrate the feasibility of proximity labeling for RNA–protein interactions

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