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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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Off-the-shelf proximity labeling

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

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Project description:BAP-seq proximity labeling of subcellular compartments

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RNA proximity labeling in log phase Caulobacter crescentus NA1000

Project description:APEX2 RNA proximity labeling is a powerful method for determining localized RNAs in vivo. APEX2 RNA proximity labeling was adapted to bacterial cells, using an APEX2 fusion to the core scaffold of BR-bodies, RNase E. As a control, APEX2 was also fused to a variant of RNase E that lacks its C-terminal IDR and is unable to form BR-bodies, RNase E delta CTD. RNA proximity labeling was performed, and we observed a similar pattern of enriched RNAs to density centrifugation isolated BR-bodies (Al-Husini et al. Mol Cell 2020).

2025-05-31 | GSE297938 | GEO

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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Bioluminescence-activated proximity labeling for spatial multi-omics

Project description:Mapping the spatial organization of proteins and cellular interactions is crucial for understanding their biological functions. Herein, we report a biocompatible, multi-functional luminescence-activated proximity labeling (LAP) strategy for profiling subcellular proteomes and cell-cell interactions in live cells and animals. Our method capitalizes on fusing the photocatalyst miniSOG to NanoLuc luciferase, whose bioluminescence activates miniSOG via a resonance energy transfer mechanism, generating reactive oxygen species in situ to mediate proximity labeling. We achieved local transcriptome profiling by combining LAP with next-generation sequencing.

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Bioluminescence-activated proximity labeling for spatial multi-omics

Project description:Bioluminescence-activated proximity labeling for spatial multi-omics

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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.

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