Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Rattus norvegicus Homo sapiens

PROVIDER: GSE227266 | GEO | 2024/03/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

BAP-seq proximity labeling of subcellular compartments

Project description:HEK293T cells expressing BS2 in different compartments (cytosol, mitochondria, nucleus, nucleolus) were labeled with AC-2. Subsequent enrichment of labeled RNAs, PolyA capture and RNA-seq reveals RNA populations in those compartments.

2024-04-05 | GSE229451 | GEO

Off-the-shelf proximity labeling

Project description:In this study we developed a new assay to perform proximity biotinylation in cells without the requirement for genetic manipulation or transfection to fuse a biotin ligase to a protein of interest. We show the specificity by targeting H3K9me3 and performing ChIP-seq for the biotin modification. Targeting IgG was used as a control. By doing so, we identified flywch1 as a new protein binding to H3K9me3 regions, which we validated using ChIP-seq (IgG ChIP was used as a control)

2021-07-09 | GSE169317 | GEO

Profiling stress-triggered RNA condensation with photocatalytic proximity labeling

Project description:Stress granules (SGs) are highly dynamic cytoplasmic membrane-less organelles that assemble when cells are challenged by stress. At different stages of assembly, various RNA molecules are sorted into SGs where they play important roles in maintaining the structural stability of SGs and regulating gene expression. Despite recent efforts of fluorescence microscopy and biochemical fractionation analysis, there still lacks a complete description of the dynamic changes in the molecular inventory of SG components during different stages of assembly and disassembly. In this study, we applied a proximity-dependent RNA labeling method, CAP-seq, to comprehensively investigate the content of local transcriptome in SGs, in the context of live mammalian cells. CAP-seq captures 457 and 822 RNAs in arsenite- and sorbitol-induced SGs in HEK293T cells, respectively, revealing that SG enrichment is positively correlated with RNA length and AU content, but negatively correlated with translation efficiency. The high spatial specificity of CAP-seq dataset is validated by single-molecule FISH imaging. We further applied CAP-seq profile RNA components in microscopically invisible SG cores, both before stress and after recovery from stress, thus mapping the dynamic changes in SG-proximal transcriptome along the time course of granule assembly/disassembly processes. Our data portray a model of AU-rich and translationally repressed SG nanostructure that are memorized long after the removal of stress.

2023-10-11 | GSE223295 | GEO

Targeting and Plasticity of Mitochondrial Proteins Revealed by Proximity-Specific Ribosome Profiling

Project description:Nearly all mitochondrial proteins are nuclear-encoded and are targeted to their mitochondrial destination from the cytosol. Here, we used proximity-specific ribosome profiling to comprehensively measure translation at the mitochondrial surface in yeast. The majority of inner membrane proteins were co-translationally targeted to mitochondria, reminiscent of proteins entering the endoplasmic reticulum (ER). Comparison between mitochondrial and ER localization demonstrated that the vast majority of proteins were targeted to a specific organelle. A prominent exception was the fumarate reductase Osm1, known to reside in mitochondria. We identified a conserved ER isoform of Osm1, which contributes to the oxidative protein folding capacity of the organelle. This dual localization was enabled by alternative translation initiation sites encoding distinct targeting signals. These findings highlight the exquisite in vivo specificity of organellar targeting mechanisms.

2014-11-10 | GSE61011 | GEO

Off-the-shelf proximity labeling

Project description:Off-the-shelf proximity labeling

| PRJNA716256 | ENA

Active thrombin is produced by intestinal epithelium to control mucosal biofilm

Project description:Healthy human and mouse colon epithelium is a major source of active thrombin, released in lumen. Using germ-free animals, we demonstrated that mucosal thrombin was directly regulated by the presence of commensal microbiota. Specific inhibition of lumenal thrombin activity caused macro-, microscopic damage and transcriptomic alterations of genes involved in host-microbiota interactions. Further, lumenal thrombin inhibition impaired the spatial segregation of microbiota biofilms, allowing bacteria to invade the mucus layer and to translocate across the epithelium. Thrombin proteolyzed the biofilm matrix of reconstituted mucosa-associated human microbiota. We demonstrated a previously unknown physiological role for epithelial thrombin that constrains biofilms at mucosal surfaces. We report that lung, bladder and skin epithelia also expressed thrombin, suggesting that this role may be applicable to other host-microbiome surfaces. Our discovery points route to new therapies targeting biofilms, important for a broad range of disorders, in the gut, and beyond.

2019-06-24 | PXD014315 | Pride

Expression profiles of villus and crypt layers of large intestine from C57Bl/6, Apc1638N+/-, and p21-/- mice.

Project description:Expression profiles obtained from the villus and crypt layers of murine large intestine can elucidate the process of differentiation undergone by epithelial cells as they migrate from the undifferentiated bottom of the crypt to the villus tip before being shed into the intestinal lumen. This series includes profiles from wild type mice, as well as mice harboring mutations in genes (APC and p21) which play key roles in the differentiation process. We used microarrays to characterize gene expression profiles at the base of the crypt and at the villus tip of the lumenal layer of the large intestine in order to better understand the process of differentiation and eventual shedding undergone by cells of the large intestinal epithelium. Four wild type, four APC1638+/- and four p21-/- mice were sacrified and the large intestines dissected out. Cells from the villus tip and from the bottom of the crypt were isolated from the lumenal face of the each large intestine using the Weiser method of sequential elution. RNA was extracted from each eluted sample and used to hybridize to Affymetrix 3' expression arrays.

2010-10-06 | E-GEOD-19338 | biostudies-arrayexpress

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq

Project description:We have developed Halo-seq, an RNA proximity labeling method that allows the quantification of subcellular transcriptomes. We have demonstrated the efficacy of Halo-seq here by using it to quantify chromatin-proximal, nucleolar, and cytoplasmic transcriptomes. In Halo-seq, RNA molecules in close proximity to a spatially restricted protein are specifically marked and biotinylated, facilitating their separation from bulk cellular RNA and their quantification.

2021-04-19 | GSE172281 | GEO

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking

Project description:The spatial organization of RNA within cells is a crucial factor influencing a wide range of biological functions throughout all kingdoms of life. However, a general understanding of RNA localization has been hindered by a lack of simple, high-throughput methods for mapping the transcriptomes of subcellular compartments. Here, we develop such a method, termed APEX-RIP, which combines peroxidase-catalyzed, spatially restricted in situ protein biotinylation with RNA-protein chemical crosslinking. We demonstrate that, using a single protocol, APEX-RIP can isolate RNAs from a variety of subcellular compartments, including the mitochondrial matrix, nucleus, bulk cytosol, and endoplasmic reticulum (ER), with specificity and sensitivity that rival or exceed those of conventional approaches. We further identify candidate RNAs localized to mitochondria-ER junctions and nuclear lamina, two compartments that are recalcitrant to classical biochemical purification. Since APEX-RIP is simple, versatile, and does not require special instrumentation, we envision its broad application in a variety of biological contexts.

2017-12-14 | GSE106493 | GEO

Dual agonistic and antagonistic roles of ZC3H18 provides for co-activation of distinct nuclear RNA decay pathways

Project description:The RNA exosome is a versatile ribonuclease. In the nucleoplasm of mammalian cells, it is assisted by its adaptors the Nuclear EXosome Targeting (NEXT) complex and the PolyA eXosome Targeting (PAXT) connection. Via its association with the ARS2 and ZC3H18 proteins, NEXT/exosome is recruited to capped and short unadenylated transcripts. Conversely, PAXT/exosome was considered to target longer and adenylated substrates via their poly(A) tails. Here, mutational analysis of the core PAXT component ZFC3H1 uncovers a separate branch of the PAXT pathway, which targets short adenylated RNAs and relies on a direct ARS2-ZFC3H1 interaction. We further demonstrate that similar acidic-rich short linear motifs of ZFC3H1 and ZC3H18 compete for a common ARS2 epitope. Consequently, while promoting NEXT function, ZC3H18 antagonizes PAXT activity. We suggest that this unprecedented organization of RNA decay complexes provides co-activation of NEXT and PAXT at loci with abundant production of short exosome substrates.

2024-01-26 | PXD045842 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data