Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging [scRNA-Seq]

ABSTRACT: Somatic stem cells are characterized by their low overall protein synthesis rates, a feature implicated in driving their stemness. Yet, how aging reshapes the translational landscape of stem cells and how these changes impact their regenerative capacity remains poorly understood. Here, we present an in vivo single-cell ribosome profiling strategy to monitor tissue-wide translational landscapes of the young and aged mouse skin. By implementing efficient in vivo cell isolation and switching to RNAse I-based ribonuclease for generating ribosomal footprints, we enhance the accessibility of single-cell ribosome profiling and facilitate the evaluation of triplet periodicity, a hallmark of high-quality data. Leveraging this strategy and integrating single-cell RNA sequencing with ribosome profiling, we document the translational landscapes of the major epidermal cell types, outline cell-type-specific translational efficiencies and capture heterogeneity in differentiation commitment among stem cell populations. Notably, we identify a pronounced translational reprogramming of AP-1 subunits specifically in aged epidermal stem cells. Our proof-of-concept study illustrates the power of in vivo single-cell ribosome profiling to map cell-type-specific translational landscapes and offers a scalable strategy for tissue-wide interrogation of translational landscapes at single-cell resolution.

ORGANISM(S): Mus musculus

PROVIDER: GSE280330 | GEO | 2026/07/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging

Project description:Somatic stem cells are characterized by their low overall protein synthesis rates, a feature implicated in driving their stemness. Yet, how aging reshapes the translational landscape of stem cells and how these changes impact their regenerative capacity remains poorly understood. Here, we present an in vivo single-cell ribosome profiling strategy to monitor tissue-wide translational landscapes of the young and aged mouse skin. By implementing efficient in vivo cell isolation and switching to RNAse I-based ribonuclease for generating ribosomal footprints, we enhance the accessibility of single-cell ribosome profiling and facilitate the evaluation of triplet periodicity, a hallmark of high-quality data. Leveraging this strategy and integrating single-cell RNA sequencing with ribosome profiling, we document the translational landscapes of the major epidermal cell types, outline cell-type-specific translational efficiencies and capture heterogeneity in differentiation commitment among stem cell populations. Notably, we identify a pronounced translational reprogramming of AP-1 subunits specifically in aged epidermal stem cells. Our proof-of-concept study illustrates the power of in vivo single-cell ribosome profiling to map cell-type-specific translational landscapes and offers a scalable strategy for tissue-wide interrogation of translational landscapes at single-cell resolution.

2026-07-01 | GSE280255 | GEO

Ribosome profiling and RNA-Sequencing of wild type and Pelota knockout mouse epidermis

Project description:mRNA quality control mechanisms ensure fidelity of protein translation. An evolutionarily conserved component of the quality control machinery, Dom34/Pelota (Pelo), rescues stalled ribosomes. Here we show that Pelo is required for mammalian epidermal homeostasis. Conditional deletion in murine epidermal stem cells expressing Lrig1 results in hyperproliferation and abnormal differentiation, whereas deletion in other stem cells does not. Loss of Pelo results in truncated ribosome footprints and global upregulation of translation. Translational inhibition by rapamycin-mediated down regulation of mTOR rescues the epidermal phenotype. Our study reveals a novel role for the ribosome-rescue machinery in mammalian tissue homeostasis and an unanticipated specificity in its impact on different stem cell populations.

2017-02-02 | GSE94385 | GEO

Global mRNA translational landscapes in mouse bone-marrow-derived-macrophage-mediated response to LPS (lipopolysaccharide)

Project description:We performed ribosome profiling and RNA-seq on mouse bone marrow derived macrophages (BMDMs) treated with 100ng/ml LPS for 0hr, 1hr, 2hrs, 4hrs, 6hrs to obtain global mRNA translational landscapes during this inflammatory response.

2017-07-11 | GSE99787 | GEO

Multifarious translational regulation during replicative aging in yeast

Project description:Protein synthesis is strictly regulated during replicative aging in yeast, but global translational regulation during replicative aging is poorly characterized. To conduct ribosomal profiling during replicative aging, we collected a large number of dividing aged cells using a miniature chemostat aging device. Translational efficiency, defined as the number of ribosome footprints normalized to transcript abundance, was compared between young and aged cells for each gene. We identified more than 700 genes with changes greater than twofold during replicative aging. Increased translational efficiency was observed in genes involved in DNA repair and chromosome organization. Decreased translational efficiency was observed in genes encoding ribosome components, transposon Ty1 and Ty2 genes, transcription factor HAC1 genes associated with the unfolded protein response, genes involved in cell wall synthesis and assembly, and ammonium permease genes. Our results provide a global view of translational regulation during replicative aging, in which the pathways involved in various cell functions are translationally regulated and cause diverse phenotypic changes.

2022-09-25 | GSE203147 | GEO

In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging

Project description:In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging

| PRJNA1177458 | ENA

Cell type-specific ribosome profiling in vivo.

Project description:We report cell-type specific ribosome profiling in a mouse glioma model. We report a strategy for cell-type specific ribosome profiling in vivo. Our strategy was applied to the characterization of a mouse glioma model.

2014-08-25 | E-GEOD-51424 | biostudies-arrayexpress

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

Project description:RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP-RNA interactions. STAMP does not rely on UV-crosslinking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP- and cell type-specific RNA-protein interactions for multiple RBPs and cell types in single, pooled experiments. Pairing STAMP with long-read sequencing yields RBP target sites in an isoform-specific manner. Finally, Ribo-STAMP leverages small ribosomal subunits to measure transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP-RNA interactomes and translational landscapes with unprecedented cellular resolution.

2021-05-09 | GSE166404 | GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

Project description:RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP RNA interactions. STAMP does not rely on UV crosslinking or immunoprecipitation and, when coupled with single cell capture, can identify RBP and cell type specific RNA protein interactions for multiple RBPs and cell types in single pooled experiments. Pairing STAMP with long read sequencing also yields RBP target sites for full length isoforms. Finally, conducting STAMP using small ribosomal subunits (RiboSTAMP) allows analysis of transcriptome wide ribosome association in single cells. STAMP enables the study of RBP RNA interactomes and translational landscapes with unprecedented cellular resolution.

2021-05-09 | GSE155728 | GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

Project description:RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP RNA interactions. STAMP does not rely on UV crosslinking or immunoprecipitation and, when coupled with single cell capture, can identify RBP and cell type specific RNA protein interactions for multiple RBPs and cell types in single pooled experiments. Pairing STAMP with long read sequencing also yields RBP target sites for full length isoforms. Finally, conducting STAMP using small ribosomal subunits (RiboSTAMP) allows analysis of transcriptome wide ribosome association in single cells. STAMP enables the study of RBP RNA interactomes and translational landscapes with unprecedented cellular resolution.

2021-05-09 | GSE155726 | GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

Project description:RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP RNA interactions. STAMP does not rely on UV crosslinking or immunoprecipitation and, when coupled with single cell capture, can identify RBP and cell type specific RNA protein interactions for multiple RBPs and cell types in single pooled experiments. Pairing STAMP with long read sequencing also yields RBP target sites for full length isoforms. Finally, conducting STAMP using small ribosomal subunits (RiboSTAMP) allows analysis of transcriptome wide ribosome association in single cells. STAMP enables the study of RBP RNA interactomes and translational landscapes with unprecedented cellular resolution.

2021-05-09 | GSE155708 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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