Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Using Ribo-tweezer removal RACK1 in mESC

ABSTRACT: We developed a novel tool named Ribo-Tweezer, which allows rapid removal of ribosomal proteins. We use the technology to removal RACK1 in mESC and perform TMT-MS to investigate proteomic changes.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Embryonic Stem Cell

SUBMITTER: Yuxiang Chen

LAB HEAD: Maria Barna

PROVIDER: PXD076559 | Pride | 2026-05-13

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	RACK1_RiboTweezer_mESC_lysate_with_or_without_8hIAA_10plex_replicate1.raw	Raw
	RACK1_RiboTweezer_mESC_lysate_with_or_without_8hIAA_10plex_replicate2.raw	Raw
	RACK1_RiboTweezer_mESC_lysate_with_or_without_8hIAA_10plex_replicate3.raw	Raw
	RACK1_RiboTweezer_mESC_ribosome_cushion_pellet_with_or_without_8hIAA_10plex_replicate1.raw	Raw
	RACK1_RiboTweezer_mESC_ribosome_cushion_pellet_with_or_without_8hIAA_10plex_replicate2.raw	Raw

Items per page:

1 - 5 of 8

Similar Datasets

Ribo-Tweezer: rapid removal of ribosomal proteins reveals new layers of post-transcriptional gene-regulation [Ribo-Seq]

Project description:The ribosome is a ribozyme, but it may also act as a dynamic regulator of gene expression. Although ribosomal protein (RP) composition varies, dissecting the functional contributions of individual RPs beyond their housekeeping roles is challenging by the lack of tools for their selective manipulation in situ. Here, we developed Ribo-Tweezer, a degron-based system directly tethered to mature ribosomes that enables rapid, reversible, and selective depletion of specific RPs. Using Ribo-Tweezer, we find a new role for RACK1 in stem cell fate control via translational regulation of zinc-finger transcriptional networks and in turn LINE1 expression. This translation-transcription coupling provides a mechanism by which translation control is further amplified in gene regulation. Distinct translational programs induced by RPLP0 and RPLP1 depletion further demonstrate RP-specific regulatory functions in translating the genome. Together, these findings establish Ribo-Tweezer as a powerful platform that has illuminated selective functions for RPs in gene regulation.

2026-05-18 | GSE327298 | GEO

Ribo-Tweezer: rapid removal of ribosomal proteins reveals new layers of post-transcriptional gene-regulation

2026-05-18 | GSE327296 | GEO

Ribo-Tweezer: rapid removal of ribosomal proteins reveals new layers of post-transcriptional gene-regulation [RNA-Seq]

2026-05-18 | GSE327297 | GEO

AGS-RACK1

Project description:MicroRNA microarray profiling analysis was performed on human gastric cancer AGS cells after RACK1 silenced or not

2016-03-01 | E-MTAB-2619 | biostudies-arrayexpress

HGC-RACK1

Project description:MicroRNA microarray profiling analysis was performed on human gastric cancer HGC cells after RACK1 silenced or not

2016-03-01 | E-MTAB-3484 | biostudies-arrayexpress

RACK1 function in the miRNA pathway

Project description:MicroRNAs (miRNAs) regulate plant development by post-transcriptional regulation of target genes. In Arabidopsis thaliana, DCL1 processes precursors (pri-miRNAs) to miRNA duplexes, which associate with AGO1. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) or AGO1, respectively, to facilitate efficient and precise pri-miRNA processing and miRNA loading. In this study, we show that the accumulation of plant microRNAs depends on RECEPTOR FOR ACTIVATED C KINASE 1 (RACK1), a scaffold protein found in all higher eukaryotes. miRNA levels are reduced in rack1 mutants and our data suggest that RACK1 affects the microRNA pathway via several distinct mechanisms involving direct interactions with known microRNA factors: RACK1 ensures the accumulation and processing of some pri-miRNAs, directly interacts with SERRATE and is part of an AGO1 complex. As a result, mutations in RACK1 lead to misregulation of miRNA target genes, which is important for ABA responses and phyllotaxy. In conclusion, our study discovered complex functioning of RACK1 proteins in the Arabidopsis miRNA pathway, which are important for miRNA production and therefore plant development.

2013-07-01 | GSE40579 | GEO

The role of Rack1 in microglia in AD

Project description:We found that Rack1 increased in microglia in AD mouse model. Conditional knockout of Rack1 in microglia reduced Aβ aggregation, alleviated neuroinflammation, and rescued cognitive impairments in AD mouse model. Mechanism investigation revealed that knockout of Rack1 in microglia decreased microglial numbers but increased astrocytic numbers and phagocytic activities via IGF1-IGF1R signaling.

2024-06-30 | GSE256191 | GEO

A PARP14/TARG1-Regulated RACK1 MARylation Cycle Drives Stress Granule Dynamics in Cancer Cells [Ribo-seq]

Project description:In this study we examine the role of RACK1 MARylation in stress granule assembly and translational regulation in ovarian cancer cells. In addition, we describe the role of TARG1, an ADPR hydrolase enzyme in stress granule assembly and translation.

2025-01-02 | GSE245503 | GEO

RACK1 function in the miRNA pathway

Project description:MicroRNAs (miRNAs) regulate different aspects of plant development by post-transcriptional regulation of target genes. In Arabidopsis, DICER-LIKE 1 (DCL1) processes miRNA precursors (pri-miRNAs) to miRNA duplexes, which associate with ARGONAUTE 1 (AGO1). AGO1 together with the miRNA guide strand binds complementary RNA sequences within target mRNAs. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) and AGO1, respectively, to facilitate efficient and precise pri-miRNA processing and loading into the effector protein. Here, we show that RECEPTOR OF ACTIVATED C KINASE 1 (RACK1) is a novel component of the Arabidopsis miRNA pathway. RACK1 is a seven-bladed WD-repeat protein that has previously been shown to act as a scaffold protein mediating multiple simultaneous protein-protein interactions. Our molecular analyses demonstrate that RACK1 function is required for controlling miRNA-mediated gene expression. rack1 mutants contain only low levels of mature miRNAs without affecting the first step of pri-miRNA processing. Physical and genetic interaction studies revealed that RACK1 acts in concert with AGO1 and also interacts with a SERRATE, a component of the miRNA processing machinery. These results suggest that RACK1 also functions as a scaffold protein in the miRNA pathway to orchestrates miRNA maturation steps after the initial events of pri-miRNA processing. sequencing of small RNAs from WT and rack1abc mutants (two biological replicates each)

2013-07-01 | E-GEOD-40579 | biostudies-arrayexpress

Splenic FO B and MZ B cells from Rack1(f/f) and Rack1(f/f;CD19-Cre) mice were sorted and subjected to bulk RNA-seq

Project description:Transcription factor Pax5 activates genes essential for B-cell development and function. However, the regulation of Pax5 expression remains elusive. Adaptor Rack1 can interact with multiple transcription factors and modulate their activation and/or stability. Despite that, its role in the transcriptional control of B-cell fates is largely unknown. Here we show that CD19-driven Rack1 deficiency leads to pro-B accumulation and simultaneous reduction of B cells at later developmental stages. The generation of bone marrow chimeras indicates a cell-intrinsic role of Rack1 in B-cell homeostasis. Moreover, Rack1 augments BCR and TLR signaling in mature B cells. Based on diminished CD19 expression upon Rack1 deficiency, further exploration reveals that Rack1 maintains Pax5 protein levels through direct interaction and consequent prevention of Pax5 ubiquitination. Accordingly, Mb1-driven Rack1 deficiency almost completely blocks B-cell development at the pro-B cell stage. Thus, Rack1 regulates B-cell development and function through, at least partially, binding to and stabilizing Pax5.

2024-11-06 | GSE273420 | 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