Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Translation efficiency changes measured using ribosome footprinting (Ribo-seq) in poorly and highly metastatic cancer cells

ABSTRACT: Translation efficiency changes measured using ribosome footprinting (Ribo-seq) in poorly and highly metastatic cancer cells

PROVIDER: PRJNA774895 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Translation efficiency changes measured using ribosome footprinting (Ribo-seq) in poorly and highly metastatic cancer cells

Project description:Cancer cells often co-opt post-transcriptional regulatory mechanisms to achieve pathologic expression of gene networks that drive metastasis. Translational control is a major regulatory hub in oncogenesis, however its effects on cancer progression remain poorly understood. To address this, we used ribosome profiling to compare genome-wide translation efficiencies of poorly and highly metastatic breast cancer cells and patient-derived xenografts. We developed novel regression-based methods to analyze ribosome profiling and alternative polyadenylation data, and identified HNRNPC as a translational controller of a specific mRNA regulon. Mechanistically, HNRNPC, in concert with PABPC4, binds near to poly(A) signals, thereby governing the alternative polyadenylation of a set of mRNAs. We found that HNRNPC and PABPC4 are downregulated in highly metastatic cells, which causes HNRNPC-bound mRNAs to undergo 3’ UTR lengthening and subsequently, translational repression. We showed that modulating HNRNPC expression impacts the metastatic capacity of breast cancer cells in xenograft mouse models. We also found that a small molecule, previously shown to induce a distal-to-proximal poly(A) site switching, counteracts the HNRNPC-PABPC4 driven deregulation of alternative polyadenylation and decreases the metastatic lung colonization by breast cancer cells in vivo.

2023-02-20 | GSE186639 | GEO

Ribosomal footprinting of MDA-Parental and MDA-LM2

Project description:We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines

2016-06-07 | GSE77315 | GEO

Ribosomal footprinting of CN34-Parental and CN34-LM1a

Project description:We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines

2016-06-07 | GSE77292 | GEO

Ribosomal footprinting of MDA_Ctrl and MDA_Glu overexpression cell lines

Project description:We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines

2016-06-07 | GSE77347 | GEO

Ribosomal footprinting of MDA_Ctrl and MDA_Arg overexpression cell lines

Project description:We used Illlumina Artseq Ribo Profile to perform ribosome footprinting on the above cell lines

2016-06-07 | GSE77317 | GEO

Ribo-seq of Arabidopsis mTRAN double mutants

Project description:mTRAN proteins are are plant specific-components of the mitoribosome. To asses of loss-of-function mtran1 mtran2 double mutants show decreased translation rates, we performed ribosome footprinting coupled to RNA-seq (Ribo-seq).

2023-09-01 | E-MTAB-13059 | biostudies-arrayexpress

Gene array comparison of highly and poorly chondrogenic clones of adult human mesenchymal stem cells (MSCs)

Project description:MSCs are a heterogeneous population of cells with different capacities for lineage differentiation. MSC clones were prepared from a single adult human bone marrow sample and screened for their chondrogenic capacity using cartilage tissue engineering (measured by type II collagen content). The aim was to compare genes expressed by highly and poorly chondrogenic clones to identify genes associated with those MSCs with an enhanced capacity for cartilage formation.

2015-04-30 | GSE54684 | GEO

Gene array comparison of highly and poorly chondrogenic clones of adult human mesenchymal stem cells (MSCs)

2015-04-30 | E-GEOD-54684 | biostudies-arrayexpress

Ribosome footprinting of fly heads

Project description:We applied ribosomal footprinting experiment followed by RNA-seq in order to detect circular RNA associated with ribosomes in fly heads.

2017-03-24 | GSE79626 | GEO

Nanoparticles and photochemistry for Native-like transmembrane protein footprinting

Project description:Mass spectrometry based footprinting can probe higher order structure of proteins. We bond photocatalytic nanoparticles to a lipid bilayer that, upon laser irradiation, produce high local concentrations of radicals that penetrate the lipid layer made permeable by a simultaneous laser-initiated PB reaction. This approach achieves high footprinting coverage for membrane proteins in liposomes, helps locate both ligand-binding residues in a transporter and ligand-induced conformational changes, and reveals structural aspects of the flexible unbound state. Overall, this approach proves highly effective in intramembrane footprinting and forges a connection between materials science and biology.

2021-09-26 | PXD027819 | Pride

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