Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of miRNAs which bind to YB-1 protein

ABSTRACT: To assess the direct association of the nucleic acid binding protein yb-1 with mature microRNAs in breast cancer. To do this we performed immunoprecipitation (IP) of YB-1 protein to pull-down linked RNAs Two breast cancer cell-lines, representative of Luminal A and Basal molecular subtypes were used, MCF7 and MDA-MB-435S. An input control represents the RNA present in the lysate used for the IP, prior to treatment. IPs were performed in triplicates on different cell-lysates with one input control used as a representative of the RNA added to the IP reaction.

ORGANISM(S): Homo sapiens

SUBMITTER: Cherie Blenkiron

PROVIDER: E-GEOD-50141 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Links between the oncoprotein YB-1 and small non-coding RNAs in breast cancer.

Blenkiron Cherie C Hurley Daniel G DG Fitzgerald Sandra S Print Cristin G CG Lasham Annette A

PloS one 20131118 11

<h4>Background</h4>The nucleic acid-binding protein YB-1, a member of the cold-shock domain protein family, has been implicated in the progression of breast cancer and is associated with poor patient survival. YB-1 has sequence similarity to LIN28, another cold-shock protein family member, which has a role in the regulation of small noncoding RNAs (sncRNAs) including microRNAs (miRNAs). Therefore, to investigate whether there is an association between YB-1 and sncRNAs in breast cancer, we invest ...[more]

PMID: 24260353

Similar Datasets

Identification of miRNAs which bind to YB-1 protein

Project description:To assess the direct association of the nucleic acid binding protein yb-1 with mature microRNAs in breast cancer. To do this we performed immunoprecipitation (IP) of YB-1 protein to pull-down linked RNAs Two breast cancer cell-lines, representative of Luminal A and Basal molecular subtypes were used, MCF7 and MDA-MB-435S. An input control represents the RNA present in the lysate used for the IP, prior to treatment.

2014-01-23 | GSE50141 | GEO

Effects of YB-1 protein reduction on microRNA abundance in breast cancer cell-lines

Project description:To assess the association of the nucleic acid binding protein yb-1 with mature microRNAs levels in breast cancer. To do this we performed YB-1 siRNA treatement in triplicates alongside an siRNA control Two breast cancer cell-lines, representative of Luminal A and Basal molecular subtypes were used, MCF7 and MDA-MB-435S. Two cell-lines, treated with either siYB-1 or si-Ctrl in triplicate samples.

2014-01-23 | E-GEOD-50087 | biostudies-arrayexpress

Effects of YB-1 protein reduction on microRNA abundance in breast cancer cell-lines

2014-01-23 | GSE50087 | GEO

Transcriptome (RNA-Seq), translatome (Ribo-Seq), and YB-1/YB-3-bound mRNAs (RIP-Seq) of HEK293T, HEK293TdeltaYB-1, and HEK293T+HA-YB-1 cells

Project description:We present results of RNA-Seq, Ribo-Seq, and RIP-Seq (YB-1, YB-3) experiments performed in HEK293T cells, as well as in HEK293T cells with YB-1 knockout and overexpression. The data shows YB-1 function as a global translation inhibitor and YB-3 ability to substitute YB-1 in its function in YB-1 knockout mutant.

2020-01-08 | GSE130781 | GEO

Mechanism and transcriptional program of YB-1 in breast cancer cell lines.

2008-10-31 | GSE13410 | GEO

Mechanism and transcriptional program of YB-1 in breast cancer cell lines.

Project description:YB-1 controls epithelial-mesenchymal transitions by restricting translation of growth-related mRNAs and enabling expression of EMT-inducing transcription factors. We used microarrays to characterize the direct transcriptional and indirect translational regulation of mRNAs by exogenous YB-1 in breast cancer cell lines. Keywords: gene expression profiling To evaluate this in a genome-wide manner we compared microarray expression profiles of total mRNA and mRNAs isolated from Ps (translationally active) or post-Ps (translationally inactive) fractions of MCF10AT-MSCV vs. MCF10AT-YB-1 cells

2008-10-30 | E-GEOD-13410 | biostudies-arrayexpress

Changes in transcriptome and translatome upon YB-1 or YB-3 expression in double knockout HEK293T ΔYB-1ΔYB-3 cells

Project description:In this study, we generated transcriptome profiles from HEK293T, HEK293T ΔYB-1ΔYB-3, and HEK293T ΔYB-1ΔYB-3 with the restored expression of YB-1 and/or YB-3. The data are used to explore YB-1 and YB-3 influence on transcriptome and translatome and their functional interchangeability in transcription and translation.

2024-01-18 | GSE249895 | GEO

YB-1 affects response to paclitaxel in TNBCs by modulation of EGR1

Project description:For patients with triple negative breast tumours (TNBCs), lacking receptors for oestrogen, progesterone or HER2 on their cell surface, chemotherapy is the main treatment. The taxanes, paclitaxel (PTX) and docetaxel, have become the most commonly-used chemotherapies for these kinds of breast cancer. Although several targeted therapies are currently undergoing clinical trials for TNBC, because of the heterogeneous nature of TNBCs, it is predicted that these may often be used in combination with chemotherapy. Therefore an understanding of the mechanisms of chemotherapy resistance will continue to be important for the treatment of these patients. Given the pleiotropic nature of YB-1, the aim of this study was to understand whether there were mechanisms in addition to those discussed above, by which YB-1 controls response to PTX in TNBCs. We initially followed up two previously studied mechanisms, mediated by ABCB1/MDR1 and DUSP4. We then proceeded to use genomics to identify novel mechanisms by which YB-1 regulates the response of TNBCs to PTX. This analysis identified and experimentally validated EGR1, encoding the early growth response protein 1 (EGR1) as a previously undiscovered mechanism of YB-1-driven PTX resistance.

2015-09-02 | E-GEOD-60964 | biostudies-arrayexpress

YB-1 RIP.chip - Co-immunoprecipitation of RNAs present in YB-1 containing RNP granules

Project description:The transcription factor and RNA-interacting Y-box binding protein-1 (YB-1 protein, YBX1 gene) has gained interest as a prognostic biomarker and therapeutic target in various malignancies including prostate cancer. Using a custom prostate-cancer-focussed microarray platform, we have established a transcriptome-wide profile of YB-1 target transcripts in the androgen sensitive prostate cancer cell line LNCaP, including RNAs regulated by YB-1 at the post-transcriptional level; under androgen deprived culture conditions and following stimulation with dihydrotestosterone (DHT).

2022-01-17 | GSE125337 | GEO

Requirements for multivalent Yb body assembly in transposon silencing in Drosophila

Project description:Female sterile (1) Yb (Yb) is a primary component of Yb bodies, perinuclear foci known as the site of PIWI-interacting RNA (piRNA) biogenesis in Drosophila ovarian somatic cells. Yb consists of Helicase C-terminal (Hel-C), RNA helicase and extended Tudor (eTud) domains. We previously showed that the RNA helicase domain is necessary for Yb−RNA interaction, Yb body formation and piRNA biogenesis. Here, we investigated the functions of the two other domains and found that Hel-C and eTud are necessary for Yb to self-associate and to interact with RNAs and other Yb body components, respectively. Both domains were essential for Yb body formation and transposon silencing. Without eTud, piRNA production was completely impaired. Loss of Hel-C severely reduced the levels of transposon-targeting piRNAs, although genic piRNAs unrelated to transposon silencing were still produced. Similar phenotypes were observed when mutations in flamenco, the primary source of transposon-targeting piRNAs, led to the expression of attenuated RNAs. Yb bodies are liquid-like multivalent condensates whose assembly depends on Yb self-association and widespread Yb−flamenco RNA binding.

2019-04-29 | GSE121605 | GEO

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