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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.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE50141 | GEO | 2014/01/23

SECONDARY ACCESSION(S): PRJNA216147

REPOSITORIES: GEO

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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. 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.

2014-01-23 | E-GEOD-50141 | biostudies-arrayexpress

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.

2014-01-23 | GSE50087 | GEO

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

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

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

Identification of miRNA targets in breast cancer cells (Ago2-IP)

Project description:miRNAs regulate mRNA stability and translation through the action of the RNAi-induced silencing complex. In this study, we systematically identified endogenous miRNA target genes by using AGO2 immunoprecipitation (AGO2-IP) and microarray analyses in two breast cancer cell lines, MCF7 and MDA-MB-231, representing luminal and basal-like breast cancer, respectively. The expression levels of ~70% of the AGO2-IP mRNAs were increased by DROSHA or DICER1 knockdown. In addition, integrated analysis of miRNA expression profiles, mRNA-AGO2 interaction, and the 3'-UTR of mRNAs revealed that >60% of the AGO2-IP mRNAs were putative targets of the fifty most abundantly expressed miRNAs. To identify mRNAs associated with AGO2, cell lysate was precleaned with control IgG and immunoprecipitated with anti-human Ago2 (Clone 2E12-1C9, Abnova). Total RNA from cell lysate or coimmunoprecipitated with AGO2 was extracted with Trizol and subjected to microarray analysis, with three biological repeats for each experimental condition.

2013-10-21 | E-GEOD-48158 | biostudies-arrayexpress

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

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

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