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

ABSTRACT: 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE13410 | GEO | 2008/10/31

SECONDARY ACCESSION(S): PRJNA109771

REPOSITORIES: GEO

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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

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

Somatic Primary piRNA Biogenesis Driven by Cis-Acting RNA Elements and Trans- Acting Yb

Project description:Primary piRNAs in Drosophila ovarian somatic cells arise from piRNA cluster transcripts and the 3′ UTRs of a subset of mRNAs, including Traffic jam (Tj) mRNA. However, it is unclear how these RNAs are determined as primary piRNA sources. Here, we identify a cis-acting 100-nt fragment in the Tj 3′ UTR that is sufficient for producing artificial piRNAs from unintegrated DNA. These artificial piRNAs were effective in endogenous gene transcriptional silencing. Yb, a core component of primary piRNA biogenesis center Yb bodies, directly bound the Tj-cis-element. Disruption of this interaction markedly reduced piRNA production. Thus, Yb is the trans-acting partner of the Tj-cis-element. Yb-CLIP revealed that Yb-binding correlated with somatic piRNA production but Tj-cis-element downstream sequences produced few artificial piRNAs. Thus, Yb determines primary piRNA sources by two modes of action; primary binding to cis-elements to specify substrates, and secondary binding to downstream regions to increase diversity in piRNA populations.

2015-06-05 | GSE69625 | GEO

Somatic Primary piRNA Biogenesis Driven by Cis-Acting RNA Elements and Trans- Acting Yb

2015-06-05 | E-GEOD-69625 | 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 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

HITS-CLIP analysis of Yb binding sites in Drosophila ovary cell line

Project description:piRNAs direct Piwi to repress transposons to maintain genome integrity in Drosophila ovarian somatic cells. piRNA maturation and association with Piwi occur at perinuclear Yb bodies, the centers of piRNA biogenesis. Here, we show that piRNA intermediates arising from the piRNA cluster flamenco (flam) concentrate into perinuclear foci adjacent to Yb bodies, termed Flam bodies. Although flam expression is not required for Yb body formation, Yb, the core component of Yb bodies, is required for Flam body formation. Abolishment of the RNA-binding activity of Yb disrupts both Yb bodies and Flam bodies. Loss of Zucchini, an endoribonuclease necessary for piRNA maturation, enlarges Flam bodies, which now superimpose with Yb bodies. Yb directly binds flam, but not neighboring protein-coding gene, transcripts. Thus, Yb integrates piRNA processing factors and piRNA intermediates into Yb bodies and Flam bodies, respectively, through direct binding to enhance piRNA biogenesis and formation of piRNA-inducing silencing complexes.

2014-06-24 | GSE54875 | GEO

Genome-wide analysis of transcription factor PfNF-YB in Plasmodium falciparum.

Project description:PfNF-YB is a transcription factor of Plasmodium falciparum and is known as a CCAAT-box-binding subunit B. PfNF-YB belongs to NF-Y complex family that is conserved from yeast to human. PfNF-YB is highly expressed in schizont stage and co-localized at the nucleus in mature form during intraerythrocytic stage. We found that melatonin and cAMP second messenger can modulate the PfNF-YB expression in P. falciparum. To better understand the function of PfNF-YB in P. falciparum we proposed to perform chromatin immunoprecipitation (ChIP) of PfNF-YB together with chromatin profiling by ChIP-on-chip analysis. The results showed that PfNF-YB binds to CCAAT of several genes in schizont stage.

2013-07-16 | GSE48894 | GEO

YB-1 knock.down - siRNA driven YBX1 knock.down

2022-01-17 | GSE125339 | GEO

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