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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Integrated and functional genomics analysis validates the relevance of the nuclear variant ErbB380kDa in prostate cancer progression

ABSTRACT: ChIP-on-chip experiments were performed on immortalized and tumour cell lines selected upon characterization of endogenous nuclear expression of an ErbB380kDa isoform. Among the 1840 target promoters identified, 26 were selected before ErbB380kDa-dependent gene expression was evaluated by real-time quantitative RT-PCR, providing evidence that ErbB380kDa exerted transcriptional control on those genes.

ORGANISM(S): Homo sapiens

SUBMITTER: Paule Séité

PROVIDER: E-MTAB-3504 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Integrated and functional genomics analysis validates the relevance of the nuclear variant ErbB380kDa in prostate cancer progression

Project description:ChIP-on-chip experiments were performed on immortalized and tumour cell lines selected upon characterization of endogenous nuclear expression of an ErbB380kDa isoform. Among the 1840 target promoters identified, 26 were selected before ErbB380kDa-dependent gene expression was evaluated by real-time quantitative RT-PCR, providing evidence that ErbB380kDa exerted transcriptional control on those genes.

2016-07-01 | E-MTAB-3499 | biostudies-arrayexpress

Proteomics dataset for interphase chromatin probabilities

Project description:Chromatin proteins mediate replication, regulate expression and ensure integrity of the genome. So far, a comprehensive inventory of interphase chromatin has not been determined. This is largely due to its heterogeneous and dynamic composition, which makes conclusive biochemical purification difficult, if not impossible. As a fuzzy organelle it defies classical organellar proteomics and cannot be described by a single and ultimate list of protein components. Instead we propose a new approach that provides a quantitative assessment of a protein’s probability to function in chromatin. We integrate chromatin composition over a range of different biochemical and biological conditions. This resulted in interphase chromatin probabilities for 7635 human proteins, including 1840 previously uncharacterized proteins. Quantitative protein ontologies may provide a general alternative to list-based investigations of organelles and complement Gene Ontology.

2014-02-18 | PXD000493 | Pride

SIRT6 regulates redox homeostasis in human mesenchymal stem cells by the transactivation of NRF2

Project description:We investigated the effect of SIRT6-knockout on gene expression and H3K4me3 modification profile in human mesenchymal stem cells. RNAs isolated from SIRT6+/+ and SIRT6-/- hMSCs at early and late passages were sequenced, respectively. And, H3K4me3 ChIP-seq was performed upon the SIRT6 deleted hMSC and WT at early stage, respectively.

2016-01-04 | E-GEOD-64642 | biostudies-arrayexpress

Chromatin immunoprecipitation of human prostate cell lines indicates an H3K4me3/H3K27me3 epigenetic signature of prostate carcinogenesis

Project description:This work offers a dynamic picture of epigenetic switches in carcinogenesis and contributes to an overall understanding of coordinated regulation of gene expression in cancer. Our data indicate an H3K4me3/H3K27me3 epigenetic signature of prostate carcinogenesis.

2009-02-12 | E-TABM-635 | biostudies-arrayexpress

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Project description:Burkholderia contaminans 1840

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Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions

Project description:One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the Cohesin in chromatin and identified transcription factors, RNA-binding proteins, and chromatin regulators associated with Cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to Cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with Cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in Cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of Cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with Cohesin that warrant further investigation.

2023-06-05 | PXD036004 | Pride

Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions

2023-06-05 | PXD035893 | Pride

Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions

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Quantitative ChIP-MS analysis of proteins associated with H3K4me1- and H3K4me3-enriched mono-nucleosomes purified from crosslinked IMR-90 cells

Project description:Here we used ChIP-MS to quantitatively profile chromatin-associated proteins that are specifically associated with H3K4me1- and H3K4me3-modified nucleosomes in IMR-90 chromatin.

2023-12-10 | PXD042826 | Pride

The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer (ChIP-seq)

Project description:This study was aimed at understanding the genome-wide binding and regulatory role of the DAXX transcriptional repressor, recently implicated in PCa. ChIP-Seq analysis of genome-wide distribution of DAXX in PC3 cells revealed over 59,000 DAXX binding sites, found at regulatory enhancers and promoters. ChIP-Seq analysis of DNA methyltransferase 1 (DNMT1), which is a key epigenetic partner for DAXX repression, revealed that DNMT1 binding was restricted to a small number of DAXX sites. DNMT1 and DAXX bound close to transcriptional activator motifs. DNMT1 sites were found to be dependent on DAXX for recruitment by analyzing DNMT1 ChIP-Seq following DAXX knockdown (K/D), corroborating previous findings that DAXX recruits DNMT1 to repress its target genes. Massively parallel RNA sequencing (RNA-Seq) was used to compare the transcriptomes of WT and DAXX K/D PC3 cells. Genes induced by DAXX K/D included those involved in autophagy, and DAXX ChIP-Seq peaks were found close to the transcription start sites (TSS) of autophagy genes, implying they are more likely to be regulated by DAXX. To determine DAXX binding sites in the prostate cancer (PCa) genome, the PC3 cell line was used. A stable DAXX shRNA knockdown (K/D) PC3 cell line and a control shRNA counterpart, were compared in a ChIP-Seq study.

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