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Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL crosslinking and affinity purification

ABSTRACT: Short-read sequencing of DNA fractions of the BioTAP-XL pull-downs on human EZH2 and interacting proteins.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53495 | GEO | 2014/02/01

SECONDARY ACCESSION(S): PRJNA232134

REPOSITORIES: GEO

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Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL crosslinking and affinity purification

Project description:Short-read sequencing of DNA fractions of the BioTAP-XL pull-downs on human EZH2 and interacting proteins. ChIP-seq-like pulldown/input samples

2014-02-01 | E-GEOD-53495 | biostudies-arrayexpress

Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification.

Project description:Understanding the composition of epigenetic regulators remains an important challenge in chromatin biology. Traditional biochemical analysis of chromatin-associated complexes requires their release from DNA under conditions that can also disrupt key interactions. Here we develop a complementary approach (BioTAP-XL), in which cross-linking (XL) enhances the preservation of protein interactions and also allows the analysis of DNA targets under the same tandem affinity purification (BioTAP) regimen. We demonstrate the power of BioTAP-XL through analysis of human EZH2, a core subunit of polycomb repressive complex 2 (PRC2). We identify and validate two strong interactors, C10orf12 and C17orf96, which display enrichment with EZH2-BioTAP at levels similar to canonical PRC2 components (SUZ12, EED, MTF2, JARID2, PHF1, and AEBP2). ChIP-seq analysis of BioTAP-tagged C10orf12 or C17orf96 revealed the similarity of each binding pattern with the location of EZH2 and the H3K27me3-silencing mark, validating their physical interaction with PRC2 components. Interestingly, analysis by mass spectrometry of C10orf12 and C17orf96 interactions revealed that these proteins may be mutually exclusive PRC2 subunits that fail to interact with each other or with JARID2 and AEBP2. C10orf12, in addition, shows a strong and unexpected association with components of the EHMT1/2 complex, thus potentially connecting PRC2 to another histone methyltransferase. Similarly, results from CBX4-BioTAP protein pulldowns are consistent with reports of a diversity of PRC1 complexes. Our results highlight the importance of reciprocal analyses of multiple subunits and suggest that iterative use of BioTAP-XL has strong potential to reveal networks of chromatin-based interactions in higher organisms.

| S-EPMC3932854 | biostudies-literature

The miRNA miR-139-5p is a regulator of metastatic pathways in breast cancer.

Project description:Whole transcriptome Identification of direct targets of miR-139-5p using biotinylated pull-downs found that this miRNA has roles in breast cancer invasion and migration.

2013-12-01 | GSE40411 | GEO

Identification of RNAs that co-purify with the Caulobacter sRNA, GsrN

Project description:Purpose: To identify RNAs that interact with GsrN, a small regulatory RNA from Caulobacter crescentus. Methods: Pseudomonas phage 7 (PP7) viral coat protein fused to maltose binding protein (MBP) was immobilized on amylose resin. PP7 coat protein binds to PP7 RNA hairpins (PP7hp). A strain expressing GsrN tagged with a genetically encoded PP7hp at base 37 (GsrN(37)-PP7hp) was captured on this column, washed, and eluted in biological triplicate (pos_rep). As a negative control, we incubated the PP7 coat protein column with independent duplicate lysates from a Caulobacter strain expressing PP7hp fused to a non-functional 3' isoform of GsrN (mock). We generated RNA-seq libraries for each of three independent GsrN(37)-PP7hp fractions, and the duplicate mock fractions. Results: We quantified levels of RNAs in the GsrN(37)-PP7hp (pos) fractions with fractions from parallel PP7hp-3'GsrN(mock) pull-downs by RNA-seq. From these data, we identified a group of RNAs that were enriched in the GsrN(37)-PP7hp fraction.

2017-10-26 | GSE106171 | GEO

BCL-XL inhibition induces an FGFR4 mediated rescue response in colorectal cancer

Project description:The heterogeneous therapy response observed in colorectal cancer is in part due to cancer stem cells (CSCs) that resist chemotherapeutic insults. The anti-apoptotic protein BCL-XL plays a critical role in protecting CSCs from cell death, where its inhibition with high doses of BH3-mimetics can induce apoptosis. To identify pathways that can regulate sensitivity to BCL-XL inhibition, we screened a compound library for synergy with low dose BCL-XL inhibitor A-1155463 and reveal that FGFR4 inhibition effectively sensitizes to A-1155463 both in vitro and in vivo. Mechanistically, we identify a rescue response that is activated upon BCL-XL inhibition and leads to rapid FGF2 secretion and subsequent FGFR4-mediated post-translational stabilization of MCL-1. FGFR4 inhibition prevents MCL-1 upregulation and thereby sensitizes CSCs to BCL-XL inhibition. Altogether, our findings suggest a cell transferable induction of a FGF2/FGFR4 rescue response in CRC that is induced upon BCL-XL inhibition and leads to MCL-1 upregulation.

2021-12-22 | GSE159504 | GEO

Transcriptome wide target profiling for miR-3118-3p and miR-4307-3p.

Project description:Whole transcriptome Identification of direct targets of miR-3118-3p and miR-4307-3p using biotinylated pull-downs found that both miRNAs have roles relevant to pancreatic cancer.

2014-12-31 | GSE40409 | GEO

Transcriptome wide target profiling for miR-23b and miR-27a.

Project description:Whole transcriptome Identification of direct targets of miR-23b and miR-27a using biotinylated pull-downs found that both miRNAs have roles relevant to the mammalian cell cycle and cancer.

2014-12-31 | GSE40410 | GEO

MicroRNA expression data from Bcl-xL silenced A549 lung adenocarcinoma cells

Project description:Bcl-xL is an anti-apoptotic protein that is frequently found to be overexpressed in non-small cell lung cancer leading to an inhibition of apoptosis and poor prognosis. Recently, the role of miRNAs in regulating apoptosis and cell survival during tumorigenesis has become evident, with cancer cells showing perturbed expression of various miRNAs. We utilized miRNA microarrays to determine if miRNA dysregulation in bcl-xL silenced lung adenocarcinoma cells could be involved in regulating apoptotic behavior, and identified dysregulated miRNAs with putative targets involved in signal transduction pathways regulating apoptosis, cell proliferation and cell progression. Short interfering RNA-based transfection of A549 was carried out inducing a reduction in bcl-xL expression levels. 24 hours post-transfection total RNA was isolated using TRIzol reagent and hybridized onto Affymetrix GeneChip miRNA Arrays. A global miRNA expression profile was then established, which compared total RNA, extracted from siRNA-transfected and non-transfected A549 cells. All experiments were carried out with three independent biological replicates.

2013-05-18 | E-GEOD-47059 | biostudies-arrayexpress

The effect of Bcl-xL overexpression on H3K3me3

Project description:To detect H3K4me3 histone modifications globally in HA-Bcl-xL overexpressing BON1 cells, we performed CUT&RUN assays.

2023-08-04 | GSE221629 | GEO

Transcriptome wide target profiling for miR-199a-5p and miR-424-3p.

Project description:Whole transcriptome Identification of direct targets of miR-199a-5p and miR-424-3p using biotinylated pull-downs found that both miRNAs are likely to have a role in the cell cycle.

2013-12-02 | GSE40406 | GEO

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