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Series GSE84432 Query DataSets for GSE84432
Status Public on Oct 06, 2016
Title Analysis of active enhancers and direct androgen receptor target genes in VCaP prostate cancer cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Androgen receptor (AR) is typically overexpressed in castration-resistant prostate cancer (CRPC). CRPC-derived VCaP cells display an excessive number of chromatin AR-binding sites (ARBs). This study analyzed direct transcription programs of the AR, the prevalence of AR enhancers and the transcriptional regulators involved in the regulation of at the enhancer regions. The analysis utilized global nuclear run-on sequencing (GRO-seq). The GRO-seq data were integrated with the ARB and VCaP cell-specific transcription factor-binding data. Androgen in 30 min activated and repressed transcription of a large number of genes including novel AR targets IGF-1 receptor and EGF receptor. GRO-seq analysis also revealed that only a fraction of the ARBs resides at functional enhancers. Activation of AR bound enhancers was most potent at the sites that also bound PIAS1, ERG and HDAC3. Our genome-wide data provide new insights how AR can directly control growth-signaling pathways in CPRC cells.
Overall design ChIP-seq samples were collected from cells treated with vehicle (ethanol, EtOH) or 10 nM R1881 (synthetic androgen methyltrienolone). IgG sample was collected from EtOH- and R1881-treated cells and used as background control. Biological duplicate samples of the AR (R1881-treated) and CTCF (vehicle- and R1881-treated) ChIP-seq samples were analyzed by using Illumina HiSeq 2000 platform 1.9. Single IgG and H3K9me3 (R1881-treated) samples were analyzed with the same platform. GRO-seq was used to determine androgen-induced changes in nascent transcription in VCaP and LNCaP cells.
Contributor(s) Toropainen S, Niskanen EA, Malinen M, Sutinen P, Kaikkonen MU, Palvimo JJ
Citation(s) 27641228
Submission date Jul 14, 2016
Last update date May 15, 2019
Contact name Sari Toropainen
Organization name University of Eastern Finland
Department School of Medicine
Lab Biomedicine
Street address Yliopistonranta 1 E
City Kuopio
ZIP/Postal code 70211
Country Finland
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (20)
GSM2235679 VCaP_GROseq_EtOH_rep1
GSM2235680 VCaP_GROseq_EtOH_rep2
GSM2235681 VCaP_GROseq_R1881_30min_rep1
BioProject PRJNA329137
SRA SRP078536

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Supplementary file Size Download File type/resource
GSE84432_VCaP_AR_R1881_30min_rep1+2_peaks.bed.gz 582.5 Kb (ftp)(http) BED
GSE84432_VCaP_AR_R1881_4h_rep1+2_peaks.bed.gz 626.3 Kb (ftp)(http) BED
GSE84432_VCaP_CTCF_EtOH_rep1+rep2_peaks.bed.gz 366.5 Kb (ftp)(http) BED
GSE84432_VCaP_CTCF_R1881_rep1+rep2_peaks.bed.gz 391.7 Kb (ftp)(http) BED
GSE84432_VCaP_DHT_gene_expression.xlsx 3.9 Mb (ftp)(http) XLSX
GSE84432_VCaP_H3K9me3_R1881_ucsc.bedGraph.gz 161.2 Mb (ftp)(http) BEDGRAPH
GSE84432_VCaP_gene_expression.xlsx 3.6 Mb (ftp)(http) XLSX
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