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Series GSE47806 Query DataSets for GSE47806
Status Public on Aug 15, 2013
Title LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs [GRO-seq II]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary While thousands of long non-coding RNAs (lncRNAs) are expressed in higher eukaryotes, the potential regulatory roles of lncRNAs in regulated gene transcription programs remain rather poorly understood. Here, we report that two lncRNAs highly overexpressed in aggressive prostate cancer, PRNCR1 and PCGEM1, bind successively to the androgen receptor (AR) and strongly enhance both ligand-dependent and ligand-independent AR-mediated gene activation programs and proliferation in prostate cancer cells. Binding of PRNCR1 to the C-terminally acetylated AR on enhancers and its association with DOT1L appear to be required for recruitment of the second lncRNA, PCGEM, to the N-terminally methylated AR. Unexpectedly, recognition of the H3K4me3 promoter mark by the PHD finger-domain of Pygopus2, recruited by PCGEM1, proves to enhance selective looping of AR-bound enhancers to target gene promoters in these cells, revealing a novel aspect of ligand-induced enhancer-promoter interactions. In “resistant” prostate cancer cells, these overexpressed lncRNAs can interact with, and are required for the robust activation of both truncated and full length AR, causing DHT-independent activation of the AR transcriptional program and cell proliferation. Conditionally-expressed short hairpin RNA (shRNA)-mediated targeting of these lncRNAs in these resistant cancer cell lines strongly suppressed xenograft growth in vivo. Together, these results suggest that these overexpressed lncRNAs can potentially serve as a required component of castration-resistance in prostatic tumors.
 
Overall design Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq); after knocking-down lincRNAs PCGEM1 and PRNCR1.
LNCaP cells were grown to 30-50% confluence and siRNA/ASO transfections were carried out using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s instructions. Control samples were transfected with scramble ASO and control siRNA, respectively. On the following day of transfection, the cells were cultured in UltraCULTURE (Phenol red free) + 5% Charcoal Dextran Stripped (CDS) serum for 48 hours. For androgen induction, we treat cells with DHT from a 100 uM stock in 70% ethanol to a final concentration of 100 nM for 1 hour
Scramble ASO, -DHT
Scramble ASO, +DHT
PRNCR1 ASO, -DHT
PRNCR1 ASO, +DHT
PCGEM1 ASO, -DHT
PCGEM1 ASO, +DHT
 
Contributor(s) Yang L, Lin C, Tanasa B, Li W, Jin C, Yang J, Meng D, Ohgi KA, Zhang J, Evans CP, Rosenfeld MG
Citation(s) 23945587
Submission date Jun 10, 2013
Last update date May 15, 2019
Contact name MICHAEL G ROSENFELD
E-mail(s) mrosenfeld@ucsd.edu
Organization name HHMI/UCSD
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (6)
GSM1159899 minusDHT_ASO_CTL_hs15l7_1
GSM1159900 minusDHT_ASO_PCGEM1_hs15l4_3
GSM1159901 minusDHT_ASO_PRNCR1_hs15l7_3
This SubSeries is part of SuperSeries:
GSE47807 LncRNA-dependent mechanisms of androgen receptor-regulated gene activation programs
Relations
BioProject PRJNA207828
SRA SRP024674

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Supplementary file Size Download File type/resource
GSE47806_RAW.tar 1.7 Gb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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