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Series GSE63202 Query DataSets for GSE63202
Status Public on Jan 22, 2015
Title Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activation, based on DNA nicking to relieve torsional stress from eRNA synthesis. Using dihydrotestosterone (DHT)-induced binding of androgen receptor (AR) to prostate cancer cell enhancers as a model, we show rapid recruitment, within minutes, of DNA topoisomerase I (TOP1) to a large cohort of AR-regulated enhancers. Furthermore, we show that the DNA nicking activity of TOP1 is a prerequisite for robust eRNA synthesis and enhancer activation and is kinetically accompanied by the recruitment of ATR and the MRN complex, followed by additional components of DNA damage repair machinery to the AR-regulated enhancers. Together, our studies reveal a linkage between eRNA synthesis and ligand-dependent TOP1-mediated nicking - a strategy exerting quantitative effects on eRNA expression in regulating AR-bound enhancer-dependent transcriptional programs.
Overall design Genome-wide binding analysis of AR, TOP1, MRE11 in prostate cancer cell line LNCaP with or without 5alpha-dihydrotestosterone (DHT) treatment.
Nascent RNA analysis by global nuclear run-on (GRO-seq) in LNCaP cells transfected with siRNA with or without DHT treatment.
Distribution of transcriptionally engaged RNA Pol II in LNCaP cells with or without DHT treatment by precision nuclear run-on and sequencing (PRO-seq).

Contributor(s) Puc J, Kozbial P, Li W, Tan Y, Liu Z, Suter T, Ohgi KA, Zhang J, Aggarwal AK, Rosenfeld MG
Citation(s) 25619691
Submission date Nov 12, 2014
Last update date May 15, 2019
Contact name Michael G Rosenfeld
Organization name University of California, San Diego
Department School of Medicine
Lab Rosenfeld Lab
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0648
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (26)
GSM1543774 LNCaP_AR_ChIP-seq_1h_dht
GSM1543775 LNCaP_MRE11_ChIP-seq_0min
GSM1543776 LNCaP_MRE11_ChIP-seq_15min_dht
BioProject PRJNA266983
SRA SRP049720

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE63202_15073summitsIn26321decreasedTOP1regions.bed.gz 104.8 Kb (ftp)(http) BED
GSE63202_43653summitsIn64569increasedTOP1regions.bed.gz 290.4 Kb (ftp)(http) BED
GSE63202_RAW.tar 1.8 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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