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| 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
Other
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| 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.
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| 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).
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| 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 |
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| Submission date |
Nov 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael G Rosenfeld |
| E-mail(s) |
mrosenfeld@ucsd.edu
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| Organization name |
University of California, San Diego
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| Department |
School of Medicine
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| Lab |
Rosenfeld Lab
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0648 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (26)
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| GSM1543777 |
LNCaP_GRO-seq_siControl_1h_vehicle_replicate-A |
| GSM1543778 |
LNCaP_GRO-seq_siControl_1h_dht_replicate-A |
| GSM1543779 |
LNCaP_GRO-seq_siTOP1_1h_vehicle_replicate-A |
| GSM1543780 |
LNCaP_GRO-seq_siTOP1_1h_dht_replicate-A |
| GSM1543781 |
LNCaP_GRO-seq_siControl_1h_vehicle_replicate-B |
| GSM1543782 |
LNCaP_GRO-seq_siControl_1h_dht_replicate-B |
| GSM1543783 |
LNCaP_GRO-seq_siMRE11_1h_vehicle_replicate-B |
| GSM1543784 |
LNCaP_GRO-seq_siMRE11_1h_dht_replicate-B |
| GSM1543785 |
LNCaP_GRO-seq_siNKX3.1_1h_vehicle_replicate-A |
| GSM1543786 |
LNCaP_GRO-seq_siNKX3.1_1h_dht_replicate-A |
| GSM1543787 |
LNCaP_GRO-seq_siControl_1h_vehicle_replicate-C |
| GSM1543788 |
LNCaP_GRO-seq_siControl_1h_dht_replicate-C |
| GSM1543789 |
LNCaP_GRO-seq_siMRE11_1h_vehicle_replicate-C |
| GSM1543790 |
LNCaP_GRO-seq_siMRE11_1h_dht_replicate-C |
| GSM1543791 |
LNCaP_TOP1_ChIP-seq_30min_vehicle |
| GSM1543792 |
LNCaP_TOP1_ChIP-seq_30min_dht |
| GSM1543793 |
LNCaP_PRO-cap_1h_vehicle |
| GSM1543794 |
LNCaP_PRO-cap_1h_dht |
| GSM1543795 |
LNCaP_background_control_for_TOP1_ChIP-seq_repeat1-3 |
| GSM1543796 |
LNCaP_GRO-seq_siControl_1h_vehicle_replicate-D |
| GSM1543797 |
LNCaP_GRO-seq_siControl_1h_dht_replicate-D |
| GSM1543798 |
LNCaP_GRO-seq_siTOP1_1h_vehicle_replicate-D |
| GSM1543799 |
LNCaP_GRO-seq_siTOP1_1h_dht_replicate-D |
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| Relations |
| BioProject |
PRJNA266983 |
| SRA |
SRP049720 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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