Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-AR | Santa Cruz Biotechnology | Cat# sc-7305; RRID: AB_626671 |
| Rabbit polyclonal anti-AR | Santa Cruz Biotechnology | Cat# sc-815; RRID: AB_630864 |
| Mouse monoclonal anti-ERα | Santa Cruz Biotechnology | Cat# sc-8005; RRID: AB_627556 |
| Mouse monoclonal anti-FUS | Santa Cruz Biotechnology | Cat# sc-373698; RRID: AB_10917550 |
| Mouse monoclonal anti-TAF15 | Invitrogen | Cat# PA5-84610; RRID: AB_2791761 |
| Rabbit polyclonal anti-Histone H3 | GenScript | Cat# A01502; RRID: AB_1968828 |
| Mouse monoclonal anti-FLAG M2 | Sigma-Aldrich | Cat# F1804; RRID: AB_262044 |
| Mouse monoclonal anti-Myc | Cell Signaling Technology | Cat# 2276S; RRID: AB_331783 |
| Rabbit polyclonal anti-GAPDH | Santa Cruz Biotechnology | Cat# sc-25778; RRID: AB_10167668 |
| Streptavidin-HRP | Jackson ImmunoResearch Laboratories | Cat# 016-030-084; RRID: AB_2337238 |
| Bacterial and Virus Strains | ||
| DH5α Chemically Competent E. coli. | New England Biolabs | Cat# C2987I |
| Rosetta (DE3) E. coli. | Sigma-Aldrich | Cat# 70954 |
| DB3.1 E. coli | Invitrogen | Cat# 11782-018 |
| STBL3 Chemically Competent E. coli. | Life Technologies | Cat# C737303 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 5α-Dihydrotestosterone (DHT) | Sigma-Aldrich | Cat# D-073 |
| 1,6-Hexanediol (1,6-HD) | Sigma-Aldrich | Cat# 240117 |
| 2,5-Hexanediol (2,5-HD) | Sigma-Aldrich | Cat# H11904 |
| Puromycin | Sigma-Aldrich | Cat# P9620 |
| Hygromycin B | Life Technologies | Cat# 10687010 |
| G418 | Life Technologies | Cat# 10131027 |
| Biotin | Sigma-Aldrich | Cat# B4501 |
| Polybrene | Sigma-Aldrich | Cat# H9268 |
| cOmplete™ Protease Inhibitor Cocktail | Roche | Cat# 11836145001 |
| Ni-NTA Agarose | Qiagen | Cat# 30210 |
| Lipofectamine™ 2000 | Life Technologies | Cat# 11668019 |
| Lipofectamine™ 3000 | Life Technologies | Cat# L3000015 |
| Poly-D-lysine | Sigma-Aldrich | Cat# P7280 |
| Formaldehyde | Sigma-Aldrich | Cat# F8775 |
| Paraformaldehyde | Sigma-Aldrich | Cat# P6148 |
| PA-JF646 Halo ligand | Gift from Dr. Luke Lavis lab | N/A |
| Doxycycline | Clontech | Cat# 631311 |
| Trypsin/Lys-C Mix, Mass Spec Grade | Promega | Cat# V5071 |
| SUPERase-In™ RNase Inhibitor | Life Technologies | Cat# AM2696 |
| N-Lauroylsarcosine sodium salt solution (Sarkosyl) | Sigma-Aldrich | Cat# L7414 |
| 5-Bromouridine 5′-triphosphate sodium salt (BrUTP) | Sigma-Aldrich | Cat# B7166 |
| Antarctic phosphatase | New England BioLabs | Cat# M0289S |
| anti-BrdU agarose beads | Santa Cruz Biotechnology | Cat# sc-32323 AC |
| poly-A polymerase | New England BioLabs | Cat# M0276S |
| SuperScript™ III RT kit | Life Technologies | Cat# 18080-051 |
| CircLigase™ ssDNA Ligase | Epicentre | Cat# CL4111K |
| Ape1 | New England BioLabs | Cat# M0282S |
| Phusion® High-Fidelity DNA Polymerase | New England BioLabs | Cat# M0530L |
| Gibson Assembly® Master Mix | New England BioLabs | Cat# E2611L |
| Proteinase K, recombinant, PCR Grade | Roche | Cat# 3115879001 |
| RNase | Sigma-Aldrich | Cat# R6513 |
| TRIzol™ LS Reagent | Life Technologies | Cat# 10296028 |
| T4 PNK | New England BioLabs | Cat# M0201S |
| DNase I | Life Technologies | Cat# AM2222 |
| Benzonase® Nuclease | EMD Millipore | Cat# 70746 |
| MyOne™ Streptavidin T1 Dynabeads™ | Life Technologies | Cat# 65602 |
| Nanolink® Streptavidin Magnetic beads | Solulink | Cat# M-1002-010 |
| AcTEV™ Protease | Life Technologies | Cat# 12575015 |
| PEG8000 | Sigma-Aldrich | Cat# 89510 |
| BioRad protein assay | BioRAD | Cat# 5000001 |
| Critical Commercial Assays | ||
| pCR™8/GW/TOPO™ TA Cloning Kit | Life Technologies | Cat# K250020 |
| Gateway™ LR Clonase™ II Enzyme mix | Life Technologies | Cat# 11791100 |
| Dual-Glo® Luciferase Assay System | Promega | Cat# E2940 |
| Antifade mountant with DAPI | Life Technologies | Cat# P36931 |
| RNeasy Mini Kit | Qiagen | Cat# 74106 |
| iScript™ Select cDNA Synthesis Kit | BioRAD | Cat# 1708897 |
| SsoAdvanced™ Universal SYBR® Green Supermix | BioRAD | Cat# 1725275 |
| QIAquick spin columns | Qiagen | Cat# 28115 |
| KAPA Hyper Prep kit | Kapa Biosystems | Cat# KK8504 |
| Nextera DNA Library Prep Kit | Illumina | Cat# FC-121-1030 |
| Deposited Data | ||
| Raw and processed sequencing data for ChIP-seq | This paper | GEO: GSE215161 |
| Raw and processed sequencing data for ATAC-seq | This paper | GEO: GSE215160 |
| Raw and processed sequencing data for GRO-seq | This paper | GEO: GSE215162 |
| AR ChIP-seq | Malinen et al.39 | GEO: GSE83860 |
| H3K27ac ChIP-seq | Hazelett et al.40 | GEO: GSE51621 |
| Experimental Models: Cell Lines | ||
| Human: LNCaP | ATCC | Cat# CRL-1740 |
| Human: U2OS | ATCC | Cat# HTB-96 |
| Human: SH-SY5Y | ATCC | Cat# CRL-2266 |
| Human: HEK293T | ATCC | Cat# CRL-3216 |
| Human: U2OS 2-6-3 | Janicki et al.51 | N/A |
| Human: LNCaP-pInducer20-AR stable lines for wildtype and mutants | This paper | N/A |
| Human: LNCaP-TetR stable line | This paper | N/A |
| Human: LNCaP-TetR-BioID-AR stable lines for wt, ΔIDR, and pQ69 | This paper | N/A |
| Human: LNCaP-BirA-TetR stable line | This paper | N/A |
| Human: LNCaP-BirA-TetR-BLRP-AR stable lines for wt, ΔIDR, and pQ69 | This paper | N/A |
| Oligonucleotides | ||
| Primers or oligos for qPCR and GRO-seq see METHOD DETAILS | This paper | N/A |
| Recombinant DNA | ||
| shAR | Sigma-Aldrich | TRCN0000003718 |
| shControl | Sigma-Aldrich | SHC002 |
| shControl | Sigma-Aldrich | SHC202 |
| pET-His-GFP-gw | This paper | N/A |
| pET-His-GFP-ARNTD for wildtype and mutants | This paper | N/A |
| pEGFP-C3-gw | This paper | N/A |
| pEGFP-C3-AR for wildtype and mutants | This paper | N/A |
| pCRY2PHR-mCherryN1 | Addgene | Plasmid ID: #26866 |
| pCRY2PHR-mCherry-gw | This paper | N/A |
| pCRY2PHR-mCherry-AR for NTD and ΔIDR | This paper | N/A |
| eYFP-gw-LacI | This paper | N/A |
| eYFP-AR-LacI for wt, ΔIDR, 7FS, and pQ69 | This paper | N/A |
| mCherry-gw | This paper | N/A |
| mCherry-AR for wt, ΔIDR, and 7FS | This paper | N/A |
| mCherry-MED1 | This paper | N/A |
| pHalo-gw-NLS | This paper | N/A |
| pHalo-ARNTDwt-NLS | This paper | N/A |
| pHalo-ARNTDpQ69-NLS | This paper | N/A |
| pInducer20 | Addgene | Plasmid ID: #44012 |
| pInducer20-AR for wildtype and mutants | This paper | N/A |
| pCMV-Renilla-3XARE-TATA-luciferase | This paper | N/A |
| pRetroX-mycBioID-MCS | This paper | N/A |
| pRetroX-mycBioID-AR for wt, ΔIDR, and pQ69 | This paper | N/A |
| pRetroX-BLRP-MCS | This paper | N/A |
| pRetroX-BLRP-AR for wt, ΔIDR, and pQ69 | This paper | N/A |
| pCL-Ampho | Novus Biologicals | Cat# NBP2-29541 |
| pMD2.G | Addgene | Plasmid ID: #12259 |
| psPAX2 | Addgene | Plasmid ID: #12260 |
| Software and Algorithms | ||
| SLIMfast | Teves et al.76 | https://doi.org/10.7554/eLife.22280.022 |
| ImageJ Macros script and MATLAB code for quantifying protein binding residence times from SPT data | Chong et al.13 | http://doi.org/10.5281/zenodo.8292534 |
| Bowtie v1.1.2 | Langmead et al.85 | http://bowtie-bio.sourceforge.net/index.shtml |
| MACS2 v2.1.1.20160309 | Zhang et al.86 | https://github.com/taoliu/MACS |
| ChIPseeker v1.10.3 | Yu et al.87 | https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
| Integrative Genomics Viewer (IGV) | Robinson et al.89 | https://software.broadinstitute.org/software/igv/ |
| MaxQuant software v1.5.5.1 | Max-Planck-Institute of Biochemistry | https://www.biochem.mpg.de/227318/MaxQuant |
| Prism 5 | GraphPad | https://graphpad-prism.software.informer.com/5.0/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |