KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit Anti-TAF15 | abcam | Cat# ab134916; RRID:AB_2614922 |
| Rabbit Anti-SFPQ | abcam | Cat# ab177149; RRID:N/A |
| Rabbit Anti-Nucleolin | abcam | Cat# ab22758; RRID:AB_776878 |
| Mouse Anti-SFPQ | abcam | Cat# ab11825; RRID:AB_298607 |
| Mouse Anti-PML | abcam | Cat# ab96051; RRID:AB_10679887 |
| Rabbit Anti-FBL | Cell Signaling | Cat# 2639; RRID:AB_2278087 |
| Rabbit Anti-DKC1 | Gene Tex | Cat# GTX109000; RRID:AB_11165396 |
| Rabbit Anti-TDP-43/TARDBP | Novus Biologicals | Cat# NB110-55376SS; RRID:AB_838957 |
| Rabbit Anti-Phospho-RNA polymerase II CTD Ser2 | Novus Biologicals | Cat# NB100-1805; RRID:AB_10001499 |
| Mouse Anti-SC-35 | Novus Biologicals | Cat# NB100-1774; RRID:AB_10128431 |
| Mouse Anti-NOP56 | Novus Biologicals | Cat# NBP2-36778; RRID:N/A |
| Mouse Anti-hnRNPA1 | Novus Biologicals | Cat# NB100-672SS; RRID:AB_10003087 |
| Mouse Anti-EWSR1 | Novus Biologicals | Cat# NBP1-92686SS; RRID:AB_11008755 |
| Mouse Anti-Nucleolin | Novus Biologicals | Cat# NBP2-44612; RRID:N/A |
| Rabbit Anti-NONO | Proteintech | Cat# 11058-1-AP; RRID:AB_2152167 |
| Rabbit Anti-NHP2L1 | Proteintech | Cat# 15802-1-AP; RRID:AB_2251452 |
| Mouse Anti-FUS/TLS | Santa Cruz | Cat# sc-47711; RRID:AB_2105208 |
| Mouse Anti-UBF | Santa Cruz | Cat# sc-13125; RRID:AB_671403 |
| Mouse Anti-RPA194 | Santa Cruz | Cat# sc-48385; RRID:AB_675814 |
| Mouse Anti-U3-55k | Santa Cruz | Cat# sc-515661; RRID:N/A |
| Mouse Anti-NPM1 | Sigma-Aldrich | Cat# B0556; RRID:AB_2154872 |
| Mouse Anti-MYC | MBL | Cat# M192-3; RRID:N/A |
| Anti-GFP FluoTag-Q ATTO488 | NanoTag | N0301-At488-L; RRID:N/A |
| Anti-mouse IgG | Santa Cruz | Cat# sc-2025; RRID:AB_737182 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 4-hydroxytamoxifen | Sigma-Aldrich | Cat# SML1666 |
| THZ1 | Sigma-Aldrich | Cat# 532372 |
| DRB | Sigma-Aldrich | Cat# D1916 |
| Triptolide | Sigma-Aldrich | Cat# T3652 |
| Actinomycin D | Sigma-Aldrich | Cat# A1410 |
| Formaldehyde | Sigma-Aldrich | Cat# F8775 |
| Biotinyl tyramide | Sigma-Aldrich | Cat# SML2135 |
| Hydrogen peroxide solution | Sigma-Aldrich | Cat# H1009 |
| RVC | New England Biolabs | Cat# S1402S |
| CX5461 | Selleck Chemicals | Cat# S2684 |
| Trizol | Thermo Fisher Scientific | Cat# 15596026 |
| Protease and Phosphatase Inhibitor Cocktail | Thermo Fisher Scientific | Cat# 78445 |
| yeast tRNA | Thermo Fisher Scientific | Cat# AM7119 |
| Protein G Dynabeads | Thermo Fisher Scientific | Cat# 10004D |
| RNase A | TaKaRa | Cat# 740505 |
| Proteinase K | Thermo Fisher Scientific | Cat# 25530049 |
| AMP Pure beads | Beckman Coulter | Cat# A63881 |
| SPRISelect beads | Beckman Coulter | Cat# B23317 |
| RNAiMAX | Thermo Fisher Scientific | Cat# 13778150 |
| Critical Commercial Assays | ||
| PureLink™ Genomic DNA Mini Kit | Thermo Fisher Scientific | Cat# K182002 |
| QIAquick PCR Purification Kit | Qiagen | Cat# 28106 |
| Ultralow V2 DNA-Seq Library Preparation Kit | NuGEN | Cat# 0344NB-A01 |
| High-Capacity RNA-to-cDNA™ Kit | Applied Biosystems | Cat# 4387406 |
| Deposited Data | ||
| SFPQ/TAF15 ChIP-seq | This paper | GEO: GSE166623, Table S1 |
| UBF/SFPQ TSA-seq | This paper | GEO: GSE166623, Table S1 |
| Experimental Models: Cell Lines | ||
| U2OS | ATCC | HTB-96 |
| RPE | Clontech | N/A |
| HeLa | ATCC | CCL-2 |
| MRC5 | ATCC | CCL-171 |
| U2OS AsiSI | Gifted from Dr. Legube | N/A |
| U2OS GFP-TAF15 | This study | N/A |
| U2OS GFP-FUS | This study | N/A |
| U2OS GFP-SFPQ | This study | N/A |
| U2OS iCas | This study | N/A |
| DLD1 mAID-POLR2A-mClover | Gifted from Dr. Maeshima | N/A |
| Oligonucleotides | ||
| See Table S3 | This paper | N/A |
| Plasmids | ||
| pX330-GFP-SFPQ | Gifted from Dr. Archa Fox | Addgene #97084 |
| pUC57-GFP-SFPQ-RT | Gifted from Dr. Archa Fox | Addgene #97090 |
| iCas | Gifted from Dr. Meng How Tan | Addgene #84232 |
| pLH-sgRNA1 | Gifted from Dr. Thoru Pederson | Addgene #75388 |
| pEGFP-C1-TAF15 | This study | N/A |
| pEGFP-C1-FUS | This study | N/A |
| Software and Algorithms | ||
| ImageJ | Schneider et al., 2012 | https://imagej.nih.gov/ij/ |
| FIJI | Schindelin et al., 2012 | https://fiji.sc/ |
| Galaxy | Afgan et al., 2018 | https://usegalaxy.org/ |
| Integrative Genomics Viewer | Robinson et al. 2011 | http://software.broadinstitute.org/software/igv/ |
| GraphPad Prism 8 | GraphPad Software, Inc | https://www.graphpad.com/scientificsoftware/prism/ |
| NIS elements viewer | Nikon | https://www.microscope.healthcare.nikon.com/ |