KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-TIA1 (C-20) | Santa Cruz | Cat#sc-1751; RRID:AB_2201433 |
| Mouse monoclonal anti-UBC9 (C-12) | Santa Cruz | Cat#sc-271057; RRID:AB_10610674 |
| Rabbit polyclonal anti-p-eif2α (Ser52) | Santa Cruz | Cat#sc-101670; RRID:AB_2096507 |
| Mouse monoclonal anti-G3BP1 (H-10) | Santa Cruz | Cat#sc-365338; RRID:AB_10846950 |
| Mouse monoclonal anti-FXR1 (B-2) | Santa Cruz | Cat#sc-374148; RRID:AB_10918113 |
| Rabbit polyclonal anti-SUMO-1 | Cell Signaling | Cat#4930; RRID:AB_10698887 |
| Rabbit polyclonal anti-SUMO-2/3 | Cell Signaling | Cat#4971; RRID:AB_2198425 |
| Rabbit polyclonal anti-RanBP2 | abcam | Cat#ab64276; RRID:AB_1142517 |
| Rabbit polyclonal anti-α-Tubulin | Sigma-Aldrich | T9026; RRID: AB_477593 |
| Mouse monoclonal anti-V5-Tag | Thermo Fisher | Cat# R960–25; RRID:AB_2556564 |
| Mouse monoclonal anti-V5-Tag | Cell Signaling | Cat# 13202; RRID:AB_2687461 |
| Rabbit polyclonal anti-ASUN | ProteinTech | Cat#19892–1-AP; RRID:AB_10638473 |
| Rabbit polyclonal anti-BLM | Bethyl labratories | Cat# A300–110A; RRID:AB_2064794 |
| Rabbit polyclonal anti-CBS | ProteinTech | Cat#14787–1-AP; RRID:AB_2070970 |
| Rabbit polyclonal anti-CBX3 | Bethyl labratories | Cat# A300–984A; RRID:AB_805792 |
| Rabbit polyclonal anti-Cdc20 | ProteinTech | Cat#10252–1-AP; RRID:AB_2229016 |
| Rabbit polyclonal anti-DTL/CDT2 | Bethyl labratories | Cat# A300–948A; RRID:AB_2093890 |
| Rabbit polyclonal anti-LGRN | ProteinTech | Cat#12840–1-AP; RRID:AB_2135302 |
| Rabbit polyclonal anti-GAK | Bethyl labratories | Cat# A304–268A; RRID:AB_2620464 |
| Rabbit polyclonal anti-GSPT1 | ProteinTech | Cat#10763–1-AP; RRID:AB_2115506 |
| Rabbit polyclonal anti-GTF3C1/TFIIIC220 | Bethyl labratories | Cat# A301–292A; RRID:AB_938040 |
| Rabbit polyclonal anti-GTF3C3/TFIIIC102 | Bethyl labratories | Cat#A301–237A; RRID:AB_890670 |
| Rabbit polyclonal anti-GTF3C4/TFIIIC90 | Bethyl labratories | Cat# A301–239A; RRID:AB_890667 |
| Rabbit polyclonal anti-MYCBP | ProteinTech | Cat#12022–1-AP; RRID:AB_2148722 |
| Rabbit polyclonal anti-OGT | ProteinTech | Cat#11576–2-AP; RRID:AB_2156943 |
| Rabbit polyclonal anti-POLR3E | Bethyl labratories | Cat# A303–708A; RRID:AB_11205449 |
| Rabbit polyclonal anti-TSC2 | Bethyl labratories | Cat# A300–526A; RRID:AB_2207795 |
| Rabbit polyclonal anti-YTHDC2 | ProteinTech | Cat#27779–1-AP |
| Rabbit polyclonal anti-ZCCHC6 | ProteinTech | Cat#25196–1-AP |
| HRP-Streptavidin | Sigma-Aldrich | Cat#RABHRP3 |
| Avidin, NeutrAvidin, Texas Red conjugate | ThermoFisher | Cat# A2665 |
| Goat-anti Mouse STAR 580 | Abberior | Cat# 52403 |
| Goat anti-rabbit ATTO647n | Sigma Aldrich | Cat# 40839 |
| Rabbit anti-Mouse Alexa Fluor 568 | Invitrogen | Cat# A-11061 |
| Goat anti-Rabbit Alexa Fluor 647 | Invitrogen | Cat# A-21245 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| (+)-Sodium L-ascorbate | Sigma-Aldrich | A7631; CAS: 134-03-2 |
| Sodium Azide OR | Mallinckrodt | 1953–57; CAS: 26628-22-8 |
| (±)-6-Hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid (Trolox) | Sigma-Aldrich | 238813; CAS: 53188-07-1 |
| N-Ethylmaleimide (NEM) | Sigma-Aldrich | E3876; CAS: 128-53-0 |
| 2-D08 | Sigma-Aldrich | SML1052; CAS: 144707-18-6 |
| Biotin | Sigma-Aldrich | B4501; CAS: 58-85-5 |
| Biotin Tyramide (Biotin-Phenol) | Iris Biotech GmbH | LS-3500; CAS: 41994-02-9 |
| Tetracycline-hydrochloride | Sigma-Aldrich | T7660; CAS: 64-75-5 |
| Sodium (meta)arsenite | Sigma-Aldrich | 71287; CAS: 7784-46-5 |
| Hydrogen peroxide 30% | J.TBaker | 2186–01; CAS: 7722-84-1 |
| Sequencing Grade Modified Trypsin | Promega | Cat#V5113 |
| LysC Trypsin mix | Promega | Cat#V5071 |
| Critical Commercial Assays | ||
| Pierce Streptavidin Magnetic Beads | Thermo Fisher | 88816 |
| CellTiter-Glo® Luminescent Cell Viability Assay | Promega | G7571 |
| Experimental Models: Cell Lines | ||
| U2OS-TetR-dddFMR1/FXR1/FXR2 | Paul Anderson lab | N/A |
| U2OS-TetR-ddG3BP1/G3BP2 | Paul Anderson lab | N/A |
| U2OS-TetR_TetO-APEX-NES | Paul Anderson lab | N/A |
| U2OS-TetR-dddFMR1/FXR1/FXR2_TetO-APEX-FMR1 | This paper | N/A |
| U2OS-TetR-dddFMR1/FXR1/FXR2_TetO-APEX-FXR1 | This paper | N/A |
| U2OS-TetR-ddG3BP1/G3BP2_TetO-APEX-G3BP1 | This paper | N/A |
| U2OS-TetR-dddFMR1/FXR1/FXR2_TetO-APEX-FMR1/TetO-GFP-PR50 | This paper | N/A |
| U2OS-TetR-dddFMR1/FXR1/FXR2_TetO-APEX-FMR1/TetO-GFP | This paper | N/A |
| U2OS-TetR_TetO-APEX-NES/TetO-GFP-PR50 | This paper | N/A |
| U2OS-TetR_TetO-APEX-NES/TetO-GFP | This paper | N/A |
| U2OS-TetR_TetO-GFP-PR50 | This paper | N/A |
| U2OS-TetR_TetO-GFP | This paper | N/A |
| U2OS-TetR-ddG3BP1/G3BP2_mRFP-G3BP1 | This paper | N/A |
| U2OS-TetR-ddG3BP1/G3BP2_eGFP-G3BP1 | This paper | N/A |
| U2OS-TetR-ddG3BP1/G3BP2_mRFP-G3BP1_TetO-GFP-PR50 | This paper | N/A |
| U2OS-TetR-ddG3BP1/G3BP2_mRFP-G3BP1_TetO-GFP | This paper | N/A |
| Mouse embryonic stem cells UBC9-iKO | This paper | N/A |
| U2OS-TetR-dddFMR1/FXR1/FXR2_TetO-GFP-FMR1 | This paper | N/A |
| U2OS-TetR-dddFMR1/FXR1/FXR2_TetO-GFP-FMR1-K88R,K130R | This paper | N/A |
| Experimental Models: Organisms/Strains | ||
| w; UAS-PR36, GMR-gal4/ CyO | Fumagalli et al., 2019 | N/A |
| UAS-Lwr | Drosophila Bloomington stock center | #9324 |
| Oligonucleotides | ||
| Primers used for cloning are in Table S5 | This paper | N/A |
| MSL2 siGenome siRNA | Dharmacon | M-020828–01 |
| PIK3R2 siGenome siRNA | Dharmacon | M-003021–03 |
| RNF41 siGenome siRNA | Dharmacon | M-006922–01 |
| SAE1 siGenome siRNA | Dharmacon | M-006402-00-0005 |
| SETX siGenome siRNA | Dharmacon | M-021420–01 |
| SH3RF2 siGenome siRNA | Dharmacon | M-007145–00 |
| UBE2G2 siGenome siRNA | Dharmacon | M-009095–01 |
| UBE2I siGenome siRNA | Dharmacon | M-004910-00-0005 |
| WDR45B siGenome siRNA | Dharmacon | M-017119–01 |
| siGENOME Nontargeting siRNA #5 | Dharmacon | D-001210–05 |
| Recombinant DNA | ||
| Plasmids used are in Table S5 | N/A | N/A |
| Software and Algorithms | ||
| MaxQuant | Cox and Mann, 2008 | https://maxquant.org |
| Andromeda search engine | Cox et al., 2011 | N/A |
| Perseus | Tyanova et al., 2016 | http://maxquant.org/perseus |
| ImageJ | Schneider et al., 2012 | https://imagej.nih.gov/ij |
| Other | ||
| Empore Octadecyl C18 47mm Extraction disks | Sigma-Aldrich | Cat#66883-U |
| 50 cm EASY-spray PepMap column | Thermo Scientific | Cat#ES803 |