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 |