Appendix 1—key resources table. .
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (Homo sapiens) | HEK293 Flp-In T-REx | Thermo Fisher Scientific | Cat# R78007 RRID:CVCL_U427 |
|
| Cell line (Homo sapiens) | HEK293 Flp-In T-REx FUBI-eS30-StHA | This paper | See Materials and methods, Cell culture, cell lines, and treatments | |
| Cell line (Homo sapiens) | HEK293 Flp-In T-REx FUBI(AA)-eS30-StHA | This paper | AA: G73,74A See Materials and methods, Cell culture, cell lines, and treatments |
|
| Cell line (Homo sapiens) | HEK293 Flp-In T-REx FUBI(GV)-eS30-StHA | This paper | GV: G74V See Materials and methods, Cell culture, cell lines, and treatments |
|
| Cell line (Homo sapiens) | HEK293 Flp-In T-REx HASt-C21orf70 | (Zemp et al., 2014) DOI: 10.1242/jcs.138719 | ||
| Cell line (Homo sapiens) | HEK293 Flp-In T-REx HASt-FUBI-eS30 | This paper | See Materials and methods, Cell culture, cell lines, and treatments | |
| Cell line (Homo sapiens) | HEK293 Flp-In T-REx HASt-GFP | (Wyler et al., 2011) DOI: 10.1261/rna.2325911 | ||
| Cell line (Homo sapiens) | HeLa Flp-In T-REx | (Häfner et al., 2014) DOI: 10.1038/ ncomms5397 | Obtained from T. Mayer (University of Konstanz) | |
| Cell line (Homo sapiens) | HeLa Flp-In T-REx FUBI-eS30-StHA | This paper | See Materials and methods, Cell culture, cell lines, and treatments | |
| Cell line (Homo sapiens) | HeLa Flp-In T-REx FUBI(AA)-eS30-StHA | This paper | AA: G73,74A See Materials and methods, Cell culture, cell lines, and treatments |
|
| Cell line (Homo sapiens) | HeLa Flp-In T-REx FUBI(GV)-eS30-StHA | This paper | GV: G74V See Materials and methods, Cell culture, cell lines, and treatments |
|
| Cell line (Homo sapiens) | HeLa FRT/TetR | Other | Obtained fromM. Beck (EMBL, Heidelberg) | |
| Cell line (Homo sapiens) | HeLa FRT/TetR EGFP-USP36 | This paper | See Materials and methods, Cell culture, cell lines, and treatments | |
| Cell line (Homo sapiens) | HeLa FRT/TetR EGFP-USP36(CA) | This paper | CA: C131A See Materials and methods, Cell culture, cell lines, and treatments |
|
| Cell line (Homo sapiens) | HeLa Kyoto, HeLa K | Other | RRID:CVCL_1922 | Obtained from D. Gerlich (IMBA, Vienna) |
| Antibody | anti-AAMP (rabbit polyclonal) | This paper | WB (1:800) See Materials and methods, Antibodies |
|
| Antibody | anti-β-actin (mouse monoclonal) | Santa Cruz Biotechnology | Cat# sc-47778 RRID:AB_626632 |
WB (1:1000) |
| Antibody | anti-C21ORF70 (rabbit polyclonal) | (Montellese et al., 2020) DOI: 10.1093/nar/gkx253 | WB (1:500) | |
| Antibody | anti-EIF1AD | Proteintech | Cat# 20528-1-AP RRID:AB_10693533 |
WB (1:1000) |
| Antibody | anti-ENP1 (rabbit polyclonal) | (Zemp et al., 2009) DOI: 10.1083/jcb.200904048 | IF (1:15,000) WB (1:1000) |
|
| Antibody | anti-eS1 (RPS3A) (rabbit polyclonal) | (Wyler et al., 2011) DOI: 10.1261/rna.2325911 | WB (1:1000) | |
| Antibody | anti-eS26 (RPS26) (rabbit polyclonal) | Abcam | Cat# ab104050 RRID:AB_10710999 | WB (1:500) |
| Antibody | anti-FAU (FUBI-eS30) (rabbit polyclonal) | Abcam | Cat# ab135765 | WB (1:500) |
| Antibody | anti-FUBI (rabbit polyclonal) | This paper | WB (1:2000) See Materials and methods, Antibodies |
|
| Antibody | anti-HA (mouse monoclonal) | Enzo Life Sciences | ENZ-ABS120-0200 | IF (1:2000) WB (1:1000) |
| Antibody | anti-His (mouse monoclonal) | Sigma-Aldrich | Cat# H1029 RRID:AB_260015 |
WB (1:2000) |
| Antibody | anti-LSG1 (rabbit polyclonal) | (Wyler et al., 2014) DOI: 10.1016/j.febslet.2014.08.013 | WB (1:3000) | |
| Antibody | anti-LTV1 (rabbit polyclonal) | (Zemp et al., 2009) DOI: 10.1083/jcb.200904048 | IF (1:4000) WB (1:2000) |
|
| Antibody | anti-NMD3 (rabbit polyclonal) | (Zemp et al., 2009) DOI: 10.1083/jcb.200904048 | IF (1:1000) WB (1:10,000) |
|
| Antibody | anti-NOB1 (rabbit polyclonal) | (Zemp et al., 2009) DOI: 10.1083/jcb.200904048 | IF (1:5000) WB (1:2000) |
|
| Antibody | anti-NOC4L (rabbit polyclonal) | (Wyler et al., 2011) DOI: 10.1261/rna.2325911 | WB (1:5000) | |
| Antibody | anti-PNO1 (DIM2) (rabbit polyclonal) | (Zemp et al., 2009) DOI: 10.1083/jcb.200904048 | IF (1:2000) WB (1:2000) |
|
| Antibody | anti-RIOK1 (rabbit polyclonal) | (Widmann et al., 2012) DOI: 10.1091/mbc.E11-07-0639 | IF (1:8000) WB (1:1000) |
|
| Antibody | anti-RIOK2 (rabbit polyclonal) | (Zemp et al., 2009) DOI: 10.1083/jcb.200904048 | IF (1:5000) WB (1:5000) |
|
| Antibody | anti-RRP12 (rabbit polyclonal) | (Wyler et al., 2011) DOI: 10.1261/rna.2325911 | IF (1:2000) WB (1:1000) |
|
| Antibody | anti-Strep (mouse monoclonal) | IBA GmbH | Cat# 2-1507-001 RRID:AB_513133 |
WB (1:1000) |
| Antibody | anti-TRIP4 (rabbit polyclonal) | This paper | WB (1:50,000) See Materials and methods, Antibodies |
|
| Antibody | anti-TSR1 (rabbit polyclonal) | ##(Zemp et al., 2014)# DOI: 10.1242/jcs.138719 | WB (1:10,000) | |
| Antibody | anti-uL23 (RPL23A) (rabbit polyclonal) | (Wyler et al., 2011) DOI: 10.1261/rna.2325911 | WB (1:200) | |
| Antibody | anti-uS3 (RPS3) (rabbit polyclonal) | (Zemp et al., 2009) DOI: 10.1083/jcb.200904048 | WB (1:1000) | |
| Antibody | anti-USP10 (rabbit polyclonal) | Sigma-Aldrich | Cat# HPA006731 RRID:AB_1080495 |
WB (1:1000) |
| Antibody | anti-USP16 (rabbit polyclonal) | Bethyl Laboratories | Cat# A301-615A RRID:AB_1211387 |
WB (1:500) |
| Antibody | anti-USP36 (rabbit polyclonal) | Sigma-Aldrich | Cat# HPA012082 RRID:AB_1858682 |
IF (1:1000) WB (1:250) |
| Antibody | goat anti-mouse Alexa Fluor 594 | Thermo Fisher Scientific | A-11005, RRID:AB_2534073 | IF (1:250) |
| Antibody | goat anti-rabbit Alexa Fluor 488 | Thermo Fisher Scientific | A-11008, RRID:AB_143165 | IF (1:250) |
| Antibody | goat anti-mouse Alexa Fluor Plus 680 | Thermo Fisher Scientific | Cat# A32729 RRID:AB_2633278 |
WB (1:10,000) |
| Antibody | goat anti-rabbit Alexa Fluor Plus 800 | Thermo Fisher Scientific | Cat# A32735, RRID:AB_2633284 | WB (1:10,000) |
| Recombinant DNA reagent | pC2Pi/control | (Boneberg et al., 2019) DOI: 10.1261/rna.069609.118 | See Materials and methods, Molecular cloning | |
| Recombinant DNA reagent | pC2Pi/USP36i-g1 | This paper | USP36 guide 1 See Materials and methods, Molecular cloning |
|
| Recombinant DNA reagent | pC2Pi/USP36i-g2 | This paper | USP36 guide 2 See Materials and methods, Molecular cloning |
|
| Recombinant DNA reagent | pCDNA5/FRT/TO/FUBI-eS30-StHA | This paper | See Materials and methods, Molecular cloning | |
| Recombinant DNA reagent | pCDNA5/FRT/TO/FUBI(AA)-eS30-StHA | This paper | AA: G73,74A See Materials and methods, Molecular cloning |
|
| Recombinant DNA reagent | pCDNA5/FRT/TO/FUBI(GV)-eS30-StHA | This paper | GV: G74V See Materials and methods, Molecular cloning |
|
| Recombinant DNA reagent | pCDNA5/FRT/TO/EGFP-USP36 | This paper | See Materials and methods, Molecular cloning | |
| Recombinant DNA reagent | pCDNA5/FRT/TO/EGFP-USP36(CA) | This paper | CA: C131A See Materials and methods, Molecular cloning |
|
| Recombinant DNA reagent | pCDNA5/FRT/TO/HASt-FUBI-eS30 | This paper | See Materials and methods, Molecular cloning | |
| Recombinant DNA reagent | pDEST/LTR/Flag-HA-USP36 | Addgene (Sowa et al., 2009) DOI: 10.1016/j.cell.2009.04.042 |
Cat# 22579 RRID:Addgene_22579 |
See Materials and methods, Molecular cloning |
| Recombinant DNA reagent | pET-28b(+)/His6-FUBI-EGFP | This paper | See Materials and methods, Molecular cloning | |
| Recombinant DNA reagent | pET-28b(+)/His6-Ub-EGFP | This paper | See Materials and methods, Molecular cloning | |
| Recombinant DNA reagent | pFBD/EGFP/His10-USP36-TEV-St | This paper | pFBD: pFastBac Dual See Materials and methods, Molecular cloning |
|
| Recombinant DNA reagent | pFBD/EGFP/His10-USP36(CA)-TEV-St | This paper | pFBD: pFastBac Dual, CA: C131A See Materials and methods, Molecular cloning |
|
| Recombinant DNA reagent | pQE30/His6-FUBI-eS30 | This paper | See Materials and methods, Molecular cloning | |
| Recombinant DNA reagent | pQE30/His6-FUBI(AA)-eS30 | This paper | AA: G73,74A See Materials and methods, Molecular cloning |
|
| Sequence-based reagent | QuikChange primers for FUBI(AA)-eS30 | Sigma-Aldrich | 5'-GCAGGCCGCATGCTTGcAGcTAAAGTTCATGGTTCC-3', 5'-GGAACCATGAACTTTAgCTgCAAGCATGCGGCCTGC-3' See Materials and methods, Molecular cloning |
|
| Sequence-based reagent | QuikChange primers for FUBI(GV)-eS30 | Sigma-Aldrich | 5'-GGCCGCATGCTTGGAGtTAAAGTTCATGGTTCC-3', 5'-GGAACCATGAACTTTAaCTCCAAGCATGCGGCC-3' See Materials and methods, Molecular cloning |
|
| Sequence-based reagent | QuikChange primers for USP36(CA) | Sigma-Aldrich | 5'-CCACAACCTaGGCAACACCgcCTTTCTCAATGCCACC-3', 5'-GGTGGCATTGAGAAAGgcGGTGTTGCCtAGGTTGTGG-3' See Materials and methods, Molecular cloning |
|
| Sequence-based reagent | QuikChange primers for USP36(NdeI) | Sigma-Aldrich | 5’- CCGTGTGCAAGAGCGTCagcGAtACaTAtGACCCCTACTTGGAC-3’, 5'-GTCCAAGTAGGGGTCaTAtGTaTCgctGACGCTCTTGCACACGG-3' See Materials and methods, Molecular cloning |
|
| Sequence-based reagent | 5'ITS1 | Microsynth (Rouquette et al., 2005) DOI: 10.1038/sj.emboj.7600752 |
5'-CCTCGCCCTCCGGGCTCCGTTAATGATC-3' See Materials and methods, Northern blot analysis |
|
| Sequence-based reagent | ITS2 | Microsynth (Rouquette et al., 2005) DOI: 10.1038/sj.emboj.7600752 |
5'-GCGCGACGGCGGACGACACCGCGGCGTC-3' See Materials and methods, Northern blot analysis |
|
| Sequence-based reagent | Cy3-5'ITS1 | Microsynth (Rouquette et al., 2005) DOI: 10.1038/sj.emboj.7600752 |
5'-CCTCGCCCTCCGGGCTCCGTTAATGATC-3' See Materials and methods, Fluorescence in situ hybridization |
|
| Sequence-based reagent | si-AAMP | Microsynth | 5’-CAGGAUGGCAGCUUGAUCCUA-3 See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-control | Qiagen | Cat# 1027281 | Allstars Negative Control siRNA See Materials and methods, RNA interference |
| Sequence-based reagent | si-eS4X (RPS4X) | Qiagen | 5’-CUGGAGGUGCUAACCUAGGAA-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-FAU (FUBI-eS30) | Qiagen | 5’-CCGGCGCUUUGUCAACGUUGU-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-uS19 (RPS15) | Microsynth (Rouquette et al., 2005) DOI: 10.1038/sj.emboj.7600752 |
5’-UCACCUACAAGCCCGUAAA-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-USP10-1 | Qiagen | 5'-UCGCUUUGGAUGGAAGUUCUA-3' See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-USP10-2 | Qiagen | 5’-UACGUCAACACCCAUGAUAGA-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-USP10-3 | Qiagen | 5’-AACACAGCUUCUGUUGACUCU-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-USP10-4 | Qiagen | 5’-AAGAACUAGUUCUUACUUCAA-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-USP36-1 | Qiagen, Microsynth | 5’-CAAGAGCGUCUCGGACACCUA-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-USP36-2 | Qiagen | 5’-UCCGUAUAUGUCCCAGAAUAA-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-USP36-3 | Qiagen | 5’-CCGCAUCGAGAUGCCAUGCAU-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-USP36-4 | Qiagen | 5’-UUCCUUGUGAGUAGCUCUCAA-3’ See Materials and methods, RNA interference |
|
| Sequence-based reagent | si-XPO1 (CRM1) | Microsynth (Zemp et al., 2009) DOI: 10.1083/jcb.200904048 |
5’-UGUGGUGAAUUGCUUAUAC-3’ See Materials and methods, RNA interference |
|
| Chemical compound, drug | cycloheximide, CHX | Sigma-Aldrich | Cat# C7698 | |
| Chemical compound, drug | Leptomycin B | LC Laboratories | Cat# L-6100 | |
| Chemical compound, drug | tetracycline, tet | Invitrogen | Cat# 550205 |