KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
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| Antibodies | ||
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| HuR/ELAV1 (3A2) | Santa Cruz Biotechnology | Cat#sc-5261; RRID:AB_627770 |
| SUMO1 76–86 | Developmental Studies Hybridoma Bank (DSHB) | N/A |
| SUMO-2 8A2 | Developmental Studies Hybridoma Bank (DSHB) | N/A |
| UBC9 | Proteintech | Cat#14837-1-AP; RRID:AB_2272479 |
| V5 tag | Invitrogen | Cat#R960-25; RRID: N/A |
| His | Cytiva | Cat#27-4710-01; RRID:AB_771435 |
| FLAG M2 | Sigma-Aldrich | Cat#F1804; RRID:AB_262044 |
| RGSHis | Qiagen | Cat#34610; RRID: N/A |
| Cyclin D1 (92G2) | Cell Signaling Technology | Cat#2978; RRID:AB_2259616 |
| Cyclin A2 (BF683) | Cell Signaling Technology | Cat#4656; RRID:AB_2071958 |
| Phospho-Rb (Ser780) (D59B7) | Cell Signaling Technology | Cat#8180; RRID:AB_10950972 |
| Rb (4H1) | Cell Signaling Technology | Cat#9309; RRID:AB_823629 |
| gamma H2A.X (phospho S139) [EP854(2)Y] | Abcam | Cat#ab81299; RRID:AB_1640564 |
| β-Actin | Sigma-Aldrich | Cat#A5441; RRID:AB_476744 |
| Anti-mouse IgG, HRP-linked | Cell Signaling Technology | Cat#7076; RRID:AB_330924 |
| Anti-rabbit IgG, HRP-linked | Cell Signaling Technology | Cat#7074; RRID:AB_2099233 |
|
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| Biological samples | ||
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| Human HCC tumor and surrounding non-tumor tissue | Córdoba Node of the Andalusian Public Health System Biobank | http://www.biobancosspa.com |
| Human HCC tumor and surrounding non-tumor tissue | Basque Biobank | https://www.biobancovasco.org |
| MYC;Trp53−/− mouse liver tissue | Amaia Lujambio74 | N/A |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
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| Geneticin (G418 sulfate) selective antibiotic | Gibco | Cat#11811031 |
| ML-792 SUMO-Activating Enzyme inhibitor | MedChemExpress | Cat#HY-108702 |
| Staurosporin (STS) | Selleckchem | Cat#S1421 |
| Palbociclib, isethionate salt, >99% | LC Laboratories | Cat#P-7766 |
| Glutathione-agarose, lyophilized powder | Sigma-Aldrich | Cat#G4510 |
| Low density nickel-agarose beads | ABT | Cat#6BCL-QLNi-25 |
| Protein A/G PLUS-Agarose | Santa Cruz Biotechnology | Cat#2003 |
| Protein G Sepharose 4 Fast Flow | Cytiva | Cat#GE17-0618-01 |
| PR-619 DUB inhibitor V | Calbiochem | Cat#662141 |
| Complete mini EDTA-free protease inhibitor cocktail tablets | Roche | Cat#11836170001 |
|
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| Critical commercial assays | ||
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| QuickChange site-directed mutagenesis kit | Stratagene | Cat#200518 |
| Lipofectamine 2000 transfection reagent | Invitrogen | Cat#11668019 |
| DharmaFECT 1 transfection reagent | Horizon Discovery | Cat#T-2001-03 |
| Maxwell 16 LEV RNA FFPE purification kit | Promega | Cat#AS1260 |
| SYBR Select master mix | Invitrogen | Cat#4472908 |
| TruSeq Stranded Total RNA human/mouse/rrat kit | Illumina | Cat#RS-122-2201 |
| Annexin V FITC Apoptosis detection kit | Immunostep | Cat#ANXVKF |
| LIVE/DEAD fixable blue dead cell stain kit | Invitrogen | Cat#L23105 |
| Ac-DEVD-AFC caspase-3 fluorogenic substrate | Enzo Life Sciences | Cat#ALX-260-032 |
| Senescence detection kit | Calbiochem | Cat#QIA117 |
| MitoTracker Green FM dye | Invitrogen | Cat#M7514 |
| MitoSOX Red mitochondrial superoxide indicator | Invitrogen | Cat#M36008 |
| Tetramethylrhodamine, ethyl ester, perchlorate (TMRE) | Invitrogen | Cat#T669 |
| ATPlite luminescence assay system | Perkin Elmer | Cat#6016943 |
| NAD/NADH colorimetric assay kit | Abcam | Cat#ab65348 |
| Fura-2, AM, cell permeant | Invitrogen | Cat#F1201 |
|
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| Deposited data | ||
|
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| RIP-Seq | This paper | GEO: GSE197798 |
|
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| Experimental models: Cell lines | ||
|
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| Human: THLE-2 cells | ATCC | CRL-2706 |
| Human: PLC/PRF/5 cells | ATCC | CRL-8024 |
| Human: HuH-7 cells | JCRB Cell Bank | JCRB0403 |
| Human: HuH-7 WT HuR cells | This paper | N/A |
| Human: HuH-7 HuR [K120R] cells | This paper | N/A |
| Human: HuH-7 HuR [K182R] cells | This paper | N/A |
| Human: HuH-7 HuR [K120/182R] cells | This paper | N/A |
| Mouse: MLP-29 cells | Enzo Medico119 | N/A |
|
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| Experimental models: Organisms/strains | ||
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| Mouse: NOD SCID gamma | Charles River Laboratories | Strain code: 614 |
| Oligonucleotides | ||
| Primers for qPCR, See Table S2 | This paper | N/A |
| siRNA targeting sequence: Mouse Pias2b Sense: 5’- CCUCCUAUGUUUUUGGAUAtt-3’ Antisense: 5’- UAUCCAAAAACAUAGGAGGac-3’ | Thermo Fisher Scientific | Custom |
| siRNA targeting sequence: Mouse Senp1 Sense: 5’- AGAAAGGUGGGUUAACAAAtt-3’ Antisense: 5’- UUUGUUAACCCACCUUUCUca-3’ | Thermo Fisher Scientific | Cat#n383576 |
| siRNA targeting sequence: Mouse Senp2 Sense: 5’- GAUUAGGUACUACAUCUUUtt-3’ Antisense: 5’- AAAGAUGUAGUACCUAAUCtt-3’ | Thermo Fisher Scientific | Cat#n251444 |
| siRNA targeting sequence: Mouse Senp3 Sense: 5’- CCGACCCUCUCAUAGAAAAtt-3’ Antisense: 5’- UUUUCUAUGAGAGGGUCGGag-3’ | Thermo Fisher Scientific | Cat#s96092 |
| Primer: HuR RRM1-2 K120R Forward: 5’- ACCATGACCCAGAGGGACGTAGAAGAC-3’ |
STAB vida | Custom |
| Primer: HuR RRM1-2 K120R Reverse: 5’ - GTCTTCTACGTCCCTCTGGGTCATGGT-3’ |
STAB vida | Custom |
| Primer: HuR RRM1-2 K182R Forward: 5’- CATCACAGTGAGGTTTGCAGCCAA-3’ |
STAB vida | Custom |
| Primer: HuR RRM1-2 K182R Reverse: 5’- GTTGGCTGCAAACCTCACTGTGATG-3’ |
STAB vida | Custom |
|
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| Recombinant DNA | ||
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| Plasmid: pcDNA3-His6-Ub | Manuel S Rodríguez120 | N/A |
| Plasmid: pcDNA3-His6-SUMO-1 | Manuel S Rodríguez121,122 | N/A |
| Plasmid: pcDNA3-His6-SUMO-2 | Manuel S Rodríguez121,122 | N/A |
| Plasmid: pcDNA3-His6-SUMO-3 | Manuel S Rodríguez121,122 | N/A |
| Plasmid: pGEX-2T-Ubc9 | Manuel S Rodríguez123 | N/A |
| Plasmid: pCMV-FLAG-hPIAS1 | Manuel S Rodríguez124 | N/A |
| Plasmid: pCMV-FLAG-hPIASxα | Arora et al125 | Addgene #15209 |
| Plasmid: pCMV-FLAG-hPIASxβ | Arora et al.125 | Addgene #15210 |
| Plasmid: pCMV-FLAG-hPIASγ | Liu etal.126 | Addgene #15208 |
| Plasmid: FLAG-hSENPI | Manuel S Rodríguez124 | N/A |
| Plasmid: pFLAG-CMV-hSENP2 | Kang et al.127 | Addgene #18047 |
| Plasmid: pcDNA3-RGS-hSENP3 | Gong et al.128 | Addgene #18048 |
| Plasmid: pcDNA3-RGS-hSENP5 | Gong et al.128 | Addgene #18053 |
| Plasmid: pFLAG-CMV-hSENP6 | Dou etal.129 | Addgene #18065 |
| Plasmid: p3xFLAG-CMV-10-hSENP7 | Bawa-Khalfe et al.130 | Addgene #42886 |
| Plasmid: pcDNA3.3-TOPO | Invitrogen | Cat# K830001 |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR WT | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR [K50R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR [K72R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR[ K89R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR[ K92R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR [K104R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR [K120R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR [K156R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR [K182R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR [K191R] | This paper | N/A |
| Plasmid: pcDNA3.3-TOPO-V5-mHuR [K120/182R] | This paper | N/A |
| Plasmid: pGEX-4T2-His6-HuR RRM1-2 WT | Irene Diaz-Moreno131 | N/A |
| Plasmid: pGEX-4T2-His6-HuR RRM1-2 [K120R] | This paper | N/A |
| Plasmid: pGEX-4T2-His6-HuR RRM1-2 [K182R] | This paper | N/A |
| Plasmid: pGEX-4T2-His6-HuR RRM1-2 [K120/182R] | This paper | N/A |
|
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| Software and algorithms | ||
|
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| The Cancer Genome Atlas (TCGA) | National Cancer Institute | https://www.cancer.gov/tcga |
| The Gene Set Enrichment Analysis (GSEA) | UC San Diego and Broad Institute | https://www.gsea-msigdb.org/gsea/ |
| Ingenuity Pathway Analysis (IPA) | Qiagen | https://digitalinsights.qiagen.com/ |
| PEAKS Studio | Bioinformatics Solutions | https://www.bioinfor.com/peaks-studio/ |
| Perseus | Max Planck Institute of Biochemistry | https://www.maxquant.org/perseus/ |
| The Amber 16 Molecular Dynamics Package | Case et al.132 | https://ambermd.org/GetAmber.php |
| Origin 2018b | OriginLab | https://www.originlab.com/2018b |
| Chimera | UC San Francisco | http://www.rbvi.ucsf.edu/chimera |
| FlowJo version 10 | BD Biosciences | https://www.flowjo.com/solutions/flowjo/ |
| Microscopy Image Browser (MIB) version 2.7 | University of Helsinki | https://mib.helsinki.fi/ |
| Agilent Seahorse Analytics | Agilent | https://seahorseanalytics.agilent.com/ |
| ImageJ | National Institutes of Health | https://imagej.net/software/fiji/ |
| Prism version 8 | GraphPad | https://www.graphpad.com/ |
| BioRender | Science Suite Inc. | https://www.biorender.com |