KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies | ||
|
| ||
| BAX | Cell Signaling Technology | Cat#2772; RRID:AB_10695870 |
| BID | Cell Signaling Technology | Cat#2002; RRID:AB_10692485 |
| BrdU | Santa Cruz Biotechnology | Cat#sc-32323; RRID:AB_626766 |
| Cleaved Caspase-3 | Cell Signaling Technology | Cat#9661; RRID:AB_2341188 |
| Caspase-8 | Cell Signaling Technology | Cat#9746; RRID:AB_2275120 |
| GAPDH | Santa Cruz Biotechnology | Cat#sc-365062; RRID:AB_10847862 |
| FAM193A | Abcam | Cat#ab122832; RRID:AB_11128856 |
| FLAG tag M2 | Sigma-Aldrich | Cat#F1804; RRID:AB_262044 |
| HA-tag | Cell Signaling Technology | Cat#3724; RRID:AB_1549585 |
| Halo-tag | Promega | Cat#G9211; RRID:AB_2688011 |
| Histone H2B | Cell Signaling Technology | Cat#12364; RRID:AB_2714167 |
| Lamin B1 | Cell Signaling Technology | Cat#13435; RRID:AB_2737428 |
| MDM2 | Santa Cruz Biotechnology | Cat#sc-965; RRID:AB_627920 |
| MDM4 | Bethyl Laboratories Inc. | Cat#A300-287A; RRID:AB_263407 |
| MDM4 (−82) | Sigma-Aldrich | Cat#M0445; RRID:AB_532256 |
| myc-tag | Cell Signaling Technology | Cat#2278; RRID:AB_490778 |
| nucleolin/C23 | Santa Cruz Biotechnology | Cat#sc-8031; RRID:AB_670271 |
| p21 | Santa Cruz Biotechnology | Cat#sc-817; RRID:AB_628072 |
| p53 | Millipore Sigma | Cat#OP43; RRID:AB_10682938 |
| PIG3 | Santa Cruz Biotechnology | Cat#sc-166664; RRID:AB_2303666 |
| PUMA | Santa Cruz Biotechnology | Cat#sc-374223; RRID:AB_10987708 |
| PUMA | Cell Signaling Technology | Cat#12450; RRID:AB_902228 |
| α-Tubulin | Sigma Aldrich | Cat#T9026; RRID:AB_477593 |
| Wip1 | Santa Cruz Biotechnology | Cat#sc-376257; RRID:AB_10986000 |
| goat anti-mouse IgG, HRP linked | Biorad | Cat#1721011; RRID:AB_11125936 |
| goat anti-rabbit IgG, HRP linked | Biorad | Cat#1706515; RRID:AB_11125142 |
| horse anti-mouse IgG, HRP linked | Cell Signaling Technology | Cat#7076; RRID:AB_330924 |
| goat anti-rabbit IgG, HRP linked | Cell Signaling Technology | Cat#7074; RRID:AB_2099233 |
| Normal Rabbit IgG | Cell Signaling Technology | Cat#2729; RRID:AB_591709 |
| Normal Mouse IgG | Santa Cruz Biotechnology | Cat#sc-2025; RRID:AB_737182 |
| Rabbit anti-Mouse IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | ThermoFisher Scientific | Cat#A-11059; RRID:AB_142495 |
|
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| Bacterial and virus strains | ||
|
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| NEB Stable Competent E. coli (High Efficiency) | New England Biolabs Inc. | Cat#C3040 |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Annexin V, FITC | Life Technologies | Cat#A13199 |
| Anti-FLAG M2 Magnetic Beads | Sigma-Aldrich | Cat#M8823 |
| Doxycycline hyclate, 98% | ThermoFisher Scientific | Cat#446060050 |
| Dynabeads Protein G | ThermoFisher Scientific | Cat#10004D |
| Mouse IgG-Agarose | Sigma-Aldrich | Cat#A0919 |
| Nutlin | Cayman Chemicals | Cat#10004372 |
| 5-Fluorouracil | Sigma Aldrich | Cat#F6627 |
| Cycloheximide | EMD Millipore | Cat#239763 |
| Carfilzomib (PR-171) | Selleck Chemicals | Cat#S2853 |
| PreScission Protease | Cytiva | Cat#27-0843-01 |
| ProTEV Plus | Promega | Cat#V6101 |
| Thiazolyl Blue Tetrazolium Bromide | Sigma-Aldrich | Cat#M5655 |
| cOmplete Mini | Roche | Cat#11836153001 |
| Aprotinin | Gold Biotechnology | Cat#A-655-25 |
| Trypsin Inhibitor | MP Biomedicals | Cat#101113 |
| Leupeptin hemisulfate | Research Products International | Cat#L22035 |
| Pepstatin | BioReagents | Cat#BP267125 |
| Sodium fluoride | Mallinckrodt Chemicals | Cat#7636-04 |
| Sodium orthovanadate | Sigma-Aldrich | Cat#S6508 |
| DAPI | Sigma-Aldrich | Cat#D9542 |
| Molecular Probes ProLong Gold Antifade Mountant | ThermoFisher Scientific | Cat#P36934 |
| Lipofectamine 3000 Transfection Reagent | ThermoFisher Scientific | Cat#L3000008 |
| Polyethylenimine Linear, MW 25000 | Polysciences | Cat#23966 |
| Alt-R S.p. Cas9 Nuclease V3 | Integrated DNA Technologies Inc. | Cat#1081058 |
|
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| Critical commercial assays | ||
|
| ||
| TRI Reagent™ Solution | Invitrogen | Cat#AM9738 |
| DNeasy Blood and Tissue Kit | Qiagen | Cat#69506 |
| Agilent RNA 6000 Pico Kit | Agilent Technologies, Inc. | Cat#5067-1513 |
| Agilent High Sensitivity DNA Kit | Agilent Technologies, Inc. | Cat#5067-4626 |
| SYBR Select Master Mix for CFX | ThermoFisher Scientific | Cat#4472954 |
| HaloTag Mammalian Pull-Down System | Promega | Cat#G6504 |
| TOPO™ TA Cloning™ Kit for Sequencing | Invitrogen | Cat#K457501SC |
| CloneJET PCR Cloning Kit | Thermo Scientific | Cat#K1231 |
| SF Cell Line 4D-Nucleofector X Kit S | Lonza | Cat#V4XC-2032 |
|
| ||
| Deposited data | ||
|
| ||
| CHP212 FAM193A WT/KO RNA-seq (GSE189133) | Gene Expression Omnibus | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189133 |
| CRISPR Screen (GSE189132) | Gene Expression Omnibus | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189132 |
|
| ||
| Experimental models: Cell lines | ||
|
| ||
| CHP212 | ATCC | Cat#CRL-2273; RRID:CVCL_1125 |
| A549 | CU Anschutz Cell Technologies Shared Resource | Cat#CVCL_0023; RRID:CVCL_0023 |
| HCT116 | CU Anschutz Cell Technologies Shared Resource | Cat#CVCL_0291; RRID:CVCL_0291 |
| MCF7 | CU Anschutz Cell Technologies Shared Resource | Cat#CVCL_0031; RID:CVCL_0031 |
| SJSA | CU Anschutz Cell Technologies Shared Resource | Cat#CVCL_1697; RRID:CVCL_1697 |
| HEK293FT | ATCC | Cat#CRL-3249; RRID:CVCL_6911 |
| H4 | ATCC | Cat#HTB-148; RRID:CVCL_1239 |
| 94T778 | ATCC | Cat#CRL-3044; RRID:CVCL_U613 |
|
| ||
| Oligonucleotides | ||
|
| ||
| For RT-qPCR primers, see Table S6. | Integrated DNA Technologies Inc. | N/A |
| For ChIP-qPCR primers, see Table S7. | Integrated DNA Technologies Inc. | N/A |
| For primers used in CRISPR screen, see Table S8. | Integrated DNA Technologies Inc. | N/A |
| For primers/oligonucleotides used for knockout cell line generation/genotyping, see Table S9. | Integrated DNA Technologies Inc. | N/A |
| For primers used for cloning and mutagenesis, see Table S10. | Integrated DNA Technologies Inc. | N/A |
|
| ||
| Recombinant DNA | ||
|
| ||
| pSpCas9(BB)-2A-GFP (PX458) | Addgene (deposited by Feng Zhang) | Cat#48138; RRID:Addgene_48138 |
| pSpCas9(BB)-2A-GFP (PX458)- HGLibA_16363 (encoding sgRNA sequence targeting FAM193A: TCAGAGCAACTTGCCCGCAC) | This paper | N/A |
| pSpCas9(BB)-2A-GFP (PX458)- HGLibA_16364 (encoding sgRNA sequence targeting FAM193A: TATGCAGTTCCCACGTCACT) | This paper | N/A |
| pSpCas9(BB)-2A-GFP (PX458)- HGLibB_16341(encoding sgRNA sequence targeting FAM193A: CGAGCTTGCAGATGACACAC) | This paper | N/A |
| pSpCas9(BB)-2A-GFP (PX458)- HGLibA_64384/HGLibB_57029 (encoding control non-targeting sgRNA sequence: ACGGAGGCTAAGCGTCGCAA) | This paper | N/A |
| pENTR4-FLAG (w210-2) | Addgene (Eric Campeau, Paul Kaufman) | Cat#17423; RRID:Addgene_17423 |
| pLenti CMV TetR Blast (716-1) | Addgene (deposited by Eric Campeau, Paul Kaufman) | Cat#17492; RRID:Addgene_17492 |
| pLenti CMV/TO Puro DEST (670-1) | Addgene (deposited by Eric Campeau, Paul Kaufman) | Cat#17293; RRID:Addgene_17293 |
| pDEST-CMV-polysite | Addgene (deposited by Robin Ketteler) | Cat#122843; RRID:Addgene_122843 |
| pENTR4-HaloTag (w876-1) | Addgene | Cat#29644; RRID:Addgene_29644 |
| psPAX2 | Addgene (deposited by Didier Trono) | Cat#12260; RRID:Addgene_12260 |
| pMD2.G | Addgene (deposited by Didier Trono) | Cat#12259; RRID:Addgene_12259 |
| Human CRISPR Knockout Pooled Library (GeCKO v2) | Addgene (deposited by Feng Zhang) | Cat#1000000048 |
| pLenti-CMV/TO-3xFLAG-FAM193A-Puro | This paper | N/A |
| pDEST-CMV-Halo-FAM193A-polysite | This paper | N/A |
| pDEST-CMV-Halo-FAM193A-fragment 1 (1–250)-polysite | This paper | N/A |
| pDEST-CMV-Halo-FAM193A-fragment 2 (251–566)-polysite | This paper | N/A |
| pDEST-CMV-Halo-FAM193A-fragment 3 (567–882)-polysite | This paper | N/A |
| pDEST-CMV-Halo-FAM193A-fragment 4 (883–1203)-polysite | This paper | N/A |
| pDEST-CMV-Halo-FAM193A-fragment 5 (1199–1515)-polysite | This paper | N/A |
| pcDNA3.1-CMV-MDM4c3 | Jiandong Chen laboratory | PMID: 27114532 PMCID: PMC4868482 |
| pcDNA3.1-CMV-MDM4c3-deltaC | This paper | N/A |
| pcDNA3.1-CMV-MDM4c3-C463A | This paper | N/A |
| pLX304-MDM4-V5 | CCSB-Broad Lentiviral Expression Collection | Cat#ccsbBroad304_00993 |
|
| ||
| Software and algorithms | ||
|
| ||
| R Studio (v1.4.1106) with R (v4.1.0) | RStudio, PBC | N/A |
| FlowJo (v10.7.2) | Becton, Dickinson & Company | N/A |
| GSEA software (v 4.1.0) | Broad Institute | N/A |
| Ingenuity Pathway Analysis (v01-19-00) | Qiagen | N/A |
| bcl2fastq (v1.8.4) | Illumina | N/A |
| FASTQC (v0.11.2) | Originator: Simon Andrews of Babraham Bioinformatics | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| fastx_toolkit (v0.0.13.2) | Originator: Hannon lab | http://hannonlab.cshl.edu/fastx_toolkit/ |
| Bowtie2 (v2.2.3) | Originator: https://doi.org/10.1038/nmeth.1923 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| SAMtools (v0.1.19) | Originator: Heng Li | http://www.htslib.org/doc/samtools.html |
| FastQ Screen (v0.9.1) | Originator: Steven Wingett and Simon Andrews | https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/_build/html/index.html |
| fastq-mcf (v1.05) | EAutils | https://expressionanalysis.github.io/ea-utils/ |
| Picard tools (v2.9.4) | Broad Institute | https://broadinstitute.github.io/picard/ |
| HTSeq (v0.8.0) | Originator: Givanna Putri | https://htseq.readthedocs.io/en/master/ |
| RSeQC (v2.6.4) | Originator: SCINet project and Iowa State University | https://rseqc.sourceforge.net/ |
| DESeq2 (v1.18.1) | Originator: Michael Love et al. | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |