KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Alexa Fluor 647 mouse anti-human HLA-DR, DP, DQ antibody | BioLegend | Cat# 361704, clone Tü39, RRID: AB 2563169 |
| Alexa Fluor 488 mouse anti-human HLA-DR antibody | BioLegend | Cat# 307620, clone L243, RRID: AB 493175 |
| Brilliant Violet 510 mouse anti-human HLA-DR antibody | BioLegend | Cat# 307646, clone L243, RRID: AB 2561948 |
| Alexa Fluor 488 mouse anti-human HLA-A,B,C | BioLegend | Cat# 311413, clone W6/32; RRID: AB 493133 |
| Alexa Fluor 647 rat anti-mouse I-A/I-E antibody | BioLegend | Cat# 107618, clone M5/114.15.2, RRID: AB 493525 |
| Alexa Fluor 647 mouse anti-mouse H-2Kb antibody | BioLegend | Cat# 116512, clone AF6-88.5, RRID: AB 492917 |
| Brilliant Violet 510 mouse anti-human CD3 antibody | BioLegend | Cat# 300448, clone UCHT1, RRID: AB 2563468 |
| Brilliant Violet 605 mouse anti-human CD4 antibody | BioLegend | Cat# 317438, clone OKT4, RRID: AB 11218995 |
| BUV737 mouse anti-human CD8 antibody | BD Biosciences | Cat# 612754, clone SK1, RRID: AB 2870085 |
| PE anti-human CD45RO antibody | BioLegend | Cat# 304206, clone UCHL1, RRID: AB 314422 |
| Pacific Blue anti-human CD62L antibody | BioLegend | Cat# 304826, clone DREG-56, RRID: AB 2186977 |
| PE/Cyanine7 rat anti-mouse CD3 antibody | BioLegend | Cat# 100220, clone 17A2, RRID: AB 1732057 |
| BV650 rat anti-mouse CD4 antibody | BD Biosciences | Cat# 563232, clone GK1.5, RRID: AB 2738083 |
| PE rat anti-mouse CD8a antibody | BioLegend | Cat# 100708, clone 53 6.7, RRID: AB 312747 |
| CD3 monoclonal antibody (OKT3), functional grade | eBioscience | Cat# 16-0037-81, RRID: AB 468854 |
| CD28 monoclonal antibody (CD28.2), functional grade | eBioscience | Cat# 16-0289-81, RRID: AB 468926 |
| Purified rat anti-mouse CD16/32 antibody | BioLegend | Cat# 101302, clone 93, RRID: AB 312801 |
| Monoclonal rabbit anti-H3K27me3 antibody | Cell Signaling Technology |
Cat# 9733S, clone C36B11; RRID: AB 2616029 |
| Monoclonal mouse anti-HSP60 antibody | Santa Cruz | Cat# sc-376240, clone C-10, RRID: AB 10986282 |
| Polyclonal rabbit anti-H3K9me2 antibody | Active Motif | Cat# 39239, RRID: AB 2793199 |
| Polyclonal rabbit anti-STAT1 antibody | Merck-Millipore | Cat# 06-501, RRID: AB 310145 |
| Monoclonal mouse anti-alpha tubulin antibody | Invitrogen | Cat# 62204, clone DM1A, RRID: AB 1965960 |
| Rabbit anti-CIITA antibody | Cell Signaling Technology |
Cat# 3793S, RRID: AB 2080109 |
| Monoclonal rabbit anti-GAPDH antibody | Cell Signaling Technology |
Cat# 2118S, clone 14C10, RRID: AB 561053 |
| Polyclonal rabbit anti-WIZ antibody | Novus Biologicals | Cat# NBP1-80586, RRID: AB 11011659 |
| Polyclonal rabbit anti-FBXO11 antibody | Novus Biologicals | Cat# NB100-59826, RRID: AB 892469 |
| Myc-Tag mouse monoclonal antibody | Cell Signaling Technology |
Cat# 2276S, clone 9B11, RRID: AB 331783 |
| HA-Tag rabbit monoclonal antibody | Cell Signaling Technology |
Cat# 3724S, clone C29F4, RRID: AB 1549585 |
| β-Actin mouse monoclonal antibody | Cell Signaling Technology |
Cat# 3700S, clone 8H10D10, RRID: AB 2242334 |
| Anti-rabbit IgG (H+L), F(ab’)2 Fragment (PE conjugate) | Cell Signaling Technology |
Cat# 79408S, RRID: AB 2799931 |
| Anti-mouse IgG (H+L), F(ab’)2 Fragment (Alexa Fluor® 647 Conjugate) | Cell Signaling Technology |
Cat# 4410S, RRID: AB 1904023 |
| Anti-ubiquitin HRP-conjugated mouse monoclonal, VU-1 antibody | LifeSensors | Cat# VU101H, RRID: AB 2716558 |
| Secondary goat anti-mouse human ads-HRP | SouthernBiotech | Cat# 1010-05, RRID: AB 2728714 |
| Secondary goat anti-rabbit IgG (H+L) mouse/human ads-HRP | SouthernBiotech | Cat# 4050-05, RRID: AB 2795955 |
| Rabbit IgG, polyclonal – isotype control (ChIP Grade) | Abcam | Cat# ab171870, RRID: AB 2687657 |
| TotalSeq-C0251 anti-human Hashtag 1 antibody | BioLegend | Cat# 394661, RRID: AB 2801031 |
| TotalSeq-C0252 anti-human Hashtag 2 antibody | BioLegend | Cat# 394663, RRID: AB 2801032 |
| TotalSeq-C0253 anti-human Hashtag 3 antibody | BioLegend | Cat# 394665, RRID: AB 2801033 |
| TotalSeq-C0254 anti-human Hashtag 4 antibody | BioLegend | Cat# 394667, RRID: AB 2801034 |
| Bacterial and virus strains | ||
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| EPZ011989 (EZH2 inhibitor) | Selleck Chemicals | Cat# S8075, CAS No. 2095432-26-9 |
| A-366 (EHMT1/2 inhibitor) | Selleck Chemicals | Cat# S7572, CAS No. 1527503-11-2 |
| UNC0638 (EHMT1/2 inhibitor) | Selleck Chemicals | Cat# S8071, CAS No. 1255580-76-7 |
| Recombinant human interferon gamma | Sigma-Aldrich | Cat# SRP3058 |
| Recombinant mouse interferon gamma | Abcam | Cat# ab123747 |
| Recombinant human interleukin-2 | NIH | Cat# Ro 23-6019 |
| Recombinant mouse interleukin-3 | Peprotech | Cat# 213-13 |
| Recombinant human interleukin-6 | Peprotech | Cat# 200-06 |
| Recombinant murine SCF | Peprotech | Cat# 250-03 |
| SIINFEKL (OVA peptide 257-264) | Sigma-Aldrich | Cat# S7951, CAS No 138831-86-4 |
| OVA peptide (323-339) | GenScript | Cat# RP10610 |
| MG-132 | MedChemExpress | Cat#HY-13259 |
| Phenylmethylsulfonyl fluoride (PMSF) | Sigma-Aldrich | Cat#11359061001 |
| Iodoacetamide (IAA) | Sigma-Aldrich | Cat#I6125 |
| Sodium dodecyl sulfate (SDS) | Sigma-Aldrich | Cat#L3771 |
| PR-619 (DUB inhibitor) | Sigma-Aldrich | Cat#SML0430 |
| cOmplete, EDTA free, protease inhibitor | Roche | Cat#05056489001 |
| NP-40 Surface-Amps Detergent Solution | Thermo Fisher | Cat#85124 |
| Dynabeads Protein A | Thermo Fisher | Cat#10002D |
| Critical commercial assays | ||
| Cytometric Bead Array Mouse Th1/Th2 Cytokine Kit | BD Biosciences | Cat# 551287 |
| EasySep Human CD4+ T Cell Isolation Kit | STEMCELL Technologies | Cat# 17952 |
| eBioscience Transcription Factor Staining Buffer Set | Thermo Fisher Scientific | Cat# 00-5523-00 |
| Deposited data | ||
| ChIP-seq: MV4-11 | Göllner et al, 2017 | GEO: GSM1513828 |
| Sequencing data (CRISPR screen, RNA-seq, scRNA-seq, ChIP-seq, CUT&Tag) | This paper | GEO: GSE189773 |
| Mendeley data (unprocessed immunoblot images) | This paper | http://dx.doi.org/10.17632/j5gt4fv75f.1 |
| Experimental models: Cell lines | ||
| Human: MV4-11 | ATCC | Cat# CRL-9591, RRID: CVCL 0064 |
| Human: LM-MEL-53 | ATCC | Cat# CRL-3337, RRID: CVCL UC56 |
| Human: A375 | ATCC | Cat# CRL-1619, RRID: CVCL 0132 |
| Drosophila: S2 | ATCC | Cat# CRL-1963, RRID: CVCL Z232 |
| Human: MOLM13 | DSMZ | Cat# ACC 554, RRID: CVCL 2119 |
| Human: OCI-AML3 | DSMZ | Cat# ACC 582, RRID: CVCL 1844 |
| Human: WM852 | ESTDAB | Cat# ESTDAB-084, RRID: CVCL 6804 |
| Human: HEK293-ET | Felix Randow (MRC-LMB, Cambridge, UK) | RRID: CVCL 6996 |
| Experimental models: Organisms/strains | ||
| Mouse: B6.SJL-Ptprc<a>Pepc<b>/BoyJ | Animal Resources Centre, Western Australia |
|
| Mouse: C57BL/6-Tg(OT-I) | Joseph Trapani (Peter MacCallum Cancer Centre) | |
| Mouse: C57BL/6-Tg(OT-II) | Walter and Eliza Hall Institute | |
| Oligonucleotides | ||
| See Table S1 and Table S2. | ||
| Recombinant DNA | ||
| pHRSIN-PSFFV-Cas9-PPGK-Blasticidin | Burr et al, 2017 | |
| FUCas9Cherry | Aubrey et al, 2015 | Addgene:70182 |
| Bassik Human CRISPR Knockout Library | Morgens et al, 2017 | Addgene:101296-101934 |
| Human targeted epigenetic CRISPR library | This paper | |
| Mouse targeted epigenetic CRISPR library | Johannes Zuber (IMP, Vienna, Austria) | |
| pKLV-U6gRNA(BbsI)-PGKPuro2ABFP | Koike-Yusa et al, 2014 | Addgene:50946 |
| lentiGuide-Crimson | Canver et al, 2015 | Addgene: 70683 |
| pcDNA3 myc CIITA | Kanazawa et al, 2000 | Addgene: 14650 |
| pMSCV-CIITA-IRES-mCherry | This paper | |
| pMSCV-CIITA-IRES-GFP | This paper | |
| FLAG-HA-Fbxo11 -pcDNA3.1 - | Horn et al, 2014 | Addgene: 52501 |
| FLAG-HA-Fbxo11 -ΔFbox-pcDNA3.1 - | Horn et al, 2014 | Addgene: 52502 |
| pHRSIN-PSFFV-Fbxo11-PPGK-Puro | This paper | |
| pHRSIN-PSFFV-Fbxo11-ΔFbox-PPGK-Puro | This paper | |
| pcDNA3-OVA | Diebold et al, 2001 | Addgene: 64599 |
| pMSCV-OVA-IRES-GFP | This paper | |
| Software and algorithms | ||
| Fastx Clipper | Hannon Laboratory | http://hannonlab.cshl.edu/fastxtoolkit/ |
| Cutadapt | Martin, 2011 | https://cutadapt.readthedocs.io/en/stable/ |
| Trimmomatic | Bolger et al, 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Redundant siRNA activity (RSA) Algorithm | König et al, 2007 | https://admin-ext.gnf.org/publications/RSA/ |
| Bcl2fastq | Illumina | https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html |
| HiSAT2 | Kim et al, 2019 | http://www.ccb.jhu.edu/software/hisat/index.shtml |
| Htseq-count | Anders et al, 2014 | https://htseq.readthedocs.io/en/master/ |
| DESeq2 | Love et al, 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Picard | Broad Institute | https://broadinstitute.github.io/picard/ |
| MACS2 | Zhang et al, 2008 | https://github.com/taoliu/MACS |
| deepTools | Ramírez et al, 2014 | https://deeptools.readthedocs.io/en/develop/ |
| Samtools | Danecek et al, 2021 | http://www.htslib.org/ |
| igvtools | Broad Institute | https://software.broadinstitute.org/software/igv/igvtools |
| IGV | Robinson et al, 2011 | https://software.broadinstitute.org/software/igv/ |
| Seurat | Butler et al, 2018; Stuart et al, 2019 | https://satijalab.org/seurat/ |
| IDEAS | Amnis Corporation | https://www.luminexcorp.com/flowsight-imaging/#software |
| R Studio | RStudio Team (2022) | http://www.rstudio.com/ |
| Other | ||