Key Resource Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| HA (Rabbit) | Cell Signaling Technology | Cat#3724; RRID: AB_1549585 |
| HA (Mouse) | Cell Signaling Technology | Cat#2367; RRID: AB_10691311 |
| SMARCA4 (D1Q7F) | Cell Signaling Technology | Cat#49360; RRID: AB_2728743 |
| SMARCC1 | Cell Signaling Technology | Cat#11956; RRID: AB_2797776 |
| SMARCC2 | Cell Signaling Technology | Cat#12760; RRID: AB_2798017 |
| ARID1A | Cell Signaling Technology | Cat# 12354, RRID:AB_2637010 |
| ARID1B | Cell Signaling Technology | Cat#65747; RRID: AB_2799694 |
| ARID1B | Abcam | Cat#ab57461; RRID: AB_2243092 |
| ARID2 | Cell Signaling Technology | Cat#82342; RRID: AB_2799992 |
| GLTSCR1 | Santa Cruz Biotechnology | Cat#sc-515086 |
| DPF2 | Santa Cruz Biotechnology | Cat#sc-514297 |
| SMARCD1 | Santa Cruz Biotechnology | Cat#sc-135843; RRID: AB_2192137 |
| SMARCE1 | Bethyl Laboratories | Cat#A300-810A; RRID: AB_577243 |
| GAPDH | Santa Cruz Biotechnology | Cat#sc-365062; RRID: AB_10847862 |
| SMARCA4 | Santa Cruz Biotechnology | Cat#sc-17796; RRID: AB_ 626762 |
| SMARCA4 | Cell Signaling Technology | Cat#72182; RRID:AB_2799815 |
| SMARCC1 | Santa Cruz Biotechnology | Cat#sc-137138; RRID: AB_ 2191994 |
| SMARCB1 | Santa Cruz Biotechnology | Cat#sc-166165; RRID: AB_2270651 |
| H3K27ac | Cell Signaling Technology | Cat#8173; RRID: AB_10949503 |
| p300 | Cell Signaling Technology | Cat#86377; RRID: AB_2800077 |
| MED1 | Cell Signaling Technology | Cat#51613; RRID: AB_2799397 |
| MED26 | Cell Signaling Technology | Cat#14950; RRID: AB_2798656 |
| BRD4 | Cell Signaling Technology | Cat#13440; RRID: AB_2687578 |
| RPB1 (CTD unmodified, YSPTSPS) | Santa Cruz Biotechnology | Cat# sc-56767, RRID:AB_785522 |
| RPB1 (Ser5 phospho) | Cell Signaling Technology | Cat#13523; RRID: AB_2798246 |
| TEAD1 | Cell Signaling Technology | Cat#12292; RRID: AB_2797873 |
| TEAD1 | Santa Cruz Biotechnology | Cat#sc-393976; RRID: AB_2721186 |
| NFIA | Cell Signaling Technology | Cat#69375 |
| NFIA | Santa Cruz Biotechnology | Cat#sc-74444; RRID: AB_2153048 |
| cJUN | Cell Signaling Technology | Cat#9165; RRID: AB_2130165 |
| cJUN | Santa Cruz Biotechnology | Cat#sc-74543; RRID: AB_1121646 |
| IR800-Streptavidin | LI-COR Biosciences | Cat#926-32230 |
| IR680 anti-mouse secondary | LI-COR Biosciences | Cat#926-68070; RRID: AB_10956588 |
| IR680 anti-rabbit secondary | LI-COR Biosciences | Cat#926-32211; RRID: AB_621843 |
| Goat anti-rabbit highly cross-adsorbed 568-conjugated antibody | ThermoFisher | Cat#A-11036; RRID: AB_10563566 |
| Guinea Pig anti-Rabbit IgG (Heavy & Light Chain) antibody | Antibodies-Online | Cat#ABIN101961; RRID: AB_10775589 |
| Bacterial and virus strains | ||
| One Shot™ Stbl3™ Chemically Competent E. coli | ThermoFisher | Cat#C737303 |
| NEB® Turbo Competent E. coli (High Efficiency) | New England Biolabs | Cat#C2984H |
| Rosetta (DE3) competent cells | Novagen | Cat#70954 |
| Chemicals, peptides, and recombinant proteins | ||
| GST-tagged ARID domain WT | This study | |
| GST-tagged ARID domain DBDmut | This study | |
| Blasticidin S HCl | ThermoFisher | Cat#R21001 |
| Puromycin dihydrochloride | Sigma-Aldrich | Cat#P8833-25MG |
| Doxycycline (hyclate) | Cayman Chemical | Cat#14422 |
| Carbenecillin disodium | Gold Bio | Cat#C-103-5 |
| Chloramphenicol | Gold Bio | Cat#C-105-5 |
| TURBO DNase I | ThermoFisher | Cat#AM2238 |
| Tn5 transposase | Illumina | Cat#20034198 |
| EpiDyne Nucleosome Remodeling Assay Substrate ST601-GATC1, 50-N-66, Biotinylated | Epicypher | Cat#16-4114 |
| HeLa Polynucleosomes, purified | Epicypher | Cat#16-0003 |
| Biomag Plus Concanavalin A (ConA) magnetic beads | Polysciences | Cat#86057-3 |
| CUTANA pAG-Tn5 | Epicypher | Cat#15-1117 |
| CUTANA pAG-MNase | Epicypher | Cat#15-1116 |
| DpnII restriction enzyme | New England Biolabs | Cat#R0543S |
| Recombinant Proteinase K Solution (20mg/mL) | ThermoFisher | Cat#AM2546 |
| Magnetic Streptavidin beads | ThermoFisher | Cat#88817 |
| Protein G Dynabeads | ThermoFisher | Cat#10004D |
| Pierce Anti-HA Magnetic Beads | ThermoFisher | Cat#88837 |
| Critical commercial assays | ||
| NextSeq 500/550 High Output Kit v2.5 (75 Cycles) | Illumina | Cat#20024906 |
| NEBNext® Ultra™ II RNA Library Prep Kit for Illumina | New England Biolabs | Cat#E7770L |
| CUTANA CUT&RUN Library Prep Kit | Epicypher | Cat#14-1001 |
| MinElute Reaction Cleanup Kit | Qiagen | Cat#28206 |
| ADP-Glo Max Assay | Promega | Cat#V7001 |
| BCA Protein Assay Kit | ThermoFisher | Cat#23225 |
| SilverQuest Silver Staining Kit | ThermoFisher | Cat#LC6070 |
| Pierce High pH Reversed-Phase Peptide Fractionation Kit | ThermoFisher | Cat#84868 |
| TMTpro 16plex Label Reagent Set | ThermoFisher | Cat#A44520 |
| Protein Qubit | ThermoFisher | Cat#Q33212 |
| Deposited data | ||
| All AN3CA CUT&Tag, CUT&RUN, ATAC and RNA-Seq data | This study | GEO: GSE209961 |
| Experimental models: Cell lines | ||
| HEK293T ΔARID1A/B | Mashtalir et al.,21 | |
| U2OS | ATCC | Cat#HTB-96; RRID: CVCL_0042 |
| AN3CA | ATCC | Cat#HTB-111; RRID: CVCL_0028 |
| MDA-MB-231 | ATCC | Cat#HTB-26; RRID: CVCL_0062 |
| KLE | ATCC | Cat#CRL-1622; RRID: CVCL_1329 |
| C2C12 | ATCC | Cat#CRL-1772; RRID: CVCL_0188 |
| CRL-7250 | ATCC | Cat#CRL-7250, discontinued; RRID: CVCL_N613 |
| MCF10A | ATCC | Cat#CRL-10317; RRID: CVCL_0598 |
| MCF10-CA | Santner et al.,76 | |
| Primary rat neurons | This study | |
| Recombinant DNA | ||
| piggybac-ARID1A WT | This study | |
| piggybac-ARID1A DBDmut | This study | |
| piggybac-ARID1A ΔIDR1 | This study | |
| piggybac-ARID1A CBR | This study | |
| piggybac-ARID1A WT-eGFP | This study | |
| piggybac-ARID1A DBDmut-eGFP | This study | |
| piggybac-ARID1A ΔIDR1-eGFP | This study | |
| piggybac-ARID1A CBR-eGFP | This study | |
| piggybac-ARID1B WT-eGFP | This study | |
| piggybac-ARID1B DBDmut-eGFP | This study | |
| piggybac-Empty Vector | This study | |
| piggybac-ARID1A WT-TbID | This study | |
| piggybac-ARID1A DBDmut-TbID | This study | |
| piggybac-ARID1A ΔIDR1-TbID | This study | |
| piggybac-ARID1A CBR-TbID | This study | |
| piggybac-FUS IDR-ARID1A | This study | |
| piggybac-DDX4 IDR-ARID1A | This study | |
| piggybac-FUS IDR-ARID1A-eGFP | This study | |
| piggybac-DDX4 IDR-ARID1A-eGFP | This study | |
| piggybac-FUS IDR-ARID1A-TbID | This study | |
| piggybac-ARID1A 42YS | This study | |
| piggybac-ARID1A AQGscram | This study | |
| piggybac-ARID1A 42YS-eGFP | This study | |
| piggybac-ARID1A AQGscram-eGFP | This study | |
| piggybac-ARID1A 42YS-TbID | This study | |
| piggybac-ARID1A AQGscram-TbID | This study | |
| piggybac-ARID1B-WT | This study | |
| piggybac-ARID1B-Block 9 del | This study | |
| piggybac-ARID1B-Block 13 del | This study | |
| piggybac-ARID1B-S320_G327del | This study | |
| piggybac-ARID1B-A457_G461del | This study | |
| piggybac-ARID1B-Block 9 del-eGFP | This study | |
| piggybac-ARID1B-Block 13 del-eGFP | This study | |
| piggybac-ARID1B-S320_G327del-eGFP | This study | |
| piggybac-ARID1B-A457_G461del-eGFP | This study | |
| piggybac transposase | This study | |
| FM5-ARID1A IDR1 | This study | |
| FM5-ARID1A IDR2 | This study | |
| FM5-ARID1A N-term | This study | |
| FM5-ARID1A N-term DBDmut | This study | |
| FM5-ARID1B IDR1 | This study | |
| FM5-ARID1B IDR2 | This study | |
| FM5-ARID1B N-term | This study | |
| Software and algorithms | ||
| STAR v2.5.2b | Dobin et al.,77 | |
| deepTools v2.5.3 | Ramirez et al.,78 | |
| BEDTools | Quinlan et al79 | |
| edgeR v3.12.1 | Dobin et al.,77 Love et al.,80 | |
| Trimmomatic v0.36 | Bolger et al.,81 | |
| Bowtie2 | Langmead et al.,82 | |
| Picard v2.8.0 | Broad Institute | |
| SAMtools v 0.1.19 | Li et al.,83 | |
| MACS2 v2.1 | Zhnag et al.,84 | |
| CutRunTools | Zhu et al.,85 | |
| ngsplot v2.63 | Shen et al.,86 | |
| corpcor R package | Schafer et al.,87 Opgen-Rhein et al.,88 | |
| HOMER v4.9 | Heinz et al.,89 | |
| Integrative Genomics Viewer (IGV) | Broad Institute | |
| Geneious Prime v2023.0.4 | Geneious | |
| NARDINI | Cohan et al.,6 | |
| localCIDER | Holehouse et al.,7 | |
| FIJI | Schindelin et al90 | |
| Other | ||
| Lipofectamine 3000 | ThermoFisher | Cat#L3000015 |
| 0.2μM Nitrocellulose membrane | Biorad | Cat#1620112 |
| HA peptide | GenScript | Cat#RP11735 |
| DS1000 High Sensitivity DNA ScreenTape | Agilent | Cat#5067-5582 |
| Agencourt AMPure XP Beads | Beckman Coulter | Cat#A63881 |