KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse Anti-SMARCA4 (BRG1) (G-7) (WB) | Santa Cruz | Cat# sc-17796; RRID: AB_626762 |
| Rabbit Anti-SMARCA4 (BRG1) (D1Q7F) (IP) | Cell Signaling Technology | Cat# 49360S |
| Rabbit Anti-BCL7C (human) | This study | N/A |
| Mouse Anti-INI1 (BAF47) (A-5) (WB) | Santa Cruz | Cat# sc-166165; RRID: AB_2270651 |
| Rabbit Anti-SMARCC1 (H-76) (WB) | Santa Cruz | Cat# sc-10756; RRID: AB_2191997 |
| Rabbit Anti-SMARCC1 D7F8S (155–7) (IP) | Cell Signaling Technology | Cat# 11956S |
| Rabbit Anti-SS18 (D6I4Z) (IP) | Cell Signaling Technology | Cat# 21792S |
| Mouse Anti-ARID1A (BAF250A) (C-7) (WB) | Santa Cruz | Cat# sc-373784; RRID: AB_10917727 |
| Rabbit Anti-ARID1A D2A8U (IP) | Cell Signaling Technology | Cat# 12354S; RRID: AB_2637010 |
| Mouse Anti-ARID2 (BAF200) (E-3) (IB) | Santa Cruz | Cat# sc-166117; RRID: AB_2060382 |
| Rabbit Anti-DPF2 (WB) | Abcam | Cat# ab134942; RRID: AB_2728668 |
| Rabbit Anti-SMARCE1 (WP) | Bethyl | Cat# A300–810A; RRID: AB_577243 |
| Mouse Anti-SMARCD1 23 (WB) | Santa Cruz | Cat# sc-135843; RRID: AB_2192137 |
| Mouse Anti-SS18 A10 (WB) | Santa Cruz | Cat# sc-365170; RRID: AB_10709584 |
| Mouse Anti-GAPDH (G-9) (WB) | Santa Cruz | Cat# sc-365062; RRID: AB_10847862 |
| Mouse Anti-V5 tag (WB) | Thermo Fisher Scientific | Cat# R960–25; RRID: AB_2556564 |
| Rabbit Anti-V5 tag (D3H8Q) (IP) | Cell Signaling Technology | Cat# 13202S |
| Normal Rabbit IgG (IP) | Cell Signaling Technology | Cat# 2729S; RRID: AB_1031062 |
| Rabbit Anti-Actl6A (WB) | Bnvirogreethyl | Cat# A301–391A; RRID: AB_1309569 |
| Rabbit Anti-PBRM1 (WB) | Millipore | Cat# ABE70; RRID: AB_10807561 |
| Mouse Anti-BRD7 B-8 (WB) | Santa Cruz | Cat# sc-376180; RRID: AB_10989389 |
| Mouse Anti-GLTSCR1 (H-10)(IB) | Santa Cruz | Cat# sc-515086 |
| Rabbit Anti-BRD9 (WB) | Abcam | Cat# ab137245 |
| Rabbit Anti-ARID1B (WB) | Abcam | Cat# ab84461; RRID: AB_1859798 |
| Rabbit Anti-HA (C29F4) (WB) | Cell Signaling Technology | Cat# 3724S; RRID: AB_1549585 |
| Mouse Anti-Ubiquitin (P4D1) (WB) | Santa Cruz | Cat# sc-8017; RRID: AB_628423 |
| Rabbit Anti-SMARCA4 (D1Q7F) (WB) | Cell Signaling Technology | Cat# 49360S |
| IRDye 680RD Goat anti-Rabbit IgG (H + L) | Li-Cor Biosciences | Cat# 925–68071; RRID: AB_2721181 |
| IRDye 800CW Donkey anti-Mouse IgG (H + L) | Li-Cor Biosciences | Cat# 925–32212; RRID: AB_2716622 |
| Bacterial and Virus Strains | ||
| One-Shot Stbl 3 chemically competent cells | Invitrogen | Cat# C7373–03 |
| One Shot T0P10 Chemically Competent E. coli | Thermos Fisher Scientific | Cat#C4040–06 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Puromycin | Sigma-Aldrich | Cat# P8833–25MG |
| Blasticidin | Life Technologies | Cat# R210–01 |
| Dimethyl sulfoxide | Sigma-Aldrich | Cat# D2650 |
| DMEM, high glucose, no glutamine | Life Technologies | Cat# 11960–069 |
| IRDye 680RD NHS Ester | Li-Cor | Cat# 929–70050 |
| Hygromycin B (50 mg/mL) | Thermos Fisher Scientific | Cat# 10687010 |
| HA peptide synthetic | GenScript | NA |
| PBS, pH 7.4 | Life Technologies | Cat# 10010–049 |
| GlutaMAX | Life Technologies | Cat# 35050–079 |
| Trypsin-EDTA (0.25%), phenol red | Life Technologies | Cat# 25200–114 |
| Sodium Pyruvate | Life Technologies | Cat# 11360–070 |
| Penicillin-Streptomycin | Life Technologies | Cat# 15140–163 |
| Polybrene | Santa Cruz Biotechnology | Cat# sc-134220 |
| Cycloheximide | Sigma-Aldrich | Cat# C7698–5G |
| Polyethylenimine (PEI) (MW 40,000) | Polysciences | Cat# 24765 |
| Goat Anti-Mouse IgG Antibody, IRDye 680RD Conjugated | LI-COR Biosciences | Cat# 926–68070 |
| Goat Anti-Rabbit IgG Antibody, IRDye 800CW Conjugated | LI-COR Biosciences | Cat# 926–32211 |
| Dynabeads Protein G | Thermo Fisher Scientific | Cat# 10004D |
| NuPage LDS Sample Buffer (4X) | Life Technologies | Cat# NP0007 |
| Effectene Transfection Reagent | QIAGEN | Cat# 301425 |
| StrataClean Resin | Agilent Technologies | Cat# 400714 |
| Pierce Anti-HA Magnetic Beads | Thermo Fisher Scientific | Cat# 88837 |
| NuPAGE Novex 4–12% Bis-Tris Gel 1.0 mm, 12 well | Thermo Fisher Scientific | Cat# NP0322 |
| SFX-Insect media | GE Healthcare | Cat# SH30278.LS |
| QIAamp DNA Mini Kit | QIAGEN | Cat# 51304 |
| MG132 | Sigma | Cat# 1211877–36-9 |
| Lipofectamine 3000 Transfection Reagent | Thermo Fisher Scientific | Cat# 13778030 |
| Effectene Transfection Reagent | QIAGEN | Cat# 301425 |
| BS3 (bis(sulfosuccinimidyl)suberate), No-Weigh Format | Thermo Fisher Scientific | Cat# 21585 |
| Critical Commercial Assays | ||
| pENTR/D-TOPO Cloning Kit | Thermos Fisher Scientific | Cat# K240020 |
| SilverQuest Silver Staining Kit | Thermo Fisher Scientific | Cat# LC6070 |
| Invitrogen Novex Colloidal Blue Staining Kit | Thermos Fisher Scientific | Cat# LC6025 |
| Deposited Data | ||
| All raw cross-linking mass spectrometry data PRIDE access numbers: PXD010122 (BAF), PXD010123 (BAF), PXD010124 (Fly PBAP) | This paper | http://www.proteomexchange.org/ |
| Visualization of cross-linking mass spectrometry data | This paper | https://www.yeastrc.org/proxl_public/viewProject.do?project_id=127 |
| Experimental Models: Cell Lines | ||
| Drosophila S2 cells | Thermo Fisher | Cat # R690-07 |
| Human: HEK293T LentiX (Female) | Clonetech | Cat# 632180 |
| Human: SW13 (Female) | ATCC | Cat# CCL-105 |
| Human: MIA-PA-Ca-2(Male) | ATCC | Cat# CRL-1420 |
| Recombinant DNA | ||
| EF-1a-MCS-PGK-Blast-HA-SMARCD1 | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-SMARCD2 | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-SMARCC1 | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-SMARCB1 | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-SMARCE1 | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-DPF2 | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-BRD7 | This study | N/A |
| EF-1a-MCS-PGK-Blast- HA-ARID1A-C-term Y2254* | This study | N/A |
| EF-1a-MCS-PGK-Blast- HA-ARID1A-C-term G2087N | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-ARID1A-C-term | This study | N/A |
| EF-1a-MCS-PGK-Blast-BCL7A-HA | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-mARID2 | This study | N/A |
| EF-1a-MCS-PGK-Blast- HA-PBRM1 | This study | N/A |
| pMSCV-Flag-HA-IRES-Puro-SS18 | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-GLRSCR1L | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-BRD9 | This study | N/A |
| EF-1a-MCS-PGK-Blast-HA-PHF10 | This study | N/A |
| EF-1a-MCS-PGK-Blast-V5-PBRM1 | This study | N/A |
| EF-1a-MCS-PGK-Blast-V5-PBRM1 Δ BAH1 | This study | N/A |
| EF-1a-MCS-PGK-Blast-GFP-PBRM1 | This study | N/A |
| pMT-Puro HA-D4 | This study | N/A |
| pMCFHBD BAP60-Flag-HA | DGRC | N/A |
| BAF57 CRISPR/Cas9 KO Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-404713 |
| Ini1 CRISPR/Cas9 KO Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-401485 |
| ARID1A CRISPR/Cas9 KO Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-400469 |
| ARID1B CRISPR/Cas9 KO Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-402365 |
| Brm CRISPR/Cas9 KO Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-401049-K0–2 |
| BAF155 CRISPR/Cas9 KO Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-400838 |
| BAF170 Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-402023-NIC |
| BAF60A CRISPR/Cas9 KO Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-402641 |
| BAF60B Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-403091-NIC |
| BAF60C CRISPR/Cas9 KO Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-402707 |
| BRG-1 Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-400168-NIC |
| BRD7 Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-416299-NIC |
| ARID2 Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-401863-NIC |
| PBRM1 Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-403988-NIC |
| SS18 Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-401575-NIC |
| CREST Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-403134-NIC-2 |
| BRD9 Double Nickase Plasmid (h) | Santa Cruz Biotechnology | Cat#sc-404933-NIC |
| Software and Algorithms | ||
| MacPyMOL | Schrodinger | https://pymol.org/2/ |
| Seaborns | Seaborns/Michael Waskom | https://seaborn.pydata.org/index.html |
| Matplotlib | Matplotlib V2.3.3/ John Hunter and colleagues | https://matplotlib.org/ |
| Circos 0.69–6 | Circos | http://circos.ca/software/download/circos/ |
| ShareLaTeX | Overleaf/ShareLaTeX | https://v2.overleaf.com/project |
| GeneiousR9 | Geneious/Biomatters Limited | https://www.geneious.com/ |
| Nexus | Ranish Laboratory (Institute for Systems Biology) | https://systemsbiology.org/people/labs/ranish-lab/ [Select: Nexus] |