| Antibodies |
| Rabbit anti-Pan-TEAD (D3F7L) |
Cell Signaling Technology |
Cat# 13295S |
| Mouse anti-TEAD4 |
Abcam |
Cat# ab58310 |
| Mouse anti-TEAD1 |
BD Biosciences |
Cat# 610922 |
| Mouse anti-BAF53A (ACTL6A)(5H3L6) |
Invitrogen |
Cat# 702414 |
| Mouse anti-ARID1A (PSG3) |
Santa Cruz Biotechnology |
Cat# sc-32761 |
| Rabbit anti-BAF57 (SMARCE1) |
Bethyl Laboratories |
Cat# A300-810A |
| Rabbit anti-Phospho-YAP (Ser127) (D9W2I) |
Cell Signaling Technology |
Cat# 13008 |
| Mouse anti-Brg1 (SMARCA4) (H-10) |
Santa Cruz Biotechnology |
Cat# sc-374197 X |
| Rabbit anti-INO80 |
Bethyl Laboratories |
Cat# A303-371A |
| Mouse anti-EZH2 |
BD Biosciences |
Cat# 612666 |
| Rabbit anti-GAPDH (D16H11) XP |
Cell Signaling Technology |
Cat# 5174S |
| Mouse anti-V5 tag |
Invitrogen |
Cat# R960-25 |
| Mouse IgG |
Santa Cruz Biotechnology |
Cat# sc-2025 |
| Rabbit IgG |
MilliporeSigma |
Cat# 12-370 |
| Mouse anti-YAP |
Abnova |
Cat# H00010413-M01 |
| Rabbit anti-BAF53A (ACTL6A) |
Novus Biologicals |
Cat# NB100-61628 |
| Mouse anti-FLAG (M2) |
Sigma-Aldrich |
Cat# F1804 |
| Donkey anti-mouse IgG |
Invitrogen |
Cat# A-21202 |
| Rabbit anti-TEAD1(D9X2L) |
Cell Signaling Technology |
Cat# 12292S |
| Rabbit anti-histone H3K4me1 |
Abcam |
Cat# ab8895 |
| Rabbit anti-histone H3K4me3 |
Active motif |
Cat# 39159 |
| Rabbit anti-histone H3K27me3 |
Cell Signaling Technology |
Cat# 9733 |
| Rabbit anti-histone H3K27Ac |
Abcam |
Cat# ab4729 |
| Rabbit anti-BAF53A (ACTL6A) |
The Crabtree laboratory |
N/A |
| Rabbit anti-Brg1/BRM (SMARCA4/SMARCA2) (J1) |
The Crabtree laboratory |
N/A |
| Rabbit anti-BAF155 (SMARCC1) |
The Crabtree laboratory |
N/A |
| Rabbit anti-YAP (D8H1X) XP |
Cell Signaling Technology |
Cat# 14074S |
| Bacterial and Virus Strains |
| One-Shot Stbl3 chemically competent E. coli
|
Invitrogen |
Cat# C7373-03 |
| BL21(DE3) Competent E.coli |
New England Biolabs |
Cat# C2527I |
| Rosetta 2(DE3) competent cells |
EMD Millipore |
Cat# 71397-3 |
| Chemicals, Peptides, and Recombinant Proteins |
| Polybrene |
Santa Cruz Biotechnology |
Cat# sc-134220 |
| Polyethylenimine Max (PEI MAX) (MW 40,000) |
Polysciences |
Cat# 24765 |
| Digitonin |
Millipore |
Cat# 300410-250MG |
| Digitonin |
Promega |
Cat# G9441 |
| Spermidine trihydrochloride |
Sigma-Aldrich |
Cat# S2501-1G |
| Benzonase Nuclease |
Sigma-Aldrich |
Cat# E1014-25KU |
| Amylose resin |
New England Biolabs |
Cat# E8021L |
| Glutathione-superflow resin |
Clontech |
Cat# 635608 |
| Glutathione reduced |
Sigma-Aldrich |
Cat# G-4251 |
| Dynabeads Protein A |
Thermo Fisher Scientific |
Cat# 10002D |
| 3X FLAG Peptide |
MilliporeSigma |
Cat# F4799-4MG |
| Dynabeads Protein G |
Thermo Fisher Scientific |
Cat# 10009D |
| Geltrex |
Thermo Fisher Scientific |
Cat# A1413302 |
| Transferrin |
Roche |
Cat# 10652202001 |
| EGF |
Thermo Fisher Scientific |
Cat# PHG0311 |
| Insulin |
Sigma-Aldrich |
Cat# I5500 |
| Forskolin |
Tocris Bioscience |
Cat# 1099 |
| VX-745 |
Tocris Bioscience |
Cat# 3915 |
| RO4929097 |
Cellagen Technology |
Cat# C7649 |
| Dexamethasone |
Tocris Bioscience |
Cat# 1126 |
| Penicillin-Streptomycin |
Thermo Fisher Scientific |
Cat# 15140-163 |
| Deoxyribonuclease I |
Worthington Biochemical Corporation |
Cat# LS002058
|
| TRIsure |
Bioline |
Cat# BIO-38033 |
| Plasmocin |
InvivoGen |
Cat# ant-mpp |
| Doxycycline |
Sigma-Aldrich |
Cat# D9891 |
| Fibronectin |
Sigma-Aldrich |
Cat# F1141-1MG |
| DharmaFECT 1 transfection reagent |
Horizon Discovery |
Cat# T-2001-01 |
| 5X siRNA Buffer |
Horizon Discovery |
Cat# B-002000-UB-100 |
| Puromycin dihydrochloride |
Sigma-Aldrich |
Cat# P8833-100mg |
| ON-TARGETplus |
Horizon Discovery |
Cat# L-008243-00 |
| Human ACTL6A siRNA |
|
|
| ON-TARGETplus Non-targeting Pool |
Horizon Discovery |
Cat# D-001810-10 |
| Blasticidin S HCl |
Thermo Fisher Scientific |
Cat# R21001
|
| Critical Commercial Assays |
| NEBNext Poly(A) mRNA Magnetic Isolation Module |
New England Biolabs |
Cat# E7490S |
| NEBNext MultiplexOligos for Illumina (Dual Index Primers Set 1) |
New England Biolabs |
Cat# E7600S |
| NEBNext High-Fidelity 2X PCR Master Mix |
New England Biolabs |
Cat# M0541S |
| Qubit dsDNA HS Assay Kit |
Thermo Fisher Scientific |
Cat# Q32854
|
| ZymoPURE II Plasmid Midiprep Kit |
Zymo Research |
Cat# D4200 |
| DNA Clean & Concentrator-5 |
Zymo Research |
Cat# D4013 |
| Direct-zol RNA Miniprep Kits |
Zymo Research |
Cat# R2050 |
| High Sensitivity D1000 Reagents (Sample Buffer & Ladder) |
Agilent Technologies |
Cat# 5067-5585 |
| High Sensitivity D1000 ScreenTapes |
Agilent Technologies |
Cat# 5067-5584 |
| NextSeq 500/550 High Output Kit v2.5 (75 Cycles) |
Illumina |
Cat# 20024906 |
| Bio-Rad Protein Assay Dye (Bradford) |
Bio-Rad |
Cat# 500-0006 |
| Lenti-X GoStix |
Clontech |
Cat# 631281 |
| PhiX Control v3 |
Illumina |
Cat# FC-110-3001 |
| SensiFAST SYBR Lo-ROX Kit |
Bioline |
Cat# BIO-94020 |
| SensiFAST cDNA Synthesis Kit |
Bioline |
Cat# BIO-65054 |
| KLD Enzyme Mix |
New England Biolabs |
Cat# M0554S |
| In-Fusion HD Cloning Kit |
Clontech |
Cat# 639650 |
| NEBNext Ultra II DNA Library Prep with Sample Purification Beads |
New England Biolabs |
Cat# E7103S |
| NEBNext Ultra II Directional RNA Library Prep Kit |
New England Biolabs |
Cat# E7760S |
| Deposited Data |
| Structure of nucleosome-bound human BAF complex |
Protein Data Bank |
ID# 6LTJ |
| Deep sequencing datasets from this study |
Gene Expression Omnibus |
GSE156788 |
| H3K4me3 ChIP-seq (keratinocytes) |
ENCODE |
ENCSR075OQB |
| H3K27me3 ChIP-seq |
ENCODE |
ENCSR377MRR |
| Experimental Models: Cell Lines |
| Human Epidermal Keratinocytes, adult (HEKa) |
Thermo Fisher Scientific |
Cat# C0055C |
| HEK293T |
Takara |
Cat# 632180 |
| FaDu |
ATCC |
Cat# HTB-43 |
| NCI-H520 |
ATCC |
Cat# HTB-182 |
| T.T |
JCRB Cell Bank |
Cat# JCRB0262 |
| KYSE70 |
Sigma |
Cat# 94072012 |
| Oligonucleotides |
| Primers |
See Table S1
|
N/A |
| Recombinant DNA |
| pQCXIH-Myc-YAP |
Addgene |
Cat# 33091 |
| CYC244-Flag-NLS-hYAP |
This study |
N/A |
| N106-hACTL6A |
This study |
N/A |
| CYC103-hACTL6A |
This study |
N/A |
| pGSTag |
Addgene |
Cat# 21877 |
| pMAL-c2X |
Addgene |
Cat# 75286 |
| lentiCRISPR v2 |
Addgene |
Cat# 52961 |
| psPAX2 |
Addgene |
Cat# 12260 |
| pMD2.G |
Addgene |
Cat# 12259 |
| Software and Algorithms |
| Adobe Creative Cloud |
Adobe |
https://www.adobe.com/creativecloud.html
|
| Rstudio |
RStudio |
https://www.rstudio.com/
|
| Image Studio Lite |
LI-COR |
https://www.licor.com/bio/
|
| SnapGene |
Insightful Science |
https://www.snapgene.com/
|
| Prism 8 |
GraphPad Software |
https://www.graphpad.com/scientific-software/prism/
|
| SeqPurge |
Sturm et al., 2016
|
N/A |
| Bowtie2 |
Langmead and Salzberg, 2012
|
N/A |
| deeptools |
Ramirez et al., 2016
|
N/A |
| macs2 |
Zhang et al., 2008
|
N/A |
| Homer |
Heinz et al., 2010
|
N/A |
| DEseq2 |
Love et al., 2014
|
N/A |
| edgeR |
Robinson et al., 2010
|
N/A |
| DiffBind |
Ross-Innes et al., 2012
|
N/A |
| chromVar |
Schep et al., 2017
|
N/A |
| ChiPseeker |
Yu et al., 2015b
|
N/A |
| ChrAccR |
https://github.com/GreenleafLab/ChrAccR
|
N/A |
| PyMOL v2.4.2 |
Schrodinger |
https://pymol.org
|
