Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal TWIST1 (WT, ChIP, CUT&RUN) | Abcam | Cat# ab50887; RRID:AB_883294 |
| Mouse monoclonal ALX4 (WB, CUT&RUN) | Novus Bio | Cat# NBP2-45490; RRID:AB_3073561 |
| Rabbit polyclonal ALX1 (WB) – discontinued | Novus Bio | Cat# NBP1-88189 |
| Rabbit polyclonal MSX1 (WB) – discontinued | Origene | Cat# TA590129 |
| Mouse monoclonal PRRX1 (WB) | Santa Cruz Biotechnology | Cat# sc-293386; RRID:AB_3073562 |
| Rabbit polyclonal CTCF (WB, CUT&RUN) | Cell Signaling | Cat# 2899; RRID:AB_2086794 |
| Rabbit monoclonal HSP90 (WB) | Cell Signaling | Cat# 4877; RRID: RRID:AB_2233307 |
| Rabbit monoclonal V5 tag (WB, IP) | Abcam | Cat# ab206566; RRID:AB_2819156 |
| Mouse monoclonal Flag tag (WB) | Sigma | Cat# F1804; RRID:AB_262044 |
| Donkey polyclonal anti-rabbit IgG (H+L) HRP (WB) | Jackson Immunoresearch | Cat# 711-035-152; RRID:AB_10015282 |
| Goat polyclonal anti-mouse IgG (H+L) HRP (WB) | Jackson Immunoresearch | Cat# 115-005-003; RRID:AB_2338447 |
| Rabbit polyclonal V5 tag (ChIP) | Abcam | Cat# ab15828; RRID:AB_443253 |
| Rabbit polyclonal H3K27ac (ChIP) | Active Motif | Cat# 39133; RRID:AB_2561016 |
| Rabbit monoclonal AP-2α (ChIP, CUT&RUN) | Cell Signaling | Cat# 3215; RRID:AB_2227429 |
| Mouse monoclonal AP-2α (ChIP) | Novus Bio | Cat# NB100-74359; RRID:AB_1048155 |
| Mouse monoclonal TCF3 (E2A) (CUT&RUN) | Santa Cruz Biotechnology | Cat# sc-133074; RRID:AB_2199147 |
| Rabbit polyclonal anti-mouse IgG (H+L) (CUT&RUN) | Abcam | Cat# ab46540; RRID:AB_2614925 |
| Chemicals, peptides, and recombinant proteins | ||
| mTeSR 1 | Stem Cell Technologies | Cat# 85850 |
| Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix | Corning | Cat# 356231 |
| ReLeSR | Stem Cell Technologies | Cat# 05872 |
| mTeSR Plus | Stem Cell Technologies | Cat# 100-0276 |
| RPMI-1640 | Gibco | Cat# 11875093 |
| Antibiotic-antimycotic | Sigma-Aldrich | Cat# A5955 |
| DMEM High glucose with L-glutamine, sodium pyruvate | Cytiva | Cat# SH30243.01 |
| GlutaMAX | Gibco | Cat# 35050061 |
| Non-essential amino acids | Gibco | Cat# 1114-0050 |
| Complete ES Cell Medium with 15% FBS | Millipore | Cat# ES-101-B |
| mLIF | Millipore | Cat# ESG1107 |
| SpeI-HF | NEB | Cat# R3133S |
| XbaI | NEB | Cat# R0145S |
| Gibson assembly master mix | NEB | Cat# E2611S |
| SalI-HF | NEB | Cat# R3138S |
| BclI | NEB | Cat# R0160S |
| Polyethylenimine | Sigma | Cat# 408719 |
| Opti-MEM | Gibco | Cat# 31985070 |
| Benzonase | Millipore | Cat# 71205-3 |
| OptiPrep Density Gradient medium | Sigma-Aldrich | Cat# D1556-250ML |
| Pluronic F-68 | Gibco | Cat# 240 4-0032 |
| Turbo DNase | Invitrogen | Cat# AM2238 |
| Collagenase IV | Gibco | Cat# 17104019 |
| KnockOut DMEM | Gibco | Cat# 10829018 |
| DMEM/F12 1:1 medium, with L-glutamine; without HEPES | Cytiva | Cat# SH30271.FS |
| Neurobasal Medium | Gibco | Cat# 21103049 |
| N2 NeuroPlex | Gemini Bio | Cat# 400-163 |
| Gem21 NeuroPlex | Gemini Bio | Cat# 400-160 |
| EGF | Peprotech | Cat# AF-100-15 |
| bFGF | Peprotech | Cat# 100-18B |
| Bovine insulin | Gemini Bio | Cat# 700-112P |
| Accutase | Sigma-Aldrich | Cat# A6964-100ML |
| Human fibronectin | Millipore | Cat# FC010-10MG |
| BSA | Gemini Bio | Cat# 700-104P |
| BMP2 | Peprotech | Cat# 120-02 |
| CHIR-99021 | Selleckchem | Cat# S2924 |
| dTAGV-1 | Tocris | Cat# 6914/5 |
| Y-27632 RHO/ROCK pathway inhibitor | Stem Cell Technologies | Cat# 72304 |
| Alt-R S.p. HiFi Cas9 nuclease V3 | Integrated DNA Technologies | Cat# 1081059 |
| QuickExtract DNA Extraction Solution | Lucigen | Cat# QE9050 |
| Lipofectamine 2000 | Invitrogen | Cat# 11668019 |
| FuGENE 6 | Promega | Cat# E2691 |
| cOmplete EDTA-free protease inhibitor cocktail | Roche | Cat# 11873580001 |
| NuPAGE LDS Sample Buffer | Invitrogen | Cat# NP0007 |
| 4–12% Novex Tris-glycine gels | Invitrogen | Cat# XV04125PK20 |
| 4–20% Novex Tris-glycine gels | Invitrogen | Cat# XV04205PK20 |
| Nitrocellulose membrane | GE Healthcare | Cat# 10600003 |
| Amersham enhanced chemiluminescence (ECL) Prime reagent | Cytiva | Cat# RPN2232 |
| DNase I | Worthington | Cat# LS006331 |
| Ampure XP beads | Beckman Coulter | Cat# A63881 |
| Methanol-free 16% formaldehyde solution | Pierce | Cat# 28908 |
| RNase A | Thermo | Cat# EN0531 |
| Proteinase K | Thermo | Cat# EO0491 |
| Dynabeads Protein A | Invitrogen | Cat# 10002D |
| Dynabeads Protein G | Invitrogen | Cat# 10004D |
| Concanavalin A beads | Epicypher | Cat# 21-1401 |
| pAG-MNase | Epicypher | Cat# 15-1016 |
| E. coli spike-in DNA | Epicypher | Cat# 18-1401 |
| TRIzol | Invitrogen | Cat# 15596018 |
| 4-thiouridine | Carbosynth | Cat# NT06186 |
| Iodoacetamide | G Biosciences | Cat# 786-078 |
| 0.05% Trypsin-EDTA | Gibco | Cat# 25300054 |
| phosSTOP | Roche | Cat# 4906845001 |
| Trypsin/LysC | Promega | Cat# V5071 |
| 0.02% ProteaseMax | Promega | Cat# V2071 |
| NEBuffer 2 | NEB | Cat# B7002S |
| LightShift Poly (dI-dC) | Thermo | Cat# 20148E |
| Critical commercial assays | ||
| OptiSeal tubes | Beckman Coulter | Cat# 362183 |
| Amicon Ultra-15 100K filter | Millipore | Cat# UFC910008 |
| LightCycler 480 Probes Master | Roche | Cat# 04707494001 |
| P3 Primary Cell 4D-Nucleofector X Kit L | Lonza | Cat# V4XP-3034 |
| Quick-DNA mini prep kit | Zymo | Cat# D3024 |
| Dual-Luciferase Reporter assay kit | Promega | Cat# E1960 |
| BCA Protein Assay | Thermo | Cat# 23225 |
| TD enzyme | Illumina | Cat# 20034197 |
| DNA Clean & Concentrator-5 | Zymo | Cat# D4013 |
| NEBNext Ultra II Q5 master mix | NEB | Cat# M0544 |
| Qubit dsDNA high sensitivity | Invitrogen | Cat# Q33231 |
| TPX 1.5 ml tubes | Diagenode | Cat# c30010010-50 |
| ChIP DNA Clean & Concentrator-5 | Zymo | Cat# D5205 |
| NEBNext Ultra II DNA | NEB | Cat# E7645S |
| RNA Clean & Concentrator-5 | Zymo | Cat# R1013 |
| Qubit RNA broad range assay | Invitrogen | Cat# Q10210 |
| QuantSeq 3’ mRNA-Seq Library Prep FWD | Lexogen | Cat# 113.96 |
| Direct-zol RNA miniprep | Zymo | Cat# R2052 |
| Dynabeads Antibody Coupling kit | Invitrogen | Cat# 14311D |
| JCSG crystallization kit | Molecular Dimensions | |
| Deposited data | ||
| ChIP-seq, ATAC-seq, CUT&RUN, RNA-seq | This paper | GEO: GSE230319 |
| Crystal structure of TWIST1, TCF4, ALX4, BRG1 bound to DNA | This paper | PDB: 8OSB |
| Experimental models: Cell lines | ||
| Human: Female H9 human embryonic stem cells (hESCs) | WiCell | WA09; RRID:CVCL_9773 |
| Human: Female RS4;11 cells | ATCC | CRL-1873; RRID:CVCL_0093 |
| Human: Female HEK293 cells | ATCC | CRL-1573; RRID:CVCL_0045 |
| Human: Female 293FT cells | Invitrogen | R70007; RRID:CVCL_6911 |
| Mouse: O9-1 cells | Millipore | SCC049; RRID:CVCL_GS42 |
| Experimental models: Organisms/strains | ||
| Mouse: CD-1 | Charles River Laboratories | RRID:MGI:5649524 |
| Oligonucleotides | ||
| Primers for cloning and genotyping, see Table S5 | ||
| HDR oligos and gRNAs for CRISPR/Cas9 editing, see Table S5 | ||
| Recombinant DNA | ||
| pAAV-GFP | Gray et al84 | Addgene 32395 |
| pCAG-NLS-HA-Bxb1 | Hermann et al87 | Addgene 51271 |
| PB-iNEUROD1_P2A_GFP_Puro | Dailamy et al86 | Addgene 168803 |
| pAAV-hSOX9-dTAG-mNeonGreen-V5 | Naqvi et al46 | Addgene 194971 |
| pDGM6 | Gregorevic et al85 | Addgene 110660 |
| pRL | Promega | N/A |
| pGL3-SV40_control | Promega | N/A |
| pUC19 | NEB | Cat# N3041S |
| pGL3-noSV40 | Long et al23 | N/A |
| pGL3-noSV40humanEC1.45_min1-2 | Long et al23 | Addgene 173952 |
| pcDNA3.1_MSX1-Flag | Genscript | OHu18516D |
| pcDNA3.1_PRRX1a-Flag | Genscript | OHu23742D |
| pcDNA3.1_PRRX1b-Flag | Genscript | OHu15551D |
| pcDNA3.1_PHOX2A-Flag | Genscript | OHu18020D |
| pAAV_FKBP-V5-TWIST1 | This paper | N/A |
| pAAV_FKBP-V5-ALX1 | This paper | N/A |
| pAAV_FKBP-V5-PRRX1 | This paper | N/A |
| pAAV_MSX1-FKBP-mNeonGreen-V5 | This paper | N/A |
| pGL3-noSV40-humanEC1.45_min1-2_4XEboxMutant | This paper | N/A |
| pCAG_TWIST1 | This paper | N/A |
| pCAG_ALX4-Flag-HA | This paper | N/A |
| pcDNA3.1_ALX4-Flag | This paper | N/A |
| pcDNA3.1_V5-TWIST1 | This paper | N/A |
| pcDNA3.1_V5-NEUROD1 | This paper | N/A |
| pcDNA3.1_V5-TWIST1_NEUROD1loop | This paper | N/A |
| pcDNA3.1_V5-TWIST1_NEUROG2loop | This paper | N/A |
| pcDNA3.1_V5-TWIST1_HAND2loop | This paper | N/A |
| pcDNA3.1_V5-TWIST1_TAL1loop | This paper | N/A |
| pcDNA3.1_V5-TWIST1_NEUROD1ins | This paper | N/A |
| pcDNA3.1_V5-TWIST1_NEUROG2ins | This paper | N/A |
| pcDNA3.1_V5-TWIST1_HAND2ins | This paper | N/A |
| pcDNA3.1_V5-TWIST1_TAL1ins | This paper | N/A |
| pcDNA3.1_V5-TWIST1_P139S | This paper | N/A |
| pcDNA3.1_V5-TWIST1_L138Y | This paper | N/A |
| pcDNA3.1_V5-TWIST1_L138F | This paper | N/A |
| pcDNA3.1_V5-TWIST1_NEUROD1L | This paper | N/A |
| pcDNA3.1_V5-TWIST1_NEUROD1R | This paper | N/A |
| pcDNA3.1_V5-TWIST1_NEUROD1M | This paper | N/A |
| Software and algorithms | ||
| Dozor-MeshBest | Melnikov et al88 | N/A |
| BEST | Bourenkov and Popov89 | https://www.embl-hamburg.de/BEST/ |
| XDS | Kabsch90 | https://xds.mr.mpg.de/ |
| skewer v0.2.2 | Jiang et al91 | https://github.com/relipmoc/skewer |
| bowtie2 v2.4.1 | Langmead and Salzberg92 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| samtools v1.10 | Danecek et al93 | https://samtools.sourceforge.net/ |
| MACS2 v2.2.7.1 | Zhang et al94 | https://github.com/macs3-project/MACS |
| bedtools | Quinlan and Hall95 | https://github.com/arq5x/bedtools2 |
| DESeq2 | Love et al96 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| IGV v2.7.2 | Robinson et al97 | https://igv.org/ |
| deeptools | Ramirez et al98 | https://deeptools.readthedocs.io/en/develop/index.html |
| tximport | Soneson et al99 | https://bioconductor.org/packages/release/bioc/html/tximport.html |
| slamdunk v0.4.3 | Neumann et al100 | https://t-neumann.github.io/slamdunk/ |
| MEME Suite v5.1.1 TOMTOM | Gupta et al101 | https://meme-suite.org/meme/doc/download.html |
| MEME Suite v5.1.1 AME | McLeay and Bailey102 | https://meme-suite.org/meme/doc/download.html |
| MEME Suite v5.1.1 FIMO | Grant et al103 | https://meme-suite.org/meme/doc/download.html |
| PWMScan | Ambrosini et al104 | https://epd.expasy.org/pwmtools/pwmtools/ |
| MEME Suite v5.1.1 STREME | Bailey et al105 | https://meme-suite.org/meme/doc/download.html |
| MEME Suite v4.12.0 ceqlogo | Timothy Bailey lab | https://meme-suite.org/meme/doc/download.html |
| Preview | Protein Metrics | https://proteinmetrics.com/resources/preview-a-program-for-surveying-shotgun-proteomics-tandem-mass-spectrometry-data/ |
| Byonic | Protein Metrics | https://proteinmetrics.com/byonic/ |
| Phaser | McCoy et al106 | https://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software |
| Phenix | Adams et al107 | https://phenix-online.org/ |
| CCP4 | Winn et al108 | https://www.ccp4.ac.uk/ |
| REFMAC5 | Murshudov et al109 | https://www.ccp4.ac.uk/ |
| Coot | Emsley et al110 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
| PyMOL | 111 | https://www.pymol.org/2 |
| Fiji | Schindelin et al112 | https://fiji.sc/ |
| LD score regression v1.0.1 | Finucane et al113 | https://github.com/bulik/ldsc |
| Matching package for R v4.10-8 | Sekhon114 | https://cran.r-project.org/web/packages/Matching/index.html |
| UCSC Kent tools | Kent et al115 | https://genome.ucsc.edu/ |
| Original code | This paper | https://zenodo.org/doi/10.5281/zenodo.7847852 |
| Other | ||
| Beckman VTi 50 rotor | Beckman Coulter | N/A |
| Bioruptor Plus | Diagenode | N/A |
| Amersham ImageQuant 800 | Cytiva | N/A |
| Countess II | Invitrogen | N/A |
| NovaSeq X Plus | Illumina | N/A |
| NovaSeq 6000 | Illumina | N/A |
| HiSeq X Ten | Illumina | N/A |
| Acquity M-Class UPLC | Waters | N/A |
| Orbitrap Q Exactive HF-X | Thermo | RRID:SCR_018703 |
| Orbitrap Exploris 480 | Thermo | RRID:SCR_022215 |
| LightCycler 480 | Roche | N/A |
| Lonza 4D-Nucleofector | Lonza | N/A |