KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-mouse ASCL1 | Abcam | ab74065 |
| anti-human H2B | Abcam | ab1790 |
| anti-human H3 | Abcam | ab1791 |
| Cy5-dCTP | GE Healthcare Life Sciences | PA55021 |
| Klenow Fragment (3ÅL→5ÅL exo-) | New England Biolabs | M0212S |
| Bacterial and Virus Strains | ||
| 6HIS_pRSF_TEV | Gifft from Ronen Marmorstein lab | 6HIS_pRSF_TEV |
| FUW-TetO-Gata4 | Buganim et al., 2012 | Addgene 41084 |
| pCMW-SPORT6-Hnf1 | Dharmacon mammalian gene collection | MMM1013–202761012 |
| Tet-O-FUW-Ascl1 | Vierbuchen et al., 2010 | Addgene 27150 |
| pBABE-E12-cTAP | Yang et al., 2009 | Addgene 20916 |
| pET-28b-FoxA1 | This paper | pET-28b-FoxA1 |
| pET-28b-Gata4 | This paper | pET-28b-Gata4 |
| pET-28b-Hnf1a | This paper | pET-28b-Hnf1a |
| pET-28b-Ascl1 | This paper | pET-28b-Ascl1 |
| pET-28b-Tcf3 | This paper | pET-28b-Tcf3 |
| pRSFDUET1-Ascl1+Tcf3 | This paper | pRSFDUET1-Ascl1+Tcf3 |
| pET-28d-Brn2 | Gift from Marius Wernig | pET-28d-Brn2 |
| pET-28b-Spi1 | This paper | pET-28b-Spi1 |
| pET-28b-Cebpa | This paper | pET-28b-Cebpa |
| pET-28b-Cebpb | This paper | pET-28b-Cebpb |
| pET-28b-Cebpb-T167D | This paper | pET-28b-Cebpb-T167D |
| pET-28b-Cebpb- S163D,T167D | This paper | pET-28b-Cebpb- S163D,T167D |
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| His6x-FOXA1 | This paper | His6x-FOXA1 |
| His6x-GATA4 | This paper | His6x-GATA4 |
| His6x-HNF1α | This paper | His6x-HNF1α |
| His6x-ASCL1 | This paper | His6x-ASCL1 |
| His6x-E12α | This paper | His6x-E12α |
| His6x-ASCL1/E12α | This paper | His6x-ASCL1/E12α, |
| GST-His6x-BRN2 | This paper | GST-His6x-BRN2 |
| His6x-PU1 | This paper | His6x-PU1 |
| His6x-CEBPα | This paper | His6x-CEBPα |
| His6x-CEBPβ WT | This paper | His6x-CEBPβ WT |
| His6x-CEBPβ T167D | This paper | His6x-CEBPβ T167D |
| His6x-CEBPβ S163D,T167D | This paper | His6x-CEBPβ S163D,T167D |
| GST-MYOG | Hu et al., 2013 | GST-MYOG |
| GST-TBX20 | Hu et al., 2013 | GST-TBX20 |
| GST-NHLH2 | Hu et al., 2013 | GST-NHLH2 |
| GST-CREM1 | Hu et al., 2013 | GST-CREM1 |
| GST-IRF3 | Hu et al., 2013 | GST-IRF3 |
| GST-RBPJ | Hu et al., 2013 | GST-RBPJ |
| GST-HMGN1 | Hu et al., 2013 | GST-HMGN1 |
| GST-HMGN5 | Hu et al., 2013 | GST-HMGN5 |
| GST-HMGA1 | Hu et al., 2013 | GST-HMGA1 |
| GST-SOX5 | Hu et al., 2013 | GST-SOX5 |
| Critical Commercial Assays | ||
| MinElute PCR purification kit | QIAGEN | 28004 |
| Quick change II XL Site-Directed mutagenesis Kit | Agilent | 200521 |
| Deposited Data | ||
| ASCL1 and BRN2 ChIP-seq | Vierbuchen et al., 2013 | GEO GSE43916 |
| PU1, CEBPα and CEBPβ ChIP-seq | Heinz et al., 2010 | GSE21512 |
| FOXA1 and HNF1α ChIP-seq | Faure et al., 2012 | E-MTAB-941 |
| GATA4 ChIP-seq | Zheng et al., 2013 | GSE49132 |
| Fibroblast MNase-seq | Teif et al., 2012 | GSE40910 |
| FOXA3-DBD:DNA co-crystal structure | Clark et al., 1993 | RCSB PDB 1VTN |
| OCT4-DBD:DNA co-crystal structure | Esch et al., 2013 | RCSB PDB 3L1P |
| PU1-DBD:DNA co-crystal structure | Kodandapani et al., 1996 | RCSB PDB 1PUE |
| KLF4-DBD:DNA co-crystal structure | Schuetz et al., 2011 | RCSB PDB 2WBS |
| GATA3-DBD:DNA co-crystal structure | Chen et al., 2012 | RCSB PDB 4HC9 |
| ASCL1 | SWISS-MODEL | SMR P50553 |
| cMYC/MAX-DBD:DNA co-crystal structure | Nair and Burley, 2003 | RCSB PDB 1NKP |
| CEBPα-DBD:DNA co-crystal structure | Miller et al., 2003 | RCSB PDB 1NWQ |
| USF-DBD:DNA co-crystal structure | Ferre-D’Amare et al., 1994 | RCSB PDB 1AN4 |
| MYOG | SWISS-MODEL | SMR P15173 |
| CREM | SWISS-MODEL | SMR Q03060 |
| TBX1-DBD:DNA co-crystal structure | El Omari et al., 2012 | RCSB PDB 4A04 |
| Brachyury-DBD:DNA co-crystal structure | Muller and Herrmann, 1997 | RCSB PDB 1XBR |
| NF-kB p50-DBD:DNA co-crystal structure | Muller et al., 1995 | RCSB PDB 1SVC |
| GAL4-DBD:DNA co-crystal structure | Hong et al., 2008 | RCSB PDB 3COQ |
| PBX1-DBD:DNA co-crystal structure | LaRonde-LeBlanc and Wolberger, 2003 | RCSB PDB 1PUF |
| UBX-DBD:DNA co-crystal structure | Foos et al., 2015 | RCSB PDB 4UUS |
| Raw gel images | Mendeley | https://doi.org/10.17632/5dnznn9kwt.1 |
| Experimental Models: Cell Lines | ||
| Rosetta (DE3)pLysS Competent Cells | Novagen | Novagen # 70956–3 |
| Experimental Models: Organisms/Strains | ||
| Oligonucleotides | ||
| Table S3 | ||
| Recombinant DNA | ||
| GATCCTGTCTCCTGCTCTGTCAGCAGGGCACTGTACTTGCTGATACCAGGGAATGTTTGTTCTTAAATACCATCATTCCGGACGTGTTTGCCTTGGCCAGTTTTCCATGTACATGCAGAAAGAAGTTTGGACTGATCAATACAGTCCTCTGCCTTGGATC | This paper | 160 bp ALBN1-DNA |
| GATCCATTACTTCTGAAACAGATGACTCCCAGCAGCTGCTGCCTGTGGCCCACAGGGCTTCCTGCCCTGCATGACAGCTGCACATCACATCCTGTGGTCATACTACTTCAGCCGCTTCTACGGCCAGATACAAAAGTGGGTGGGGAACATAGGCAAGGGATC | This paper | 162 bp NRCAM-DNA |
| GATCCGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTTAGCAATGGATACTTCCCGATTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCGGATC | This paper | 162 bp CX3CR1-DNA |
| Software and Algorithms | ||
| Gene Mapper v4.1 | Thermo Fisher | Cat no. 4440915 |
| Peak Scanner module | Thermo Fisher Scientific Cloud | https://www.thermofisher.com/us/en/home/life-science/sequencing/fragment-analysis/fragment-analysis-fundamentals/fragment-analysis-software-data-analysis.html |
| Pymol | Schrodinger | https://pymol.org/2/ |
| PRISM 7 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| PROMO | Messeguer et al., 2002 | http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3 |
| GenePix Pro 7 | Molecular Devices, LLC. | http://mdc.custhelp.com/app/products/detail/p/129/~/version-7 |
| R studio | https://www.rstudio.com/ | |
| Fiji is Just ImageJ (Fiji) version 2.0.0-rc/1.51f | https://imagej.net/ | |
| SWISS-MODEL | Bienert et al., 2017 | https://swissmodel.expasy.org/ |
| Other | ||
| Human TF Protein microarrays | Hu et al., 2013 | Human TF Protein microarrays |