KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
| Antibodies | ||
| anti-DYKDDDDK Tag (Binds to same epitope as Sigma’s Anti-FLAG® M2 Antibody) | Cell Signaling Technology | Cat# 14793, RRID:AB_2572291 |
| anti-E2F1 | Cell Signaling Technology | Cat# 3742, RRID:AB_2096936 |
| anti-Histone H3 (Tri-Methyl-Lys4) | Cell Signaling Technology | Cat# 9751, RRID:AB_2616028 |
| anti-Histone H3 (Mono-Methyl-Lys4) | Abcam | Cat# ab8895, RRID:AB_306847 |
| anti-Histone H3 (Acetyl-Lys27) | Active Motif | Cat# 39034 |
| anti-c-Jun | Cell Signaling Technology | Cat# 9165, RRID:AB_2130165 |
| anti-CTCF | Cell Signaling Technology | Cat# 3418, RRID:AB_2086791 |
| anti-RB | Cell Signaling Technology | Cat# 9309S, RRID:AB_10696874 |
| anti-Phospho-RB S608 | Cell Signaling Technology | Cat# 8147S, RRID:AB_10949974 |
| anti-Phospho-RB S780 | Cell Signaling Technology | Cat# 8180S, RRID:AB_10950972 |
| anti-Phospho-RB S795 | Cell Signaling Technology | Cat# 9301P, RRID:AB_10830074 |
| anti-Phospho-RB S807/S811 | Cell Signaling Technology | Cat# 8516S, RRID:AB_11178658 |
| anti-Phospho-RB T373 | Abcam | Cat# ab52975, RRID:AB_2177344 |
| anti-a-Tubulin | Sigma-Aldrich | Cat# T9026, RRID:AB_477593 |
| anti-FLAG (M5) | Sigma-Aldrich | Cat# F4042, RRID:AB_439686 |
| anti-HA-Tag | Cell Signaling Technology | Cat# 3724, RRID:AB_1549585 |
| anti-p44/42 MAPK (Erk1/2) | Cell Signaling Technology | Cat# 9102, RRID:AB_330744 |
| anti-Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) | Cell Signaling Technology | Cat# 4370, RRID:AB_2315112 |
| anti-Cyclin D1 | Santa Cruz Biotechnology | Cat# sc-753, RRID:AB_2070433 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Doxycycline hyclate | Sigma-Aldrich | Cat# D9891 |
| Trametinib (GSK1120212) | Selleckchem | Cat# S2673 |
| Gateway LR Clonase II Enzyme mix | Invitrogen | Cat# 11791-020 |
| X-tremeGENE 9 DNA Transfection Reagent | Roche | Cat# 6365787001 |
| Polybrene | Sigma-Aldrich | Cat# 107689 |
| Geneticin | Gibco | Cat# 10131035 |
| Puromycin | Sigma-Aldrich | Cat# P9620 |
| EdU (5-ethynyl-2’-deoxyuridine) | Invitrogen | Cat# A10044 |
| Alexa Fluor 647 Azide, Triethylammonium Salt | Invitrogen | Cat# A10277 |
| DAPI (4′,6-Diamidino-2-Phenylindole, Dihydrochloride) | Invitrogen | Cat# D1306 |
| FastStart Universal SYBR Green Master | Roche | Cat# 4913914001 |
| EGS (ethylene glycol bis(succinimidyl succinate)) | Thermo Scientific | Cat# 21565 |
| RNase A | Roche | Cat# 11119915001 |
| Proteinase K | Thermo Scientific | Cat# 25530049 |
| Agencourt AMPure XP | Beckman Coulter | Cat# A63881 |
| Protein G-Dynabeads | Life Technologies | Cat# 10004D |
| Critical Commercial Assays | ||
| pENTR™/D-TOPO Cloning Kit | Invitrogen | Cat# K240020 |
| Direct-zol RNA Kit | Zymo Research | Cat# R2073 |
| TaqMan Reverse Transcription Reagents | Thermo Fisher Scientific | Cat# N8080234 |
| Qubit dsDNA HS Assay kit | Thermo Fisher Scientific | Cat# Q32851 |
| Ovation Ultralow System V2 | TECAN | Cat# 0344NB-A01 |
| NextSeq 500/550 High Output Kit v2.5 (75 Cycles) | Illumina | Cat# 20024906 |
| Deposited Data | ||
| ChIP sequencing data | This paper | GEO: GSE176035 |
| Original images for Western Blots | This paper | DOI: 10.17632/p2x5xr4vt2.1 |
| RB ChIP-seq data from K562 cell line | ENCODE Project | ENCODE accession: ENCSR670JDQ GEO accession: GSE105638 |
| RB ChIP-seq data from GM12878 cell line | ENCODE Project | ENCODE accession: ENCSR785OKZ GEO accession: GSE106046 |
| Experimental Models: Cell Lines | ||
| hTERT-RPE1 human epithelial cells | Dr. David Pellman’s laboratory, Dana Farber Cancer Institute | RRID:CVCL_4388 |
| hTERT-BJ1 human fibroblasts | ATCC | Cat# CRL-4001, RRID:CVCL_6573 |
| MCF10A human mammary epithelial cells | Dr. Lee Zou’s laboratory, MGH | RRID:CVCL_0598 |
| T47D human breast cancer | Center for Molecular Therapeutics - MGH | RRID:CVCL_0553 |
| SW1573 human lung adenocarcinoma | Center for Molecular Therapeutics - MGH | RRID:CVCL_1720 |
| NCI-H2030 human lung adenocarcinoma | Center for Molecular Therapeutics - MGH | RRID:CVCL_1517 |
| CALU-1 human lung squamous cell carcinoma | Center for Molecular Therapeutics - MGH | RRID:CVCL_0608 |
| HOP62 human lung adenocarcinoma | Center for Molecular Therapeutics - MGH | RRID:CVCL_1285 |
| Oligonucleotides | ||
| Primers for cloning A-FOS and DNDP1 cDNA in pENTR/D-TOPO, see Table S8 | This paper | N/A |
| Real Time RT-PCR primers, see Table S8 | MGH Primer Bank database | N/A |
| Recombinant DNA | ||
| pINDUCER11 | (Meerbrey et al., 2011) | Addgene plasmid# 44363 |
| pINDUCER20 | (Meerbrey et al., 2011) | Addgene plasmid# 44012 |
| pLenti-CMVtight-puro-Dest | gift from Eric Campeau | Addgene plasmid# 26430 |
| pLenti-CMVtight-eGFP-puro | gift from Eric Campeau | Addgene plasmid# 26431 |
| pINDUCER11-shRB1 (5’-CAGAGATCGTGTATTGAGATT-3’) | This paper | N/A |
| pINDUCER11-shScramble (5’-ACTAAGGTTAAGTCGCCCTCGA -3’) | This paper | N/A |
| pINDUCER20-RB wild-type | (Sanidas et al., 2019) | N/A |
| pINDUCER20-FLAG-RB wild-type | (Sanidas et al., 2019) | N/A |
| pINDUCER20-RB Δcdk | (Sanidas et al., 2019) | N/A |
| pINDUCER20-FLAG-RB Δcdk | (Sanidas et al., 2019) | N/A |
| pINDUCER20-FLAG-mP-RB mutant alleles | (Sanidas et al., 2019) | N/A |
| pLenti-CMVtight-HA-A-FOS-puro | This paper | N/A |
| pLenti-CMVtight-HA-DNDP1-puro | This paper | N/A |
| Software and Algorithms | ||
| Geneset enrichment analysis (GSEA) | (Subramanian et al., 2005) | N/A |
| HOMER | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/ |
| WebGestalt | (Liao et al., 2019) | http://www.webgestalt.org |
| Prism 6 | GraphPad | https://www.graphpad.com |
| OriginPro | Origin Lab | https://www.originlab.com/ |
| MATLAB | MathWorks | https://www.mathworks.com/products/matlab.html |
| Python | N/A | https://www.python.org/ |
| gdown (Python package) | Kentaro Wada | https://github.com/wkentaro/gdown |
| argparse (Python package) | Ben West | https://github.com/bewest/argparse |
| R | N/A | https://www.r-project.org/ |
| ggplot2 (R package) | N/A | https://cran.r-project.org/web/packages/ggplot2/index.html |
| leaflet (R package) | N/A | https://cran.r-project.org/web/packages/leaflet/index.html |
| RColorBrewer (R package) | N/A | https://cran.r-project.org/web/packages/RColorBrewer/index.html |
| DiffBind (R package) | N/A | https://doi.org/doi:10.18129/B9.bioc.DiffBind |
| BEDTools | (Quinlan and Hall, 2010) | https://github.com/arq5x/bedtools2 |
| ENCODE | (An integrated encyclopedia of DNA elements in the human genome, 2012) | https://www.encodeproject.org/ |
| Cistrome Data Browser | (Zheng et al., 2019) | http://cistrome.org/db/ |
| BART2 | (Wang et al., 2018) | https://github.com/zanglab/bart2 |
| MARGE | (Wang et al., 2016) | http://cistrome.org/MARGE |
| Cromwell | (Voss et al., 2017) | https://doi.org/10.7490/f1000research.1114634.1 |
| ENCODE ChIP-seq Pipeline | (Landt et al., 2012) | https://github.com/ENCODE-DCC/chip-seq-pipeline2 |
| PanChIP | This paper | DOI: 10.5281/zenodo.6787997 |