KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse anti-FLAG | Sigma-Aldrich | Cat# F1804-1MG |
| Rabbit anti-Histone H3 (acetyl K27) | Abcam | Cat# Ab4729 |
| Mouse anti-Cyclin T1 | Santa Cruz | Cat# sc-271348 |
| Rabbit anti-DOT1L (D1W4Z) | Cell Signaling Technology | Cat# 77087s |
| Rabbit anti-ENL | EMD Millipore | Cat# ABE2596-100UG |
| Mouse anti-β-Actin Antibody (AC-15) | Novus Biologicals | Cat# NB600-501 |
| Mouse anti-AFF4 | Santa Cruz | Cat# sc-390130 |
| Mouse anti-ELL2 | Santa Cruz | Cat# sc-376611 |
| Rabbit anti-Pol II S2P | Abcam | Cat# Ab5095 |
| Anti-mouse IgG, HRP-linked Antibody | Cell Signaling Technology | Cat# 7074s |
| Anti-rabbit IgG, HRP-linked Antibody | Cell Signaling Technology | Cat# 7076s |
| goat anti-Rabbit IgG (H+L) Alexa Fluor® 488 | Invitrogen | Cat# A32732 |
| goat anti-Mouse IgG (H+L) Alexa Fluor® 488 | Invitrogen | Cat# A32723 |
| goat anti-Rabbit IgG (H+L) Alexa Fluor® 568 | Invitrogen | Cat# A11011 |
| goat anti-Mouse IgG (H+L) Alexa Fluor® 568 | Invitrogen | Cat# A11031 |
| Bacterial and virus strains | ||
| NEB® 5-alpha Competent E. coli (High Efficiency) | NEB | Cat# C2987I |
| NEB® Stable Competent E. coli (High Efficiency) | NEB | Cat# C3040I |
| Escherichia coli (E. coli) strain BL21 (DE3) | Novagen | Cat# 69450 |
| Chemicals, peptides, and recombinant proteins | ||
| EMEM | Thermo Fisher Scientific |
Cat# MT10009CV |
| DMEM/F12 | Sigma | Cat# D8062 |
| DMEM | Thermo Fisher Scientific |
Cat# MT10013CV |
| low-glucose DMEM | Thermo Fisher Scientific |
Cat# 10567014 |
| OPTI-MEM | Gibco | Cat# 31985062 |
| Penicillin-streptomycin | Thermo Fisher Scientific |
Cat# 15-140-122 |
| FBS | HyClone | Cat# SH30910.03 |
| Lipofectamine 3000 | Invitrogen | Cat# L3000008 |
| Polyethylene Glycol 8000 (PEG) (1kg) | Fisher Scientific | Cat# BP233-1 |
| PEI MAX | Fisher Scientific | Cat# NC1038561 |
| Polybrene | EMD Millipore | Cat# TR-1003-G |
| Doxycycline | Sigma-Aldrich | Cat# D9891-1G |
| SYBR Green PCR Master Mix | Fisher Scientific | Cat# A25778 |
| Anti-Flag M2-conjugated agarose beads | Sigma-Aldrich | Cat# A2220-1ML |
| Ribonucleoside vanadyl complex (RVC) | Sigma-Aldrich | Cat# R3380-5ML |
| DPBS | Mediatech | Cat# MT21030CM |
| Janelia Fluor® 549 (JF549) | Laboratory of Mustafa A. Mir | N/A |
| Paraformaldehyde (PFA) | Sigma-Aldrich | Cat# 158127-500G |
| Triton X-100 | Fisher Scientific | Cat# BP151500 |
| Tween-20 | Fisher Scientific | Cat# BP337500 |
| Stellaris® FISH Probes, Human GAPDH_intron with Quasar® 670 Dye | Biosearch Technologies |
Cat# ISMF-2151-5 |
| Stellaris 5 × RNA FISH Wash buffer A | Biosearch Technologies |
Cat# SMF-WA1-60 |
| Stellaris RNA FISH hybridization buffer | Biosearch Technologies |
Cat# SMF-HB1-10 |
| Stellaris RNA FISH Wash Buffer B | Biosearch Technologies |
Cat# SMF-WB1-20 |
| Deionized Formamide | VWR | Cat# EM4650 |
| Fluoroshield™ with DAPI, histology mounting medium | Sigma-Aldrich | Cat# F6057-20ML |
| Goat serum | Cell Signaling Technology | Cat# 5425s |
| Bovine Serum Albumin (BSA) | Sigma-Aldrich | Cat# A7906-10G |
| 16% Paraformaldehyde Aqueous Solution, EM Grade | Electron microscope scientific | Cat# 15710 |
| Tris-HCl | Fisher Scientific | Cat# BP1531 |
| NaDOC | Sigma-Aldrich | Cat# 35915 |
| N-Lauroylsarcosine sodium salt | Sigma-Aldrich | Cat# L9150-50G |
| DTT | Sigma-Aldrich | Cat# D9163-5G |
| cOmplete™ EDTA-free Protease Inhibitor Cocktail | Sigma-Aldrich | Cat# 11836170001 |
| Protein A Dynabeads | Fisher Scientific | Cat# 10-002-D |
| EDTA | Sigma-Aldrich | Cat# E5134-500G |
| SDS | Thermo Fisher Scientific |
Cat# BP8200500 |
| Lithium chloride (LiCl) | Sigma-Aldrich | Cat# 213233-500G |
| NaCl | Fisher Scientific | Cat# BP358-1 |
| Glycerol | Fisher Scientific | Cat# BP2291 |
| 2-Mercaptoethanol | Thermo Fisher Scientific |
Cat# 21985023 |
| Glycine | Fisher Scientific | Cat# BP3815 |
| Tris Base | Fisher Scientific | Cat# BP152-1 |
| Pierce ECL Western Blotting Substrate | Pierce Endogen | Cat# 32106 |
| Blotting-Grade Blocker | Bio-Rad | Cat# 1706404 |
| MgCl | Sigma-Aldrich | Cat# M0250-500G |
| NP-40 | BioVision | Cat# 2111-100 |
| Protein K | Sigma-Aldrich | Cat# 03115879001 |
| RNase A | Fisher Scientific | Cat# 9001-99-4 |
| RNase inhibitor | Thermo Fisher Scientific |
Cat# N8080119 |
| LB Broth | Thermo Fisher Scientific |
Cat# BP1426-2 |
| Ampicillin | Fisher Scientific | Cat# BP176025 |
| Kanamycin | Fisher Scientific | Cat# BP906-5 |
| HEPES-Na | Sigma-Aldrich | Cat# H7006 |
| Polyethylene Glycol 4000 | Thermo Fisher Scientific |
Cat# A1615130 |
| sodium citrate | Sigma-Aldrich | Cat# 1613859 |
| 2-propanol | Sigma-Aldrich | Cat# I9516 |
| sodium formate | Sigma-Aldrich | Cat# 247596 |
| sodium acetate trihydrate | Sigma-Aldrich | Cat# 236500 |
| PowerUp SYBR Green Master Mix | Applied Biosystems Inc. |
Cat# A25742 |
| Alexa 488 Fluor™ 488 NHS | Invitrogen | Cat# A20000 |
| Ni IDA Beads 6FF | Smart-Lifesciences | Cat# SA00501L |
| Strep-4FF beads | Smart-Lifesciences | Cat# SA053100 |
| Alexa Fluor™ 488 | Thermo Fisher Scientific |
Cat# A30005 |
| Alexa Fluor™ 568 | Thermo Fisher Scientific |
Cat# A20003 |
| Isopropyl β-D-thiogalactoside | Sigma-Aldrich | Cat# 10724815001 |
| imidazole | Sigma-Aldrich | Cat# 12399 |
| phenylmethylsulfonyl fluoride (PMSF) | VWR Chemicals | Cat# 329-98-6 |
| Desthiobiotin | IBA Life Sciences | Cat# 2-1000-002 |
| SYPRO Orange stain | Thermo Fisher Scientific |
Cat# S6650 |
| H317-28K27ac | This paper | SciLight Biotechnology, LLC |
| H324-27K27ac | This paper | SciLight Biotechnology, LLC |
| ENL wildtype YEATS protein with his-tag, residues 1148 | This paper | Accession number: NP_005925.2 |
| ENL T1 mutant YEATS protein with his-tag, insNHL, residues 1–151 | This paper | N/A |
| ENL T2 mutant YEATS protein with his-tag, PPV-> L, residues 1–146 | This paper | N/A |
| ENL T3 mutant YEATS protein with his-tag, NPP-> K, residues 1–146 | This paper | N/A |
| ENL T4 mutant YEATS protein with his-tag, insHLR, residues 1–151 | This paper | N/A |
| Critical commercial assays | ||
| RNeasy kit | Qiagen | Cat# 74106 |
| High-Capacity cDNA Reverse Transcription Kit | Thermo Fisher | Cat# 4368814 |
| Miniprep kit | Qiagen | Cat# 27106 |
| Gel extraction kit | Qiagen | Cat# 28704 |
| PCR purification kit | Qiagen | Cat# 28106 |
| HisTrap HP 5mL column | GE Healthcare | Cat# 17524705 |
| Superdex 75 10/300 GL | GE healthcare | Cat# 10146535 |
| Deposited data | ||
| ENL T1 YEATS domain in complex with H3K27ac | This paper | PDB ID: 7X8B |
| ENL T2 YEATS domain in complex with H3K27ac | This paper | PDB ID: 7X88 |
| ENL T3 YEATS domain in complex with H3K27ac | This paper | PDB ID: 7E74 |
| ENL T4 YEATS domain in complex with H3K27ac | This paper | PDB ID: 7X8F |
| ENL T1(H116P) YEATS domain in complex with H3K27ac | This paper | PDB ID: 7X8G |
| Mendeley Database | This paper | DOI: 10.17632/bfrkxbhkw p.1 |
| Experimental models: Cell lines | ||
| HEK293 | ATCC | Cat# CRL-1573 |
| HEK293T | ATCC | Cat# CRL-3216 |
| U2OS | Laboratory of Shasha Chong | N/A |
| WiT49 | Laboratory of Herman Yeger Lab | N/A |
| Oligonucleotides | ||
| Oligonucleotides are listed in Table S1 | This paper | N/A |
| Recombinant DNA | ||
| Plasmid: mCherry-hsENL-WT-NLS | Wan et al., 2019 | N/A |
| Plasmid: mCherry-hsENL-T1-NLS | Wan et al., 2019 | N/A |
| Plasmid: mCherry-hsENL-T1 (H116P)-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T2-NLS | Wan et al., 2019 | N/A |
| Plasmid: mCherry-hsENL-T3-NLS | Wan et al., 2019 | N/A |
| Plasmid: mCherry-hsENL-T4-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T5-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T6-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T7-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T8-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T2 (N111P)-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T3 (K111P)-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-WT-YD-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T1-YD-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-WT-ΔIDR-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T1-ΔIDR-NLS | Wan et al., 2019 | N/A |
| Plasmid: mCherry-hsENL-WT-ΔAHD-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T1-ΔAHD-NLS | Wan et al., 2019 | N/A |
| Plasmid: mCherry-hsENL-ΔYD-NLS | Wan et al., 2019 | N/A |
| Plasmid: mCherry-hsENL-IDR-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-AHD-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-ΔIDR1-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-ΔIDR2-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-IDR1_Scr1-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-IDR1_Scr2-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-IDR1_K/Q21-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-IDR1_S/A21-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-IDR2_ED/A29-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-IDR2_E/Q17-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-IDR2_S/A33-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-ΔpolyS-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T1-M1-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T1-M2-NLS | This paper | N/A |
| Plasmid: mCherry-hsENL-T1-M3-NLS | This paper | N/A |
| Plasmid: mCherry-Vector | Wan et al., 2019 | N/A |
| Plasmid: EYFP-hsENL-WT-YD-LacI | This paper | N/A |
| Plasmid: EYFP-hsENL-T1-YD-LacI | This paper | N/A |
| Plasmid: EYFP-hsENL-T2-YD-LacI | This paper | N/A |
| Plasmid: EYFP-hsENL-T1 (H116P)-YD-LacI | This paper | N/A |
| Plasmid: EYFP-hsENL-T2 (N111P)-YD-LacI | This paper | N/A |
| Plasmid: mEGFP-hsENL-T1-NLS | This paper | N/A |
| Plasmid: EGFP-hsENL-T1-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-WT-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T2-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T3-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T4-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T5-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T6-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T7-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T8-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-Vector | Wan et al., 2019 | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1 (H116P)-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T2 (N111P)-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T3 (K111P)-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-WT-YD-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-YDNLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T2-YDNLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-WT-ΔIDR-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-ΔIDR-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T2-ΔIDR-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-WT-ΔAHD-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-ΔAHD-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T2-ΔAHD-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-ΔYD-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-ΔIDR1-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-ΔIDR2-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-IDR1_Scr1-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-IDR1_Scr2-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-IDR1_K/Q21-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-IDR2_ED/A29-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-IDR2_E/Q17-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-IDR1_S/A21-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-IDR2_S/A33-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-ΔpolyS-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-M1-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-M2-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-T1-M3-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-WT-M1-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-WT-M2-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-HA-hsENL-WT-M3-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-Halo-hsENL-T1-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-Halo-hsENL-T2-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-Halo-hsENL-T1(Y78A)-NLS | This paper | N/A |
| Plasmid: plenti-teton-miniCMV-3xflag-Halo-hsENL-T2(Y78A)-NLS | This paper | N/A |
| Plasmid: pSpCas9(BB)-2A–GFP (PX458) | Addgene | Cat# 48138 |
| Plasmid: pSpCas9(BB)-2A–sgAFF4-GFP | This paper | N/A |
| Plasmid: pSpCas9(BB)-2A–sgCDK9-GFP | This paper | N/A |
| pET28b-ENL wildtype and mutant YEATS, residues 1148 | This paper | N/A |
| pET28b-ENL YEATS Y78A, residues 1–148 | This paper | N/A |
| pET28b-full length ENL with N-terminal Strep II tag and C-terminal His-tag, residues 1–559 | This paper | N/A |
| Software and algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| GraphPad Prism | GraphPad | https://www.graphpad.com/ |
| Snapgene | Snapgene | https://www.snapgene.com/snapgene-viewer/ |
| Biorender | Biorender | https://biorender.com/ |
| HKL2000 | Otwinowski and Minor, 1997 | https://www.hkl-xray.com/hkl-2000 |
| MOLREP | Vagin and Teplyakov, 2010 | http://www.ccp4.ac.uk/ |
| COOT | Emsley and Cowtan, 2004 | https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ |
| PHENIX | Adams et al., 2010 | https://www.phenix-online.org |
| PYMOL | Molecular Graphics System, Version 1.8 Schrödinger |
https://pymol.org/2/ |
| CFX Manager | BioRad | N/A |
| Origin 7.0 | OriginLab | N/A |
| CCP4 | Collaborative Computational Project, Number 4, 1994 |
http://www.ccp4.ac.uk/ |
| Imaris 9.3.1 | Oxford Instruments | N/A |
| NIS-Elements AR | Nikon | N/A |
| Astra 6 software program | Wyatt Technology | N/A |