KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-KANSL2 | Sigma | Cat# HPA038497, RRID: AB_10674685 |
| Anti-KANSL3 | Sigma | Cat# HPA035018, RRID: AB_10601763 |
| Anti-KAT8 | Abcam | Cat# ab200660 |
| Anti-H4K5ac (#1) | Abcam | Cat# ab51997, RRID: AB_2264109 |
| Anti-H4K5ac (#2) | Abcam | Cat# ab114146 |
| Anti-H4K5ac (#3) | Diagenode | Cat# C1541005 |
| Anti-H4K16ac (#1) | Abcam | Cat# ab109463, RRID: AB_10858987 |
| Anti-H4K16ac (#2) | Millipore | Cat# 07-329, RRID: AB_310525 |
| Anti-H4K8ac | Abcam | Cat# ab45166, RRID: AB_732937 |
| Anti-Pol II | Cell Signaling | Cat# 14958, RRID: AB_2687876 |
| Anti-H3K4me3 | Cell Signaling | Cat# 9751, RRID: AB_2616028 |
| Anti-H3 | Abcam | Cat# ab24834, RRID: AB_470335 |
| Anti-H4 | Abcam | Cat# ab17036, RRID: AB_1209245 |
| Anti-HA | Cell Signaling | Cat# 3724S, RRID: AB_1549585 |
| Anti-FLAG | Sigma | Cat# F1804, RRID: AB_262044 |
| Anti-Vinculin | Sigma | Cat# SAB4200080, RRID: AB_10604160 |
| Anti-GAPDH | Abcam | Cat# ab181602, RRID: AB_2630358 |
| Anti-b-Actin | Abcam | Cat# ab6276, RRID: AB_2223210 |
| Anti-MSL2 | Cell Signaling | Cat# 44006, RRID: AB_2799256 |
| Anti-TAF1 | Cell Signaling | Cat# 12781, RRID: AB_2798025 |
| Goat Anti-Rabbit IgG Antibody (H+L), Peroxidase | Vector Laboratories | Cat# PI-1000, RRID: AB_2336198 |
| Horse Anti-Mouse IgG Antibody (H+L), Peroxidase | Vector Laboratories | Cat# PI-2000, RRID: AB_2336177 |
| IRDye® 800CW Goat anti-Rabbit IgG | LI-COR Biosciences | Cat# 925-32211, RRID: AB_2651127 |
| IRDye® 680RD Goat anti-Mouse IgG | LI-COR Biosciences | Cat# 926-68070, RRID: AB_10956588 |
| Bacterial and Virus Strains | ||
| DH5alpha Chemically Competent Cells | Lab prep | N/A |
| Stbl3 Chemically Competent Cells | Lab prep | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Agencourt Ampure XP beads | Beckman Coulter | A63881 |
| LIF | Lab prep | N/A |
| Polybrene | Fisher | NC9200896 |
| RetroNectin | Fisher | 50444032 |
| Protein G Sepharose 4 Fast Flow | GE Healthcare | 17061802 |
| Protein G Dynabeads | Thermo Fisher Scientific | 10004D |
| ANTI-FLAG® M2 Affinity Gel | Sigma | A2220 |
| TMTpro™ 16plex Label Reagent Set | Thermo Fisher Scientific | A44520 |
| TMT10plex Isobaric Label Reagent Set plus TMT11-131C Label Reagent | Thermo Fisher Scientific | A34808 |
| EdU (5-ethynyl-2'-deoxyuridine) | Lumiprobe | 10540 |
| Sulfo-Cyanine5 azide | Lumiprobe | A3330 |
| FITC Annexin V | BD | 556420 |
| Digitonin | Promega | G9441 |
| Critical Commercial Assays | ||
| SNAP-ChIP K-AcylStat panel | EpiCypher | 193001 |
| Illumina Tagment DNA Enzyme and Buffer | Illumina | 20034197 |
| NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® | NEB | E7645L |
| Illumina TruSeq v2 kit | Illumina | RS1222001 |
| Deposited Data | ||
| Raw and analyzed RNA-seq data | GEO | GSE158521 |
| Raw and analyzed ChIP-seq data | GEO | GSE158736 |
| Raw and analyzed ATAC-seq data | GEO | GSE157583 |
| Uncropped western blots | Mendeley | DOI: 10.17632/v7mbmfxxy5.1 |
| Raw and analyzed proteomics data | ProteomeXchange | PXD022267, PXD021943, PXD023865 |
| Experimental Models: Cell Lines | ||
| HEK293FT | Kristian Helin lab | RRID: CVCL_6911 |
| HEK293 | Kristian Helin lab | RRID: CVCL_0045 |
| HeLa | Xuejun Jiang Lab | RRID: CVCL_0030 |
| U2OS | Xuejun Jiang Lab | RRID: CVCL_0042 |
| THP-1 | Kristian Helin lab | RRID: CVCL_0006 |
| K562 | Kristian Helin lab | RRID: CVCL_0004 |
| MOLM13 | Kristian Helin lab | RRID: CVCL_2119 |
| Caki1 | MSKCC cell line core | RRID: CVCL_0234 |
| SKHEP1 | MSKCC cell line core | RRID: CVCL_0525 |
| SKMEL28 | Jedd Wolchok lab | RRID: CVCL_0526 |
| SKMEL5 | MSKCC cell line core | RRID: CVCL_0527 |
| Mouse MLL-AF9 secondary leukemia cells | Lab prep | N/A |
| E14 mouse embryonic stem cells | Joshua Brickman lab | RRID: CVCL_C320 |
| See Table S7 for primer and sgRNA sequences | ||
| Recombinant DNA | ||
| pLentiCas9-blast | Addgene | 60955 |
| pU6-sgRNA-EF1α-puro-T2A-BFP | Addgene | 52962 |
| pHR-SFFV-KRAB-dCas9-2A-CHERRY | Addgene | 60954 |
| pLenti-PGK-Hygro dest | Addgene | 19066 |
| U6-sgRNA-SFFV-puro-P2A-EGFP | This study | N/A |
| eSpCas9(1.1)-T2A-mCherry | Ian Chambers lab | N/A |
| pCRIS-PITChv2-BSD-dTAG (BRD4) | Addgene | 91792 |
| pUC19_FKBPF36V-KANSL3-targeting | This study | N/A |
| Software and Algorithms | ||
| sgRNA Designer: CRISPRko | https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design | N/A |
| CRISPRi sgRNA design | Radzisheuskaya et al., 2016 | N/A |
| Image Studio Lite software | LI-COR Biosciences | N/A |
| R/Bioconductor package ShortRead v.1.36.1 | Morgan et al., 2009 | N/A |
| twoBitToFa utility | Speir et al., 2016 | N/A |
| R/Bioconductor package Rsubread v.1.32.2 | Liao et al., 2019 | N/A |
| R/Bioconductor package Rsamtools v.2.3.3 | Morgan et al., 2016 | N/A |
| R/Bioconductor package DESeq2 v.1.20.0 | Love et al., 2018 | N/A |
| R/Bioconductor package limma v.3.42.2 | Ritchie et al., 2015 | N/A |
| R/Bioconductor package edgeR v.3.28.0 | Robinson et al., 2010 | N/A |
| bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | N/A |
| MACS2 | https://github.com/taoliu/MACS | N/A |
| BEDTools suite | http://bedtools.readthedocs.io | N/A |
| EaSeq | Lerdrup et al., 2016 | N/A |
| Homer v4.5 | http://homer.ucsd.edu | N/A |
| HiC-Pro version 2.11.0 | Servant et al., 2015 | N/A |
| HiCExplorer 3.4.3 | Ramírez et al., 2018 | N/A |
| R/Bioconductor package circlize v.0.4.8 | Krzywinski et al., 2009 | N/A |