KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| ARID2 | Santa Cruz | Cat# sc-166117; RRID: AB_2060382 |
| ARID2 | Cell Signaling | Cat# 82342; RRID:AB_2799992 |
| PBRM1 | In house | N/A |
| BRD7 | Santa Cruz | Cat# sc-376180; RRID:AB_10989389 |
| SS18 | Cell Signaling | Cat# 21792; RRID:AB_2728667 |
| SNF5 | Santa Cruz | Cat# sc-166165; RRID:AB_2270651 |
| SNF5 | Bethyl | Cat# A301-087A; RRID:AB_2191714 |
| BRG1 | Abcam | Cat# ab110641; RRID:AB_10861578 |
| BRG1 | Santa Cruz | Cat# sc-17796; RRID:AB_626762 |
| ARID1A | Bethyl | Cat# A301-041A; RRID:AB_2060365 |
| ARID1A | Santa Cruz | Cat# sc-32761; RRID:AB_673396 |
| GAPDH | Santa Cruz | Cat# sc-32233; RRID:AB_627679 |
| H3K27ac | Abcam | Cat# ab4729; RRID:AB_2118291 |
| H3K27me3 | Epicypher | Cat# 13-0030; RRID: N/A |
| H3K9me3 | Abcam | Cat# ab176916; RRID:AB_2797591 |
| FOSL2 | Santa Cruz | Cat# sc-604; RRID:AB_2107084 |
| TEAD4 | Santa Cruz | Cat# sc-101184; RRID:AB_2203086 |
| MITF | Sigma A. | Cat# HPA003259; RRID:AB_1079381 |
| MITF | Active Motif | Cat# 91201; RRID:AB_2793801 |
| CTCF | Millipore | Cat# 07-729; RRID:AB_441965 |
| REST | Millipore | Cat# 07-579; RRID:AB_11211936 |
| PHF10 | ThermoFisher | Cat# PA5-30678; RRID:AB_2548152 |
| BRM | Santa Cruz | Cat# sc-166579; RRID:AB_2302397 |
| GLTSCR1 | Santa Cruz | Cat# sc-515086; RRID: N/A |
| CHD5 | Abcam | Cat# ab124736; RRID:AB_10974578 |
| TGBR2 | Abcam | Cat# ab184948; RRID:AB_2818975 |
| Phospho-SMAD3 | Cell Signaling | Cat# 9520; RRID:AB_2193207 |
| SMAD3 | Cell Signaling | Cat# 9523; RRID:AB_2193182 |
| Bacterial and virus strains | ||
| One Shot™ Stbl3™ Chemically Competent E. coli | Invitrogen | Cat# C737303 |
| Chemicals, peptides, and recombinant proteins | ||
| DSG | Pierce (ThermoFisher) | Cat# 20593 |
| Protein A + G magnetic beads | Millipore | Cat# LSKMAGAG10 |
| Dynabeads Protein A magnetic beads | Invitrogen | Cat# 10001D |
| KAPA HiFi DNA Polymerase | Roche | Cat# 07958838001 |
| Digitonin | Promega | Cat# G9441 |
| Illumina Tagment DNA Enzyme and Buffer Small Kit | Illumina | Cat# 20034197 |
| AMPure XP beads | NEB | Cat# A63880 |
| T4 PNK | NEB | Cat# M0201S |
| 5U/uL Klenow Fragment (3′–5′ exo-) | NEB | Cat# M0212S |
| Quick T4 DNA ligase | NEB | Cat# M2200S |
| T4 DNA Polymerase | NEB | Cat# M0203S |
| DNA Polymerase Klenow Fragments | NEB | Cat# M0210S |
| dNTPs | Roche | Cat# 11969064001 |
| dATPs | Roche | Cat# 11889516103 |
| Critical commercial assays | ||
| Transit-VirusGEN Transfection Kit | Mirus Bio | Cat# MIR6700 |
| NEXTFLEX Poly(A) Enrichment Beads | PerkinElmer | Cat# NOVA-512992 |
| NEXTFLEX Rapid Directional RNA-seq Kit 2.0 | PerkinElmer | Cat# N0VA-5198-01 |
| RNeasy extraction kit | Qiagen | Cat# 74104 |
| Arima Hi-C Kit | Arima | Cat# A410030 |
| QIAquick PCR Purification Kit | Qiagen | Cat# 28106 |
| Kapa HyperPrep Kit | Kapa Biosystems | Cat# KK8500 |
| QIAquick Gel Extraction Kit | Qiagen | Cat# 28704 |
| Deposited data | ||
| Raw RNA sequencing, ATAC-sequencing, ChIP-sequencing, and Hi-C data | GEO | GSE172383 |
| Analyzed RNA sequencing, ATAC-sequencing, ChIP-sequencing, and Hi-C data, See Tables S2, S3, S6 | This paper | N/A |
| The Cancer Genome Atlas Skin Cutaneous Melanoma | Akbani et al. (2015) | https://gdc.cancer.gov/about-data/publications/skcm_2015 |
| Experimental models: Cell lines | ||
| SKmel147 | Eva Hernando Laboratory (NYU) | RRID:CVCL_3876 |
| 501mel | Eva Hernando Laboratory (NYU) | RRID:CVCL_4633 |
| 113/6-4L | Robert Kerbel Laboratory (Sunnybrook Health Sciences Center) | Cruz-Munoz et al., 2008 |
| WM1552c | Rockland | WM1552C-01-0001, RRID: CVCL_6472 |
| WM1799 | Rockland | WM1799-01-0005, RRID: CVCL_A341 |
| WM3456 | Rockland | WM3456-01-0001, RRID: CVCL_AP91 |
| Mel888 | Stuart Aaronson Laboratory (ISMMS) | RRID: CVCL_4632 |
| WM1716 | Rockland | WM1716-01-0001, RRID: CVCL_AP82 |
| LOX-IMVI | Jessie Villanueva Laboratory (Wistar Institute) | RRID: CVCL_1381 |
| WM3533 | Rockland | RRID: CVCL_0B73 |
| Experimental models: Organisms/strains | ||
| Premium specific pathogen-free (SPF) embryonated chicken eggs | Charles River Laboratories | Cat# 10100326 |
| Mouse: female, 6 to 8 weeks old, N0D/SCID/IL2γR−/− | Jackson Laboratories | Cat# 005557 |
| Oligonucleotides | ||
| Non-targeting sgRNA: CACCGTTCCGCGTTACATAACTTAG | This paper | N/A |
| ARID2.1 sgRNA: CACCGAATGGCAAACTCGACGGGGA | This paper | N/A |
| ARID2.3 sgRNA: CACCGATGATGATGAGGTACCACC | This paper | N/A |
| ARID2.5 sgRNA: CACCGTTTACTACTTGCTAATGCCG | This paper | N/A |
| ARID2 shRNA: CGTACCTGTCTTCGTTTCCTA | Sigma-Aldrich | TRCN0000166264 |
| Recombinant DNA | ||
| lentiCas9-Blast | Addgene | Cat# 52962 |
| pLKO.1 eGFP/mCherry | Brian Brown Laboratory (ISMMS) | N/A |
| pLenti-puro | Addgene | Cat# 39481 |
| pLK0.1 eGFP NTsg | This paper | N/A |
| pLKO.1 mCherry ARID2 sg1 | This paper | N/A |
| pLKO.1 mCherry ARID2 sg3 | This paper | N/A |
| lentiCRISPR v2 | Addgene | Cat# 52961 |
| FG12-GFP | Bravo-Cordero Laboratory (ISMMS) | N/A |
| psPAX2 | Addgene | Cat# 12260 |
| pMD2.G | Addgene | Cat# 12259 |
| pLKO.1 shARID2 | Sigma-Aldrich | TRCN0000166264 |
| pLL-CMV-rFLuc-T2A-GFP | System Biosciences | Cat# LL300PA-1 |
| Software and algorithms | ||
| Incucyte Life-Cell Imaging System | Essen Bioscience | https://www.sartorius.com/en/products/live-cell-imaging-analysis/live-cell-analysis-software/incucyte-base-software |
| FCS Express | De Novo Software | https://denovosoftware.com/ |
| STAR | Version 2.6.0c, Dobin, 2013 | https://github.com/alexdobin/STAR |
| Rsubread | Version 2.4.3, Liao et al., 2014 | http://subread.sourceforge.net |
| DEseq2 | Version 1.30.1, Love et al. (2014) | https://github.com/mikelove/DESeq2 |
| Bowtie | Version 1.1.12, Langmead et al. (2009) | https://github.com/BenLangmead/bowtie |
| MACS2 | Version 2.1.0, Zhang et al. (2008) | https://pypi.org/project/MACS2/ |
| fastQC | Version 0.11.7, Andrews, 2019 | https://github.com/s-andrews/FastQC |
| PICARD | Version 2.2.4 | https://github.com/broadinstitute/picard/releases |
| Samtools | Version 1.9, Li et al. (2009) | http://www.htslib.org/ |
| SICER | Version 2.0, Zang et al. (2009) | https://zanglab.github.io/SICER2/ |
| deepTools | Version 3.2.1, Ramírez et al., 2016 | https://deeptools.readthedocs.io/en/develop/ |
| Bowtie2 | Version 2.1.0, Langmead et al., 2009 | https://github.com/BenLangmead/bowtie2 |
| Topdom | Version 0.0.1, Shin et al., 2015 | https://github.com/HenrikBengtsson/TopDom |
| Hi-C bench | Lazaris et al. (2017) | https://github.com/NYU-BFX/hic-bench |
| BedTools | Version 2.29.2, Quinlan and Hall (2010) | https://bedtools.readthedocs.io/ |
| ChIPSeeker | Version 1.26.2, Yu et al. (2015) | https://github.com/YuLab-SMU/ChIPseeker |
| HOMER | Version 4.11, Heinz et al. (2010) | https://github.com/IGBIllinois/HOMER |
| clusterProfiler | Version 3.18.1, Yu et al., 2012 | https://github.com/YuLab-SMU/clusterProfiler |
| Prism | Version 9 | https://www.graphpad.com |
| ImageJ | Version 2.1.0/1.53c | https://imagej.nih.gov/ij/index.html |
| RStudio | Version 1.1.46 | https://rstudio.com |