KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-H3 antibody | Cell Signaling Technology | Cat#4620; RRID: AB_1904005 |
| anti-H3K27Ac | Abcam | Cat#ab4729; RRID: AB_2118291 |
| anti-Ser5P PolII | Abcam | Cat#ab5131; RRID: AB_449369 |
| anti-NIPBL | Bethyl Laboratories | Cat#A301-779A; RRID: AB_1211232 |
| normal rabbit IgG | EMD Millipore | Cat#12-370; RRID: AB_145841 |
| PolII | Santa Cruz Biotechnology | N20x; Cat#sc-899; RRID: AB_632359 |
| Spt5 | Santa Cruz Biotechnology | H-300x; Cat#sc-28678; RRID: AB_668824 |
| Ikaros D10E5 Rabbit mAb | Cell Signaling Technology | Cat#9034; RRID: AB_2797691 |
| Aiolos D1C1E Rabbit mAb | Cell Signaling Technology | Cat#15103; RRID: AB_2744524 |
| E2A | Cell Signaling Technology | Cat#12258; RRID: AB_2797860 |
| ZEB1 | Proteintech | Cat#21544-1-AP; RRID: AB_10734325 |
| YY1 | Santa Cruz Biotechnology | Cat#sc-7341; RRID: AB_2257497 |
| PU.1 | Cell Signaling Technology | Cat#2258; RRID: AB_2186909 |
| Helios D8W4X | Cell Signaling Technology | Cat#42427; RRID: AB_2799221 |
| IRF4 | Cell Signaling Technology | Cat#4964; RRID: AB_10698467 |
| MEF2B | Abcam | Cat#ab33540; RRID: AB_2142738 |
| BCL6 | Cell Signaling Technology | Cat#5650; RRID: AB_10949970 |
| IRF8 | Cell Signaling Technology | Cat#5628; RRID: AB_10828231 |
| NFKB1 | Cell Signaling Technology | Cat#12540; RRID: AB_2687614 |
| ELF1 | Bethyl laboratories | Cat#A301-443A; RRID: AB_960983 |
| ELF2 | Invitrogen | Cat#PA5-52247; RRID: AB_2640985 |
| p65 | Cell Signaling Technology | Cat#8242; RRID: AB_10859369 |
| c-Rel | Cell Signaling Technology | Cat#12659; RRID: AB_2797983 |
| Nuclear Pore Proteins | Abcam | Cat#ab24609; RRID: AB_448181 |
| Rad21 | Cell Signaling Technology | Cat#4321; RRID: AB_1904106 |
| Pax5 | Novus | Cat#NBP2-29905 |
| YY2 | Sigma | Cat#HPA030335; RRID: AB_2673434 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Ampure XP beads | Beckman Coulter | Cat#A63880 |
| Gene Pulser Electroporation Buffer | BioRad | Cat#1652676 |
| Proteinase K | Cell Signaling Technology | Cat#10012 |
| T4 DNA ligase | Promega | Cat.#M1804 |
| T7 endonuclease I | New England Biolabs | Cat#M0302 |
| Blasticidin | InvivoGen | Cat# ant-bl-5 |
| Dynabeads MyONE C1 streptavidin beads | Life Technologies | Cat#65002 |
| Hexammine cobalt (III) chloride | Sigma Life Sciences | Cat#H7891 |
| PEG8000 | Sigma Life Sciences | Cat#P2139 |
| micrococcal nuclease | Cell Signaling Technology | Cat#10011 |
| Protein G Magnetic beads | Cell Signaling Technology | Cat#70024 |
| SimpleChIP DNA Purification Buffers and Columns | Cell Signaling Technology | Cat#14209 |
| Hygromycin | EMD Millipore | Cat#400050 |
| Dynabeads Protein G beads (ChIP-seq of H3, H3K27Ac, Ser5P PolII, PolII and Spt5) | Invitrogen | Cat#10004D |
| Protease inhibitor cocktail complete, EDTA free | Roche Merck | Cat#5056489001 |
| Critical Commercial Assays | ||
| SimpleChIP enzymatic Chromatin IP kit | Cell Signaling Technology | Cat#9003 |
| iTaq universal SYBR green supermix | Bio-Rad | Cat#1725121 |
| Phusion Hot Start Flex DNA polymerase | New England Biolabs | Cat#M0535L |
| In-Fusion | Takara | Cat#638911 |
| TruSeq ChIP Sample Preparation kit | Illumina | Cat#IP-202-1012 |
| Ultra II DNA Library Prep Kit | New England Biolabs | Cat#E7645 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE139810 |
| ChIP-seq data for MYC | Seitz et al., 2011 | GSE30726 |
| ChIP-seq data for NIPBL, H3K4me1 and H3K4me3 | Qian et al., 2014 | GSE62063 |
| Experimental Models: Cell Lines | ||
| human: Ramos cell line | Laboratory of Michael Neuberger | N/A |
| human: 293T cell line | ATCC | CRL-3216 |
| chicken: DT40 cell line | Laboratory of Jean-Marie Buerstedde | N/A |
| Oligonucleotides | ||
| Primers for NIPBL ChIP, see Table S3 | This paper | N/A |
| Primers for splinkerette, see Table S3 | This paper | N/A |
| Primers for HTISA, see Table S3 | This paper | N/A |
| chr11 gRNA-1: AAACAATGTCCGCCTACCCT | This paper | N/A |
| chr11 gRNA-2: AGCTTCGGTGCCACACAACG | This paper | N/A |
| chr22 gRNA-1: CCTAATTCAGCATGCGTTGG | This paper | N/A |
| chr22 gRNA-2: AAGCCTAATTCAGCATGCGT | This paper | N/A |
| Recombinant DNA | ||
| Px458 | Ran et al. (2013) | Addgene plasmid #48138 |
| pExpress | Forman and Samuels, 1991 | N/A |
| pIgLGFP2 | Blagodatski et al., 2009 | N/A |
| pGFP7 | This paper | N/A |
| GFPnovo2 | Arakawa et al., 2008 | N/A |
| pRV3 | Senigl et al., 2012 | N/A |
| SuperDIVAC | Williams et al., 2016 | N/A |
| psPAX2 | unpublished | Addgene plasmid # 12260 |
| pVSV-G | Clontech | Cat#631530 |
| Software and Algorithms | ||
| CRISPR Design | http://zlab.bio/guide-design-resources | |
| Broad Institute’s sgRNA designer | Doench et al. (2016) | https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design |
| Bowtie 1.1.2 | Langmead et al. (2009) | https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/ |
| MACS 1.4.3 | Zhang et al., 2008 | https://pypi.org/pypi/MACS/1.4.3 |
| UCSC database | Karolchik et al., 2004 | https://genome.ucsc.edu |
| UCSC Genome Browser | Kent et al., 2002 | https://genome.ucsc.edu |
| Bedtools | Quinlan and Hall, 2010 | https://github.com/arq5x/bedtools2 |
| R | R Development Core Team (2008) | https://www.r-proiect.org/ |