library_construction_protocol: mESCs were trypsinized (Gibco, 12604-013) and counted prior to crosslinking. Cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS for 5 min then quenched with 2.5 M glycine. Crosslinked cells were washed twice with cold PBS then lysed with 10 ml of cold Lysis Buffer 1 (50mM Hepes–KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) by rotating for 10 min at 4°C. After pelleting at 1350xg for 5 min at 4°C, nuclei were lysed in 5 ml Lysis Buffer 2 (10mM Tris–HCl pH 8, 200mM NaCl, 1mM EDTA, and 0.5mM EGTA) by rotating for 20 min at 4°C. After pelleting at 1350 × g for 5 min at 4°C, supernatant was removed and tubes were washed with 1 ml of cold Shearing Buffer (10mM Tris pH 7.5, 1mM EDTA, 0.1% SDS) and spun at 1350 × g for 5 min. Chromatin (pellet) was resuspended in 1 ml of Shearing Buffer and 5% of HEK293T chromatin (extracted using the same protocol) was added prior to sonication to be used later for spike-in normalization. Sonication of chromatin was performed using a Covaris E220 in milliTUBEs (Covaris, 520130) with the following settings: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 20 min. Following sonication, insoluble material was pelleted and removed by spinning samples for 10 min at 15,000 rpm at 4°C. ChIPs were performed using RAD21 antibody (5ug, Abcam ab992), WDR5 antibody (4uL, CST D9E1I), SP1 antibody (5ug, Millipore 07-645), or Rabbit IgG antibody (5ug, Bethyl P120-101) incubated with 50uL Protein A Dynabeads (Invitrogen 10002D), or using NFYA antibody (2.5ug, Santa Cruz sc-17753) or Mouse IgG (2.5ug, Santa Cruz sc-2025) incubated with 50uL Protein G Dynabeads (Invitrogen 10004D). Antibodies were incubated with beads for 4-6 h prior to the IP. Beads were washed three times with PBS to remove unbound antibody prior to the addition of chromatin. 2% Input was removed, then chromatin from 1 × 107 cells was added to antibody-conjugated beads and incubated in ChIP buffer (20mM Tris pH 8, 2mM EDTA, 0.1% SDS, 225mM NaCl, and 1.5% Triton X-100), rotating overnight at 4°C. The next day, beads were washed with cold Wash Buffer 1 twice (20mM Tris pH 8, 2mM EDTA, 0.1% SDS, 150mM NaCl, and 1% Triton X-100), then with cold High Salt Wash Buffer (20mM Tris–HCl pH 8, 500mM NaCl, 2mM, EDTA, 0.1% SDS, and 1% Triton X-100), cold LiCl Wash Buffer (10mM Tris–HCl pH 8, 250mM LiCl, 1mM EDTA, and 1% NP-40), and cold TE Wash Buffer (10mM Tris pH 8, 1mM EDTA, and 50mM NaCl), each for 5 min rotating at 4°C. All buffers listed above were supplemented with 1X protease inhibitor cocktail (PIC) (Sigma Aldrich, 11697498001) and 1mM PMSF (ThermoFisher 36978). Chromatin was eluted from beads by adding 100uL IP Elution Buffer (50mM Tris pH 8, 10mM EDTA, and 1% SDS) and incubating at 65°C for 1 hour, vortexing every 15 min. Supernatant (and 2% Input chromatin samples) was incubated at 65°C overnight with addition of 5uL Proteinase K (NEB, P8107S) to reverse crosslinks. The next day, DNA was purified using a ChIP DNA Clean and Concentrate kit (Zymo, D5205), per manufacturer's instructions. Samples were then used for ChIP-qPCR and/or ChIP-seq. ChIP-Sequencing libraries were prepared using a Hyper Prep kit (Roche/Kapa Biosciences, KK8502) according to manufacturer's instructions. 50bp paired-end sequencing was performed on NovaSeq 2000 P2, NextSeq 2000 P3, and NovaSeq 6000 S1 platforms using Illumina reagents according to manufacturer's instructions by the High Throughput Sequencing Facility at UNC Chapel Hill.