ChIP-qPCR.

Roughly 10 μg of chromatin was used for each ChIP. TRExBCBL1-RTA cells were treated with 1 μg/mL Doxy for 0 or 24 h, and cross-linked with 1% formaldehyde for 10 min at room temperature (RT) then quenched using 0.125 M glycine. Cells were washed with ice-cold 1× PBS then resuspended in ice-cold swelling buffer (5 mM Pipes pH 8.0, 85 mM KCl, 1% Igepal). Cells were then homogenized using a glass douncer, then incubated in nuclei lysis buffer (50 mM Tris-Cl pH 8.1, 10 mM ethylenediaminetetraacetic acid [EDTA], 1% sodium dodecyl sulfate [SDS]) plus protease inhibitor on ice for 30 min, then subjected to sonication using Bioruptor Pico (Diagenode). The nuclei lysates were then diluted at least fivefold with ice-cold IP buffer (50 mM Tris pH 7.4, 150 mM NaCl, 1% Igepal, 0.25% deoxycholic acid, 1 mM EDTA) with protease inhibitor, then incubated with antibody of interest overnight in 4 °C. Magnetic protein A/G beads (Pierce) were used to pull down each ChIP for 2 h at 4 °C, then the immunoprecipitant was washed twice with IP wash buffer 1 (same as IP dilution buffer, without the protease inhibitor) then twice with IP wash buffer 2 (100 mM Tris-Cl pH 9.0, 500 mM LiCl, 1% Igepal, 1% deoxycholic acid), both at RT. The final antibody/chromatin complexes were eluted using IP elution buffer. After elution, DNA was purified using MinElute PCR clean up kit (Qiagen) and subjected to qPCR or further processed as ChIP-seq library. Primer sequences used for ChIP-qPCR are found in SI Appendix, Table S1.