M2 monoclonal

Strains DMF11, DMF14, RPB081, and DMF36 were used for all ChIP experiments. Subcultures were grown in LB at 37°C with aeration to an OD₆₀₀ of 0.5–0.7. Cultures were harvested, crosslinked, sonicated, and immunoprecipitated as previously described [74] (link), with minor modifications. Anti-FLAG (2 µL per IP, M2 monoclonal; Sigma) or anti-σ⁷⁰ (1 µL per IP; Neoclone) antibodies were used for all immunoprecipitations, both for ChIP-qPCR and ChIP-seq. ChIP and input DNA was purified using Zymo PCR Clean and Concentrate kit. Samples were analyzed using qPCR as previously described [74] (link). Oligonucleotides used to amplify the bglB control region and regions of interest are described in Table S6. ChIP-qPCR experiments were utilized 3–7 biological replicates per strain. Complete ChIP-qPCR data is presented in Table S1.

The following antibodies were used in immunoblotting, immunprecipitation and ChIP:
TRIM33 (3E9, Euromedex for WB and IP; A301-059A, Bethyl for ChIP), SPT16 (sc-28734, Santa Cruz), SSRP1 (10D1, Biolegend), PU.1 (sc-352X, Santa Cruz), ATP1B3 (ab137055, Abcam), RNA POLII (sc-9001X, Santa Cruz), H3K4me3 (07-473, Millipore), H3K79me2 (ab3594, Abcam), H3K36me3 (ab9050, Abcam), FLAG (M2 monoclonal, Sigma Aldrich).
Primer sequences for RT-qPCR are available upon request.