Mouse kidneys were minced in ice-cold nuclei EZ lysis buffer (Sigma, #NUC101) with scissors and homogenized with 10 (pestle A) and 5 (pestle B) strokes of 2-ml Dounce tissue grinders (DWK, #8853000002).  The homogenized samples were filtered by 100-µm and 30-µm strainers (Miltenyi, #130110917, #130110915). Nuclei were centrifuged at 300 g for 5 min at 4°C and resuspended in CUT&RUN wash buffer. Reagents in CUT&RUN Assay Kit (CST, #86652) were used throughout the assays. 500k nuclei were bound to Concanavalin A beads and incubated at 4°C overnight with antibodies (H3K9me3: abcam, #ab176916; RPB1-S2P/S5P: CST, #13546; IgG: CST, #66362). Note that RPB1-S2P/S5P antibody recognizes the Pol II C-terminal domain phosphorylated at both serine 2 and serine 5 and is used to target elongating Pol II. Following the incubation with pAG-MNase at 4°C for 1 h, DNA was digested in the presence of calcium chloride at 4°C for 1 h. STOP buffer containing yeast spike-in DNA was added to stop the digestion. The targeted DNA was eluted from nuclei at 37°C for 10 min and purified by DNA Clean & Concentrator (Zymo, #D5205). Libraries were prepared using KAPA HyperPrep Kit (Roche) with minor modifications. End repair and A-tailing reactions were carried out at 20°C for 30min, followed by inactivation at 50°C for 30 min. 100 fmol UDI barcodes (Revvity, NOVA-514150) was used for adapter ligation. The ligated DNA was cleaned up by x1.2 volume of AMPure XP beads (Beckman Coulter, #A63881). Following PCR amplification, the libraries were cleaned up three times by x1.2 volume of AMPure XP beads. The pooled libraries were sequenced by NextSeq 2000 (Illumina) to obtain 2x 51 bp paired end reads.