For ChIP, mouse ES cells (C57BL/6N x 129/Sv background) stably expressing FHA-Srap1 were fixed in 1% paraformaldehyde for 10 min at 37 °C, followed by quenching with 125 mM glycine for 5 min. Cells were lysed and processed using the MAGnify ChIP system (Life Sciences). Lysates were sonicated using an ultrasonic processor (Cole Parmer) at power setting 3 in 30 s pulses followed by 1 min on ice, for a total of 6 min sonication. Nucleoprotein complexes were immunoprecipitated using a mixture of M2 Flag and HA antisera (2.5 mg each) or equivalent amounts of isotype-matched mouse IgG per sample. Library preparation was performed using the Kapa HyperPrep kit, followed by 12 cycles of PCR amplification with Kapa HiFi HotStart polymerase. Amplified libraries were pooled, purified twice with 0.9X Ampure XP beads and analyzed on the Illumina HiSeq2000 or NextSeq500 for single-end reads.