ChIP-seq Analysis Protocol

ChIP analysis was conducted as described [33 (link)]. Briefly, DNA was fragmented by sonication to an average size of 400–500 bp for standard ChIP or of 100–200 bp for high-resolution ChIP. Immunoprecipitation was conducted using Dynabeads Protein G (Invitrogen, Carlsbad, CA, USA), anti-FLAG-tag antibody (Sigma-Aldrich, St. Louis, MO, USA; M2), anti-PA-tag antibody (FujiFilm Wako Pure Chemical Corporation, Osaka, Japan; NZ-1), and polyclonal antibody against Rap1 (Santa Cruz Biotechnology, Dallas, TX, USA; yC-19) or Hmo1 [29 (link)]. Real-time quantitative PCR analyses were performed using a KAPA SYBR Fast qPCR kit (Kapa Biosystems, Wilmington, MA, USA). Each experiment was performed in triplicate, and the mean and standard deviation of the ratio of immunoprecipitated DNA to input DNA (IP/input) were calculated. Primer pairs used for quantitative PCR are described in the S1 text.