The chromatin remodeler Ino80 mediates alternative RNAPII pausing site determination

Promoter-proximal pausing of RNAPII is a critical step in early transcription elongation to precisely regulate gene expression. Here, we observed evidence of promoter-proximal pausing like distributions of RNAPII in S. cerevisiae. We find that Ino80p loss caused the transition of RNAPII pausing to the alternative pausing site at which is tightly associated with the +1 nucleosome. These Ino80p dependent genes showed better nucleosome positioning around the main pausing site which suggested the regulation of RNAPII pausing by Ino80p in a nucleosome context-dependent manner. Furthermore, we examined the similar INO80 dependent RNAPII pausing site determination in mESCs. Altogether, we hypothesize a highly conserved role of the chromatin remodeling Ino80 complex in controlling the early RNAPII elongation to establish intact pausing in various organisms, from budding yeast to mouse. Overall design: For S. cerevisiae: PRO-seq and PRO-cap libraries that were generated in Ino80p-AID cells and various deletion mutants. A fixed amount of S. pombe cells were used for spike-in control. For mouse embryonic stem cells (mESCs): PRO-seq libraries that were generated in mESCs transfected with either siEGFP or siINO80.