(A) Three different types of Pol II pausing induced by CPA recognition of the PAS, R-loop formation, and heterochromatin patches. Elongating Pol II (red) is shown transcribing the DNA template, with extruded, capped RNA transcript (blue) indicated. Nucleosomes are depicted by yellow barrels, with histone N-terminal tails indicated. Pol II CTD is shown as an extended tail. Red dots on the CTD and histone tails denote methylation. The hand denotes Pol II pausing. (B) Pol II arrested by base J or Reb1 DNA binding protein. Pol II is then ubiquitinated and degraded by the proteasome.