Figure 6. Proposed pathways of transcription through a nucleosome by Pol II- or Pol III-type mechanisms: the structure of the EC+49 dictates the fate of the nucleosome on transcription.

As different RNAPs enter the nucleosome and pause within the +45 region (complex 1 or 1’), they form structurally different complexes at the position +49. Pol II forms a stable intranucleosomal Ø-loop-containing intermediate 2. Further transcription by Pol II results in uncoiling of the downstream nucleosomal DNA (complex 3) and nucleosome survival. In contrast, during transcription by Pol III-type mechanism DNA is uncoiled behind the enzyme in the EC+49 and the Ø-loop forms with much lower efficiency (complex 2’). In this case, further transcription would result in partial uncoiling of DNA from the octamer in front of the enzyme (complex 3’), formation of a larger intranucleosomal DNA loop and nucleosome translocation.