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. Author manuscript; available in PMC: 2014 Jan 1.
Published in final edited form as: Biochim Biophys Acta. 2012 Sep 6;1829(1):76–83. doi: 10.1016/j.bbagrm.2012.08.015

Fig. 3.

Fig. 3

Mechanism of single-round transcription through a nucleosome by Pol II in vitro (modified from [35]). Primary pathway (likely operates in vivo): as Pol II approaches a nucleosome (complex 1), (smaller arrows indicate direction of transcription), upstream nucleosomal DNA is partially uncoiled from the octamer (2). As Poll II proceeds, it encounters strong DNA-histone interactions and pauses immediately upstream of the position +49. As DNA re-coils on the octamer behind the enzyme, a transient Ø-loop is formed at position +49 (3), and Pol II displaces the promoter-distal end of nucleosomal DNA from the octamer surface (4, see Fig. 4), allowing its own further transcription. Strong sequence-specific interactions of H3/H4 histones with the PBS (polar barrier sequence) DNA region (complex 3) can prevent uncoiling of the downstream DNA and cause Pol II arrest. Otherwise Pol II continues transcription and the DNA-histone contacts upstream of the enzyme serve as an anchor to recover the nucleosome behind Pol II (5). An H2A/H2B dimer is lost during transcription (6); alternatively, 5–50% templates lose the entire octamer (complex 6′).