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. Author manuscript; available in PMC: 2010 Dec 1.
Published in final edited form as: Nat Struct Mol Biol. 2010 May 9;17(6):745–752. doi: 10.1038/nsmb.1798

Figure 2.

Figure 2

Transcription through a nucleosome shows a distinctive 10 bp periodicity pausing pattern. (a) RNAP transcribed through a nucleosome in the forward direction of the 601 NPE as indicated by the template cartoon (identical to Fig. 1d). PAGE analysis of transcription through naked DNA and nucleosomal DNA shows that as RNAP proceeded into the nucleosome, a distinctive periodicity of ~ 10 bp highlighted all nucleosome-induced pause sites within Regions 1 and 2. Transcription pause sites are marked as distances from the dyad. (b) RNAP transcribed through a nucleosome from the reverse direction of 601 NPE as indicated by the template cartoon. Although RNAP effectively transcribed a different sequence, all nucleosome-induced pauses were again highlighted by a distinctive ~ 10 bp periodicity within Regions 1 and 2. The pause site at the end of the 601 NPE might be intrinsic pausing (compare transcription through naked DNA and nucleosomal DNA). Also note that at this pause site the leading edge of the RNAP was ~ 20 bp downstream of the 601 NPE.