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. 2016 Aug 3;44(21):10091–10105. doi: 10.1093/nar/gkw684

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© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 4. — The +1 nucleosome is implicated in Pol II pausing. (A) The +1 nucleosome placement is further downstream of TSS in Tetrahymena than in yeast. Nucleosome distribution around TSS (± 1 kb) is aggregated over 15,841 well-annotated genes in Tetrahymena (Supplemental File S2) and 2231 genes in yeast (71). Note the downstream placement of the +1 nucleosome (yeast: 56 bp; Tetrahymena: 138 bp), increase in NRL (yeast: 167 bp; Tetrahymena: 200 bp), and a lack of nucleosome arrays upstream of TSS, when Tetrahymena is compared with yeast. (B) Poly (dA:dT) tract distribution relative to TSS in Tetrahymena (red) and yeast (beige). A5/T5 (AAAAA or TTTTT) distribution around TSS (± 1kb) is calculated using the 5 bp bin. C) Distribution of nucleosome, Pol II, and H3K4 methylation (from top to bottom) in a genomic region. Raw coverage of the input (nucleosome) and ChIP-Seq DNA fragments (Pol II and H3K4 methylation) was shown. Note the enrichment of Pol II and H3K4 methylation at the 5′ end of the gene body. (D) Zoom-in of a region containing a single gene. Note Pol II enrichment at the +1 nucleosome. (E) Composite analysis of Pol II distribution in the gene body. Well-modeled long genes (≥1.5 kb) are ranked from high to low by their expression levels and divided into 10 quantiles. Normalized Pol II distribution around TSS is aggregated over all genes in a quantile. (F) Composite analysis of H3K4 methylation in the gene body.