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. 2015 Nov 17;44(5):2110–2124. doi: 10.1093/nar/gkv1214

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© The Author(s) 2015. 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/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Positioning of nucleosomes on landmark transcriptional sites is largely transcription-independent. (A) Individual (heatmap, T40, log2-MNase-Seq/gDNA ratio) and average (line-graph, T-all) MNase-seq occupancy profiles around transcriptional landmark sites normalized by gDNA. The bottom panels show corresponding GC-content profiles. Ten-thousand non-overlapping random sites were selected uniformly across the genome as control. Note: for TSS and TTS individual occupancy profiles are sorted based on the mRNA abundance of the corresponding gene, while all other profiles are sorted based on distance to another landmark site (as indicated). Dashed grey line indicates the approximate position of the neighbouring landmark site. Heatmaps displaying individual profiles for all landmark sites sorted in three different ways (hierarchical clustering, mRNA abundance, distance to nearest landmark site) can be found in Supplementary Figure S4. (B) Frequency profiles of longer than 6 nt homopolymeric tracks (poly dA (red), poly dT (blue)) around transcription landmark sites. (C) Average normalized profiles (top) and GC-content profiles (bottom) for euchromatic genes in T40 separated into four different mRNA abundance quartiles. Darker colours reflect higher mRNA abundance.