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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 5. — The nucleosome landscape can be predictive for functional DNA motifs. Smoothened, gDNA-corrected average nucleosome occupancy profiles around the top 394 or 726 scoring occurrences with P-value ≤ 8.43 × 10⁻⁵ of the TGCATGCA motif that are located in (A) upstream or (B) coding regions. (C and D) Screenshot of the nucleosome landscape (MNase-Seq-over-gDNA ratio for sub + mono-nucleosomal fragments) around two TGCATGCA motifs. Motif +/− 25 nt upstream of genes PF3D7_1312700 (C) and PF3D7_0114000 (D) is highlighted (blue and pink) and used for DNA pulldown experiments. Blue gene: forward strand; Red gene: reverse strand. (E and F) Scatterplot displaying the quantitative proteomic analysis of duplicate, label-swap DNA pulldowns performed with 500 μg mixed-stage nuclear extract. Statistically significant outliers (FDR < 5%) displaying preferential binding to TGCATGCA (green) or mutated-motif (red) containing probes upstream of genes PF3D7_1312700 (E) or PF3D7_0114000 (F) are marked. The y-axis of plot (F) is not auto-scaled and excludes a single data-point located at (x,y)-coordinates (−0.48, 5.06). (G) Table displaying steady-state mRNA level heatmaps (log2(Cy5/Cy3)-ratio from (59)) and the consensus-motif recognized by recombinant DNA-binding-domain for PF3D7_1107800 (from (44)) and PF3D7_1466400 (from (56)).