Defining flexible vs. inherent promoter architectures

Figures & data

Figure 1. Promoter architecture is influenced by NDR placement. Nucleosome occupancy 400 bp upstream to the TSS, in unstressed cells (left) or 60 min after treatment with 0.4 mM H₂O₂ (right) from.⁸ Upstream nucleosome occupancy is shown for 493 DPN genes (A) or 543 OPN genes (B), as defined by Tirosh and Barkai;¹⁴ genes were organized by hierarchical clustering of the upstream regions. Occupancy is shown on the same scale for both gene groups, according to the key.

Figure 2. Two classes of promoters based on NDR accessibility. Data are shown as described in Figure 1. (A) 1,069 genes with no nucleosome signal in unstressed cells, before (left) and 60 min after treatment with 0.4 mM H₂O₂ (right) from.⁸ (B) 288 genes whose promoters rank in the top 5% based on nucleosome signal in the NDR. Genes in both classes were organized by position of the NDR. The contrast was increased for genes in (B) to distinguish the NDR.

Huebert DJ, Kuan PF, Keleş S, Gasch AP. Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 2012; 32:1645 - 53; http://dx.doi.org/10.1128/MCB.06170-11; PMID: 22354995

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Tirosh I, Barkai N. Two strategies for gene regulation by promoter nucleosomes. Genome Res 2008; 18:1084 - 91; http://dx.doi.org/10.1101/gr.076059.108; PMID: 18448704

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