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Fig. 7 | Epigenetics & Chromatin

Fig. 7

From: Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing

Fig. 7

Sequence motifs enriched in regions of variant nucleosomes in KDM5B-depleted ES cells. a Hierarchical clustering of transcription factor binding site motifs in linker regions of shifted nucleosomes relative to the TSS (+ 1 nucleosome, upstream shift; + 1 nucleosome, downstream shift; − 1 nucleosome, upstream shift; − 1 nucleosome, downstream shift) in KDM5B-depleted ES cells. The color scale indicates enrichment (red) or underrepresentation (black) of motif occurrences. AutoSOME [68] was used to generate pair-wise affinity values. b Average MNase-Seq profiles around NANOG [69], OCT4, SOX2, and ZFX transcription factor binding sites in shLuc (left panel) and shKdm5b ES cells (right panel; red, highest ChIP-Seq signal; green, lowest ChIP-Seq signal). c Hierarchical clustering heatmap of oligonucleotide occurrences at shifted nucleosomes relative to the TSS (+ 1 nucleosome, and − 1 nucleosome) in KDM5B-depleted ES cells. The positional profiles of 6-mer motifs in 10-bp windows 130 bp upstream and downstream of the nucleosome summit are represented in the heatmap. Each row represents one k-mer. Color scale: the normalized frequency of k-mers corresponds to over- or underrepresentation. d MEME-ChIP confirmation of GC and AT motifs at sequences of shifted nucleosomes. Representative sequence logos of GC- and AT-rich motifs are shown

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