Supplementary Figure 1: De novo analysis of the CTCF binding motifs and footprints in mouse erythroid cells. | Nature Cell Biology

Supplementary Figure 1: De novo analysis of the CTCF binding motifs and footprints in mouse erythroid cells.

From: Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

Supplementary Figure 1

(a) CTCF consensus binding motif in forward and reverse orientation resulting from MEME motif analysis of CTCF ChIP-seq (2 independent experiments in which 2 animals were analysed in total) in erythroid cells. Core (C), upstream (U), and downstream (D) sequence elements are identified with preferential spacing to the core motif (spacer, red bar histograms). (b) Plots of the average DNaseI footprints of C, UC, and UCD motif containing CTCF binding sites in forward orientation (top panel) and reverse orientation (lower panel). Upper (red, +) and lower (blue, -) strand specific DNaseI cleavage signals are shown. Footprints are averaged over the total number of sites in each category (indicated between parentheses). (c) Normalised CTCF ChIP-seq (RPKM, 2 independent experiments in which 2 animals were analysed in total) annotated with the CTCF site names and orientation at the α-globin locus in erythroid cells. Gene annotation is Refseq. DNaseI footprints and top CTCF binding motif hit for each of the CTCF binding sites. Motif P-values are shown (as explained in Fig. 1c). Orientation is indicated by the colour of the arrow over the core motif (C); forward (red) or reverse (blue). Upstream motif (U) is shown in green and downstream motif (D) in yellow.

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