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Fig. 7 | Genome Biology

Fig. 7

From: Chromatin accessibility plays a key role in selective targeting of Hox proteins

Fig. 7

In vivo motif preferences for Hox binding in the presence of Exd/Hth. a Constrained pattern matching on in vivo binding regions defines 3 classes of consensus sequences. Matches to the pattern TGATTDAT (where D = A or G or T), based on the in vitro SELEX Exd-Hox sites [16], in defined sets of binding regions were used to create the three matrices. The binding regions used were class 1 unique Exd/Hth enhanced Lab bound, class 2 unique Exd/Hth enhanced Pb or Dfd or Scr bound, and class 3 unique Exd/Hth enhanced Antp or Ubx or Abd-A or Abd-B bound. The pattern matching allowed one mismatch. b The Class 1, 2 and 3 consensus sequences (highlighted) are the most enriched 8-mers in unbiased k-mer enrichment analysis on Exd/Hth-enhanced Hox binding regions (Hox ENH). Enrichment of the top 15 k-mers in each binding region set is plotted as a heatmap. c Correspondence of in vivo and in vitro binding specificities. The left plot shows the percentage of regions from the Exd/Hth-enhanced Hox binding regions with perfect matches to the class 1, 2, and 3 consensus sequences. The right plot shows the affinity scores for SELEX 16-mers which contain the three Class consensus sequences for the different SELEX Hox+Exd experiments in Slattery et al. [16]; class 1: green, class 2: blue; class 3: red

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