Skip to main content
Fig. 6 | Epigenetics & Chromatin

Fig. 6

From: Roles of cofactors and chromatin accessibility in Hox protein target specificity

Fig. 6

Abd-B specific and cofactor-dependent Ubx peaks in DNase1-inaccessible chromatin. a Comparative overlap analysis between Abd-B/Ubx common and Abd-B specific peaks with DNase1 peaks. Almost all (97 %) of the Abd-B/Ubx common peaks overlap with DNase1, while only 58 % of the Abd-B specific peaks overlap with DNase1. Hox peak sets were derived by the overlap analysis of Abd-B and Ubx Experiment 1; using q-value 1e−10 peaks. DNase1 peaks are q-value 1e–2. b Comparative overlap analysis between Ubx + Hth/Ubx common and Ubx + Hth specific peaks with DNase1 peaks. Almost all (96 %) of the Ubx + Hth/Ubx common peaks overlap with DNase1, while only 71 % of the Ubx + Hth specific peaks overlap with DNase1. Hox peak sets were derived by the overlap analysis of Ubx + Hth and Ubx Experiment 2; using q-value 1e−10 peaks. DNase1 peaks are q-value 1e–2. c For each selected peak set, the median bedGraph score per peak was calculated and the distribution plotted, showing that Abd-B specific and cofactor-dependent Ubx (Ubx + Hth specific) peaks have markedly reduced DNase1 accessibility. Hox peak sets were derived by overlap analysis as described in a and b but using q-value 1e–2 peaks. d Using the colour-coded chromatin state classification scheme described in Kc cells [25], the plot shows the prevalence of different chromatin states across the Kc cell genome. e Chromatin state prevalence plots for DNase1 (all q-value 1e–2 peaks), Ubx (all q-value 1e–2 peaks, Experiment 1), Abd-A (all q-value 1e–2 peaks) and Abd-B (all q-value 1e–2 peaks). f Chromatin state prevalence plots for Abd-B/Ubx common (highest 1000 peaks) and Abd-B specific (highest 1000 peaks). Peak sets were derived as described in c. The Abd-B specific peaks are strongly shifted towards the ‘repressed’ blue and black states. g Chromatin state prevalence plots for cofactor-independent Ubx peaks (Ubx + Hth/Ubx common; highest 1000 peaks) and cofactor-dependent Ubx peaks (Ubx + Hth specific; highest 1000 peaks). Peak sets were derived as described in c. The cofactor-dependent Ubx peaks are strongly shifted towards the ‘repressed’ states

Back to article page