Fig. 7

Characteristics of Abd-B peaks in DNase1-inaccessible chromatin. a Enrichment of a set of core Hox binding 5-mers (as described in Fig. 5) in Abd-B peaks in accessible (Abd-B and DNase1) and inaccessible (Abd-B not DNase1) chromatin. Peak sets were derived by the overlap analysis of Abd-B and DNase1; using q-value 1e–2 peaks. Although the DNase1-inaccessible peaks generally have higher 5-mer enrichments, the profiles are similar. b Density analysis of matches to the Abd-B PWM (MA0165.1, JASPAR database) on the left and to the Ubx PWM (MA0094.2, JASPAR database) on the right. The Abd-B peaks in inaccessible chromatin (AbdBnotDNase1) and the Abd-B specific peaks (AbdBnotUbx) have a higher density of matches to the Abd-B PWM compared to peaks in accessible chromatin (AbdBandDNase1) or Abd-B/Ubx common peaks (AbdBandUbx). Similarly, the cofactor-dependent Ubx peaks (UbxHthnotUbx) have a higher density of matches to the Ubx PWM compared to cofactor-independent peaks (UbxHthandUbx). Peak sets were derived by the overlap analysis of Abd-B and DNase1, Abd-B and Ubx Experiment 1, Ubx + Hth and DNase1, and Ubx + Hth and Ubx Experiment 2; using q-value 1e–2 peaks. c Comparative DNA shape analysis, showing that the average predicted minor groove width for Abd-B peaks in inaccessible chromatin (Abd-B not DNase1) is narrower in a region of 200 bp centred on the peak summit, compared to the Abd-B peaks in accessible chromatin (Abd-B and DNase1) where the average predicted minor groove width is wider. This narrowing in the minor groove width is not observed in the Ubx + Hth peaks occurring in inaccessible chromatin. DNase1 peak summits have a local increase in minor groove width. Peak sets were derived as described in b. DNase1 peaks are q-value 1e−2. d Comparative GC composition analysis, showing that Abd-B peaks in inaccessible chromatin (Abd-B not DNase1) are associated with a lower GC content compared to Abd-B peaks in accessible chromatin (Abd-B and DNase1). This lower GC content is not observed in the Ubx + Hth peaks occurring in inaccessible chromatin. DNase1 peak summits have a prominent local increase in GC content. Peak sets are the same as in c