Fig. 2

DamID and ChIP profiles of Polycomb-binding sites correlate. a–a′ Wild-type WID (a) and scrib¹ WID stained with DAPI (cyan) and phalloidin (red). Scale bar: 100 µm. b Characteristic DNA smear formed by DamID methylation-dependent PCR products obtained from hsflp-induced samples isolated from WT WIDs (lane 1 and 2) or scrib¹ WIDs (lanes 3 and 4). c Box plot comparing the distribution of the Pc-binding intensities (log₂) at individual GATC fragments (normalized to Dam) in WT and scrib¹ DamID-seq samples. Pc-binding intensities averaged over two biological replicates are shown. d Heat-scatterplot showing the correlation of Pc-binding intensities (log₂) at individual GATC fragments (normalized to Dam) in WT and scrib¹. (Pearson’s correlation, r = 0.47). e ChIP-chip Pc-binding profiles (modENCODE) from three different sources (S2 cells, DmBG3 cells and embryo) and DamID-seq profiles mapped to individual GATC fragments obtained in this study (WT and scrib¹ WID) visualized across the BX-C cluster (demarcated by dotted lines). GATC motifs mapping to the genome sequence are indicated below. e′ Pearson’s correlations for a comparison of Pc-binding intensities in ChIP-chip profiles (modENCODE) from three different sources (S2 cells, DmBG3 cells and embryo) and Pc-binding intensities WT and scrib¹ WID DamID-seq Pc profiles at GATC fragments mapping to microarray probe sequences. f Percentage of genomic sites in scrib¹ compared to WT WID that lose (loss), acquired new (gain) and had no change (no change) in Pc-binding visualized for each chromosome and the whole genome. Loss, gain and no-change transitions were determined by transitions between ‘enriched’, ‘intermediate’ and ‘depleted’ Pc-binding states classified by a three-state HMM analysis. Note that the no-change category contains GATC fragments that were classified as ‘enriched’, ‘intermediate’ and ‘depleted’ for Pc-binding and thus includes Pc target and non-target genes