Fig. 3

Polycomb-binding is altered only at specific loci in scrib¹ wing discs. a Schematic representation of the workflow used to analyse transition in Pc-binding states on transcription-associated GATC fragments (taGATCf) that are mapping to a regulatory region surrounding a TSSs of a gene that was differentially expressed in scrib¹ versus WT RNA-seq samples. b Graph visualizes the distribution of GATC fragments classified according to a gain or loss in Pc-binding in sc–rib¹ compared to WT profiles, and according to the change in expression level of the gene in sc–rib¹ to whose TSS the GATC fragment had been mapped to. Group I (RNA—upregulated; Pc-binding—gain); group II (RNA—downregulated; Pc-binding—gain); group III (RNA—upregulated; Pc-binding—loss); group IV (RNA—downregulated; Pc-binding—loss). c Profiles visualize Pc-binding in WT and scrib¹ WIDs at indicated loci that represent known Pc target genes involved in tumorigenesis, and novel Pc target genes belonging to group II and III loci. Pc-binding levels on each GATC fragments were classified by a three-state HMM analysis to be either ‘enriched’ (red), ‘intermediate’ (orange) and ‘depleted’ (green) and visualized by centring a fragment around individual GATC motifs. GATC fragments not recovered by our DamID-Seq analysis in either genotype are shown in grey and were excluded for both genotypes in our analysis. Intron–exon structure, TSS and position of GATC motifs are indicated for each gene. Scalebar is 5 kb. d Profiles visualize the presumptive regulatory region 2.5 kb upstream to 1.5 kb downstream of the TSS of indicated genes. Domains bound by Pc in S2 cells (modENCODE) (orange), domains enriched for H3K27me3 (dark grey) and Pc (light grey) by ChIP-Seq analysis in wing discs [42] and domains with loss transitions DamID_Seq profiles in scrib¹ (light blue)