Fig. 6

Gene expression changes mediated by loss of STAG2 are linked with altered domain structure. a ChIP-Seq generated binding profile tracks for STAG2, STAG1 and CTCF across the HOXA cluster region, displaying consistent STAG1 and CTCF binding profiles in the absence of STAG2. ChIP-Seq generated H3K27ac and H3K273me tracks show increased H3K27ac across the HoxA locus, with decreased H3K273me across the region encompassing HOXA1-7 in ΔSTAG2 cells, compared to STAG2-WT cells. In keeping with this, the normalised RNA-seq read count track demonstrates increased transcription/gene expression across the HOXA1-7 region in the Δ STAG2 cells compared to STAG2-WT cells (different scales were used to display H3K27ac, H3K273me and RNA-Seq read count tracks across the HOXA1-7 and HOXA9-13 regions in order to highlight the differences in these regions between STAG2-WT and ΔSTAG2 cells). b Heatmap showing the % change in gene expression between STAG2-WT and ΔSTAG2 cells of all genes located within the HOXA cluster represented above, in each replicate (Rep) RNA-Seq experiment carried out. c Virtual 4C plot displaying interactions anchored at the CTCF site located within the SKAP2 gene located upstream of the HOXA cluster. CTCF binding tracks along with RefSeq gene tracks have been included for comparison. Additionally, v4c generated interaction loops across the region have been drawn, indicating the reduced interaction frequency between the SKAP2 and the C7/9 CTCF sites, and the increased interaction frequency between the SKAP2 and the C10/11 CTCF sites in ΔSTAG2 cells compared to the STAG2-WT cells. This demonstrates altered 3D structure within the HOXA cluster in ΔSTAG2 cells and indicates the inclusion of early HOX genes (HOXA1-A7) within the transcriptionally active TAD controlling expression of the late HOX genes (HOXA9-13) in these cells