Fig. 3

Loss of STAG2 alters domain architecture and interaction frequency of the 3D genome. a Representative HiChIP contact matrixes displaying interactions covering an 8 Mb region of chromosome 2 and a 28 Mb region of chromosome 4, highlighting the reduced interaction frequency of smaller loop domains, maintenance of intermediate sized domains and formation of larger domains in ΔSTAG2 cells compared to STAG2-WT cells. b Density plot showing the distribution of domain scores generated using the Arrowhead algorithm on CTCF HiChIP data generated from STAG2-WT and ΔSTAG2 cells indicating reduced domain interaction frequency in ΔSTAG2 cells, compared to STAG2-WT cells. Dotted lines represent the median domain scores. c Density plot showing distribution of domain lengths called in the STAG2-WT and ΔSTAG2 cells demonstrating loss of smaller domain interactions, maintenance of intermediate size interactions and increased frequency of larger domain interactions in ΔSTAG2 cells compared to STAG2-WT cells. Dotted lines represent the median domain lengths. d Virtual 4C (V4c) plot displaying interactions anchored at a domain boundary region 11 Mb into chromosome 2 and 30.7 Mb into chromosome 4 demonstrating significantly reduced interaction frequency with this anchor point in ΔSTAG2 cells compared to STAG2-WT cells. e Density plot showing distribution of loop lengths called in the STAG2-WT and Δ STAG2 cells, indicating the formation of similar sized loops in both STAG2-WT and ΔSTAG2 cells. Dotted lines represent the median loop sizes. f Aggregate Peak Analysis plots using loops called in the STAG2-WT cells as inputs, scaled internally indicating significantly reduced loop signal intensity in Δ STAG2 cells in comparison to STAG2-WT cells