Figure 7. Changes in CTCF- and RAD21-mediated contacts suggests loop extrusion as a mechanism for forming new interactions.
(A) Metaplots of HS over Ctrl log2 FC of RAD21 HiChIP signal showing HS-induced increase in interactions escaping lost CTCF loops on F-R, F- F and R-R anchors.
(B) Metaplots of HS over Ctrl log2 FC of H3K4me1 HiChIP signal showing HS-induced increase in interactions escaping lost CTCF loops on F-R, F- F and R-R anchors.
(C) NIPBL knockdown impairs rearrangements of H3K4me1 interactions found in (B) based on H3K4me1 HiChIP in siNIPBL cells.
(D) Metaplots of RAD21 HiChIP on forward-reverse (F-R, top) and forward-forward (F-F, middle) CTCF loops showing extrusion lines in the same direction as CTCF motifs. The extrusion lines from the left F anchors of F-F loops continue after passing the right F anchor, whereas the line from left F anchors of F-R loops is greatly reduced after passing the right R anchor. Subtraction of FR from the FF metaplots more clearly shows the differences in the extrusion lines between these two types of loops, indicating the preferential pause of the cohesin complex at F-R sites.
(E) (Top) Metaplot of actual RAD21 HiChIP data on all F-R CTCF loops showing increase of signal on extrusion lines from the left F anchor to the right R anchor. Regions between F and R anchors were scaled to 10 bins. A: Forward CTCF anchor. B-F: non-CTCF bins inside loops used as control random extrusion start sites in Figure 7F.
(Middle) Metaplot of simulated RAD21 HiChIP signals based on the assumption that RAD21 starts extrusion from random sites inside F-R CTCF loops, showing increased signal on the extrusion lines from the left F to the right R anchor. Red dashed line indicates the same line in Figure 7G.
(Bottom) Metaplot of simulated RAD21 HiChIP signals based on the assumption that RAD21 starts extrusion from CTCF sites of F-R CTCF loops. Results show constant signal on the extrusion lines from the left F to the right R anchors. Green dashed line indicates the same line in Figure 7G.
(F) Slopes of signals of actual Hi-C enrichment on lines starting at CTCF forward motif and non-CTCF anchors A, B, C, D, E, F shown in Figure 7E (top). Same colors under A-F in Figure 7E (top) diagrams were used for lines starting at A-F locus.
(G) Slopes of signals from actual and simulated Hi-C enrichment on lines starting at CTCF forward motif. Red dotted lines were labeled in Figure 7E (middle) representing slopes anchoring the CTCF site in random-starting simulation matrix, green dotted lines were labeled in Figure 7E (bottom) representing slopes anchoring the CTCF site in CTCF-starting simulation matrix.