Fig.3: Cohesin is required for proper folding of the inactive X chromosome at day 7 of differentiation.

(A) Schematic of expected cohesin levels versus TAD, compartment, and superstructures detected on the X chromosome at different stages of XCI, based on prior studies. Levels corresponding to day 7 DMSO control and dTAG-13 treated cells indicated.

(B) Metaplot and heatmaps of active (Xa) and inactive (Xi) X chromosome RAD21 binding by cChIP-seq in day 7 RAD21-FKBP^degron embryoid bodies treated for 8 hours with 500nM dTAG-13 or DMSO.

(C) TAD scores calculated from day 7 Xa and Xi RAD21-FKBP^degron allelic Hi-C interaction maps binned at 100kb. DMSO and dTAG-13 samples as in (B). Representative Hi-C maps shown for the indicated regions (50kb resolution, clones merged).

(D) Chromosome-wide day 7 Xi RAD21-FKBP^degron allelic Hi-C maps (250kb resolution, clones merged) and log2-ratio map (1Mb resolution). Treatment as in (B). Inset, 50kb resolution.

(E) Day 7 composite X, Xi, and Xa Hi-C maps at Dxz4-Firre superloop (100kb resolution, clones merged). RAD21 and H3K27me3 cChIP-seq at superloop anchors shown for reference. Treatment as in (B).

(F) Day 7 composite X, Xi, and Xa Hi-C maps at Kdm5c-Ogt loop (250kb resolution, clones merged). RAD21 and H3K27me3 cChIP-seq at loop anchors shown for reference. Treatment as in (B).

(G) Day 7 composite X, Xi, and Xa Hi-C maps at Bcor-Bcorl1 loop (100kb resolution, clones merged). RAD21 and H3K27me3 cChIP-seq at loop anchors shown for reference. Treatment as in (B).

(H) First Principal Component (PC1) tracks of day 7 Xa and Xi RAD21-FKBP^degron Hi-C maps. Treatment as in (B).

(I) Saddle plot analysis of compartment strength in RAD21-FKBP^degron Xi and Xa Hi-C maps (clones merged). Scores represent B-B (Xi: S2-S2), B-A (Xi: S2-S1), and A-A (Xi: S1-S1) compartment interaction strength. Treatment as in (B).

(J) Cumulative distribution plots of allelic chromosome X and chromosome 13 expression by PRO-seq in RAD21-FKBP^degron linesTreatment as in (B).