Extended Data Figure 9: Eigenvector change upon Nipbl deletion is activity-dependent and uncorrelated with changes in gene expression or epigenetic marks. | Nature

Extended Data Figure 9: Eigenvector change upon Nipbl deletion is activity-dependent and uncorrelated with changes in gene expression or epigenetic marks.

From: Two independent modes of chromatin organization revealed by cohesin removal

Extended Data Figure 9

a, Correlation of cis eigenvector values of 100-kb genomic bins before and after Nipbl deletion, split by the functional state of chromatin. Top row, left to right: genome-wide relationship; bins showing constitutive lamin-B1 association across four mouse cell types (cLADs); bins showing variable (facultative) lamin-B1 association (fLADs); binds not showing any association (non LADs). Bottom row: bins assigned the inert ChromHMM simplified state; bins assigned the repressed state; bins assigned the active state. b, Scatter plot of genome-wide ChIP–seq signal binned at 200 bp in wild-type versus ΔNipbl cells. Top, H3K27ac; bottom, H3K4me3. c, Stacked heatmap of histone ChIP–seq signal over input ± 10 kb around putative TSS sites sorted by total H3K27ac signal in the wild type and oriented by TSS strand. From left to right: H3K4me3 in wild-type and ΔNipbl, followed by H3K27ac in wild-type and ΔNipbl. d, ChIP–seq signal for histone marks of activity versus eigenvector value of 20-kb bins. Top row, H3K27ac; bottom row, H3K4me3. Left column, wild-type cells; middle column, ΔNipbl cells; right column, correlation of changes in both signals upon Nipbl deletion. e, Change in compartment structure upon Nipbl deletion cannot be attributed to the sign of the local expression change. The heatmap shows the number of 100-kb genomic bins as a function of the ranks of expression change and the eigenvector change. The attached plots show the correspondence between the values of expression change (top) or eigenvector change (right) and their ranks.

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