Figure 7. Cohesin depletion alters the domain landscape.

(A) Contact map of mitotic chromatin in wild-type cells reveals the presence of CAR domains and their boundaries. Contact map showing the interaction in the 100–550 kb region of chromosome V overlays with the tracks for Mcd1p ChIP-seq signal. Triangles indicate the CAR domains’ position. Dashed lines indicate the position of the CAR domain boundaries. (B) The signal composing CAR domains in wild-type is lost upon cohesin depletion. The wild-type (WT) domains are rescaled to the same length with left and right boundaries aligned on the plot (black bar). Genome-wide average domain/boundary strength for WT, BRN1-AID, MCD1-AID, and asynchronous cells were plotted as distance-normalized matrices over the CAR domains called in the wild-type (n = 306). (C) Cohesin is enriched at the boundaries of CAR domains in wild-type, but not at domains formed upon cohesin depletion. Mcd1p ChIP-seq data from wild-type cells were plotted separately over ±5 kb region (top) and cumulative curves were plotted separately as the function of log2 ratio of Mcd1p ChIP-seq signal (bottom) around the boundaries of CAR domains in wild-type (WT) (blue), the boundaries present upon Mcd1p-depletion (pink), or the boundaries present in asynchronous cells (grey). (D) CARs at wild-type domain boundaries have higher levels of cohesin binding than other CARs genome-wide. Cumulative curves show the probability distribution of Mcd1p ChIP-seq signal (log2) from CARs present at the wild-type CAR boundaries (WT) (blue), and from the other CARs (purple). Below the curves are plotted the corresponding Mcd1p ChIP-seq values of each CAR (blue dots for CARs at the CAR boundaries and purple dots for the other CARs). Box and whiskers plot indicates the median values and the quartiles distribution.

Figure 7—figure supplement 1. Cohesin depletion alters the chromatin domain landscape.

(A) Chromosome domains are reorganized after cohesin removal. Wild-type (WT) (top), cohesin-depleted cells (MCD1-AID) (middle), and asynchronous cells (bottom) Micro-C XL contact maps are plotted at a 2 kb resolution across chromosome V: 100–450 kb region. Above each contact map, the corresponding domains called by hicexplorer are indicated with blue/yellow bars, and their respective boundaries are indicated with a red line above. Finally, Mcd1p ChIP-seq signal is overlaid with the contact maps in the same region at the very top of the figure. (B) Comparison of domain strength between wild-type, MCD1-AID, BRN1-AID, and asynchronous cells. The score of domain strength in wild-type was plotted at x-axis against the score in each condition at y-axis, respectively. Colormap codes the density of scatter dots. (C) Box plot showing the distribution of domain strength in each condition. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The whiskers extend to the most extreme data points not considered outliers, and the outliers are plotted individually using the 'o' symbol. (D) CAR domain boundaries are enriched at terminators, while domains in cohesin-depleted and asynchronous cells are enriched at promoters. Bar chart shows the log2 enrichment of domain boundaries from wild-type (WT) in blue, cohesin-depleted cells (MCD1-AID) in red, and asynchronous cells (Async) in grey, at promoter or terminator.