The chromatin landscape of cohesin-deficient thymocytes is characterized by the loss of cohesin-based interactions and the detection of alternative interactions. (A) Outline of approach used to score interactions between specific chromatin features located within architectural compartments as assigned by eigenvector analysis of chromosomal organization (SIMA) (Lin et al. 2012). Open compartments (1, 2, …, n) are indicated by gray boxes. Orange, green, and black symbols (features 1, 2, etc.) represent chromatin features, and purple lines indicate “featureless” control sites. Hi-C interactions between features are indicated by dashed lines. For each compartment, we counted Hi-C reads connecting features of the same type (homotypic interactions, illustrated for feature 1), and Hi-C reads connecting different features (heterotypic interactions, illustrated for features 2 and 3), assigning Hi-C reads that mapped within 10 kb of each feature (Lin et al. 2012). We compared interactions in control and cohesin-deficient cells for each feature and pair of features within each open compartment and combined these scores as a measure for the cohesin dependence of long-range interactions between specific features. (B) Impact of cohesin deficiency on homotypic cohesin-based and alternative interactions. SIMA was used to determine the enrichment of Hi-C reads in interactions connecting “like” features in control and cohesin-deficient thymocytes. The difference between normalized enrichment ratios in each condition was assessed by the Wilcoxon signed-rank test (see Methods). (C) Impact of cohesin deficiency on all pairwise feature-based interactions. SIMA results for homotypic interactions are shown together with those associated with interactions connecting different features (heterotypic interactions). Refer to B for details. Homotypic RAD21-RAD21 interactions are the most decreased, followed by CTCF-RAD21 interactions. Interactions between features associated with active transcription are strongly increased in cohesin-deficient thymocytes, as are interactions involving the repressive histone modification H3K27me3 (Zhang et al. 2012) with marks of active transcription. (D) Cytoscape representation of SIMA results in C. Edge color and width correspond to the Wilcoxon signed-rank test effect size and significance, respectively. (E) Length scale of lost and gained cohesin-dependent feature-based interactions. Boxplots are based on SIMA comparisons stratified into three classes according to compartment size (≤1 Mb, 1–3 Mb, >3 Mb). Effect sizes for decreased interactions (RAD21-RAD21, CTCF-RAD21, CTCF-CTCF) and increased interactions (remainder) were grouped and are indicated separately. The effect of reduced cohesin-based interactions is most pronounced within smaller compartments and decreases when larger compartments are considered (Pearson's correlation coefficient r = −0.73, P < 0.05), whereas alternative interactions increased with compartment size (r = 0.7, P < 0.001). Outliers are not depicted.
