Fig. 1: Cohesin acetylation restricts the length of architectural stripes and chromatin loops.
From: The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism
a, Immunoblot analysis of ∆ESCO1 cells. The ∆ESCO1 cell line displays reduced levels of acetylated SMC3 (AcSMC3). This experiment was performed three times, with similar results. b, Immunoblot analysis of ∆HDAC8 cells; these cells have increased levels of acetylated SMC3. This experiment was performed three times, with similar results. c, Hi-C contact matrices for G1 cells of the indicated genotypes. A locus at chromosome 4 is shown at 20-kb resolution. Matrices were normalized to 100 million contacts per sample. The arrows indicate examples of architectural stripes whose length has changed in ∆ESCO1 and ∆HDAC8 cells. d, Aggregate stripe analysis to quantify signal enrichment emanating from CTCF sites at 100-kb resolution. Typically, interactions are formed close to the diagonal and decay over distance. These so-called expected contacts were obtained from a distance-normalized contact matrix; we then calculated enrichment of the observed (obs) contacts over the expected (exp) contacts at 100-kb resolution. This method reveals the presence of architectural stripes emanating from CTCF sites. ∆ESCO1 cells are enriched for long interactions while ∆HDAC8 cells display shorter interactions. e, Cartoon illustrating the difference between primary and extended loops. f, APA for extended loops. Differential APA plots for extended loops compared with wild type (WT). ∆ESCO1 (∆1) cells show an increase in extended loops while ∆HDAC8 (∆8) cells show a decrease.
