Brown Nat Protocols Fig 3

Figure 3 | Comparison of chromatin structure and TAD shapes. Super-resolution 3D-SIM imaging of human RPE-1 cells after a control IF treatment or indicated FISH protocol using a KIF23 TAD-specific probe. a, Central mid-sections of SYTOX Green stained nuclei show a rather inhomogeneous distribution of chromatin with strings of domain-like features separated by distinctive interchromatin space in both the IF control and after RASER-FISH. In contrast, 4 min and 30 min+dry nuclei show both a more homogeneous chromatin distribution with much reduced interchromatin regions. Insets are pseudocoloured for intensity and demonstrate the retention of interchromatin space in the RASER-FISH sample. Scale bar, 5 µm and 1 µm (insets). b, Exemplary TAD FISH signals selected from several cells highlight more defined and distinct edges of the TAD signal after RASER detection compared to 4 min, 4 min+dry (bottom row of middle section) and 30 min+dry heat denaturation. Images show false colour representations of maximum intensity projections. Scale bar, 1 µm.