Figure 1. Chromatin contact maps (Hi‐C) and matched gene expression (CAGE) data in murine neuronal differentiation system.

1. Scheme of the murine differentiation system of our study, from ESC to NPC and post‐mitotic neurons.
2. Cells express stage‐specific markers as detected by immunofluorescence: ESC express Oct4, NPC the neuronal precursor marker nestin and Neurons Tubb3 (Tuj1 antibody). Scale bar, 100 μm.
3. ESC and NPC are actively cycling, whereas Neurons are negative for BrDNA after 24‐h BrdU incorporation. Nuclei were counterstained with DAPI.
4. Examples of interaction patterns in Hi‐C matrices across the whole chromosomes show extensive higher‐order dynamic contacts, which change during terminal neuronal differentiation. Hi‐C interaction data are plotted in log scale.
5. Matched CAGE data sets were produced from total RNA extracted from ESC, NPC and Neurons. The expression levels confirm specific expression of stage‐specific markers. CAGE expression reported as a percentage relative to highest expression.