Fig. 4: Gene regulatory dynamics in Purkinje neurons.

a, t-SNE map of Purkinje neurons showing pseudotime and the differentiation trajectory. b, TFs involved in the gene regulatory network as identified using DELAY. The nodes are sized by centrality. c, t-SNE map of nuclei simulated from the DELAY network using BoolODE. Colour represents the expression of NHLH2, LHX5 and ESRRB. d, Heat maps of Purkinje marker genes expressed along the pseudotime trajectory and the corresponding prediction based on the DELAY network. e, Trend lines of important factors in ESRRB gene progression. The vertical lines mark important events. Top to bottom: expression of LHX5 and TFAP2B; accessibility of cCREs regulating ESRRB; expression of the ESRRB gene; and enrichment of the ESRRB-binding site in target peaks. f, Chromatin accessibility landscape around the ESRRB gene. Nine cCREs were identified to regulate ESRRB expression. Two are highlighted that occur close to each other but open up at different stages in differentiation. g, The contribution scores of two cCREs regulating ESRRB expression (an early and a late cCRE), corresponding to the marked peaks in f. The top plot shows the contribution score (importance of nucleotide for prediction); the bottom plot shows the effect of mutating each nucleotide variant of a region on the prediction score (saturation mutagenesis). The early example contains two binding sites for TFAP2B, whereas the late cCRE contains an LHX5-binding site.