Fig. 3: A neuronal microexon in Gfra1 regulates neuron projection development.

a A generalized additive model (GAM) was fitted to scaled expression scores for genes significantly upregulated (logFC > 0, FDR < 0.05) in Gfra1 microexon deletion cells (KO, n = 103; red) and non-targeting controls (NT, n = 278; gray) across pseudotime (adjusted R² = 0.72; KO vs. NT estimate = 0.39; P = 6.7 × 10⁻⁹) (Methods). Colored lines represent the smoothed estimate of mean z-score across pseudotime. Shaded areas represent the 95% confidence interval of the fit. b Heatmap of the log(odds ratio) of the top ten (sorted by odds ratio) significantly enriched GO terms in bulk RNA-seq and CHyMErA-seq following Gfra1 microexon deletion. Benjamini-Hochberg corrected P < 0.05 shown (two-sided hypergeometric test). c Empirical cumulative distribution function (eCDF) of differentially expressed genes (FDR < 0.05; n = 1481) associated with Gfra1 microexon deletion compared to wild-type neurons are plotted according to their associated neuronal lineage correlation (Methods). P value calculated by two-sided Wilcoxon rank sum test. d Immunofluorescence microscopy detection of microtubule associated protein 2 (MAP2) in wild-type (‘WT’) and Gfra1 microexon-deleted differentiating neurons at day in vitro 7. Nuclei are stained with DAPI. Scale bar = 15 μm. e Quantification of neurite length in wild-type (‘WT’) (n = 123) and Gfra1 microexon deletion neurons (n = 212) (p = 0.0056, two-tailed unpaired t-test). The boxes mark the first and third quantile and the lines inside the boxes mark the median, whiskers extend from the box to the farthest point lying within 1.5 times the inter-quartile range (outliers not shown). Source data are provided as a Source Data file.