Fig. 3: Integrative analysis reveals spatial alternative splicing programs in adult mouse brain enriched for synaptic and membrane trafficking functions.
From: Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM
a, Workflow overview. CA, cornu ammonis; DG, dentate gyrus. b, Comparison of SV in gene expression (x axis) versus isoform usage (y axis) in the CBS2 sample. Points colored by expression perplexity (effective number of isoforms per gene). Inset: number of events significant in both CBS1 and CBS2 replicates (adjusted P < 0.05), categorized as SVP or spatially variably expressed but not variably processed (SVENP) genes. c, Pathway enrichment analysis comparing SVP versus SVENP genes, with terms arranged by precision differences between the two groups. d, Unsupervised clustering based on gene-level expression of SVE genes (left) or relative isoform ratios of SVP genes (right). Isoform counts were locally smoothed to compensate for data sparsity. e, Selected isoform usage programs identified through hierarchical clustering of SVP genes. f, Distributions of AS event types among SVP and SVE genes. g, Selected exon features of 214 skipping or mutually exclusive exons in SVP and 1,349 exons in SVENP genes, showing per-exon median relative position (left) and median exon number of transcripts containing each exon. Boxplots show median (center line), interquartile range (box) and 1.5× interquartile range (whiskers). P values from two-sided t-test. h, Unsupervised clustering based on 1,028 SVE RBP expression from SR sequencing data. i, Top RBPs ranked by number of significantly associated targets, color-coded by availability of documented motifs (CISBP-RNA) or CLIP data (POSTAR3). Right: log-normalized expression of selected RBPs. j, Differential isoform usage P values for Rbfox3 (left) and Celf5 (right) in two 50-μm spaced adjacent technical replicates. Red points indicate validated targets with RBP binding near regulated events in brain-CLIP data. k, Gnas transcript structure and spatial log-normalized expression patterns. HSPC, hematopoietic stem and progenitor cell. Panel a created using BioRender.com.
