Regulation of RNA splicing is pivotal in neural development, with established gene isoform expression patterns. However, the specific roles of isoform diversity across cell types in both healthy and diseased brains warrant further investigation. Here, we employed a combination of metabolic RNA labeling using 4-thiouridine (4sU) and long-read sequencing based single-cell full-length transcriptome sequencing to capture newly synthesized transcripts within the developing mouse cortices. This approach allowed us to identify predetermined cell states supported by new RNAs and the driving isoforms of transcription factors that regulate the development of deep- and upper-layer neurons. Through detailed single-cell isoform expression analysis, we discovered novel cell type-specific isoforms and uncovered isoform switch events that modulate neuron differentiation. Additionally, we investigated isoform regulation associated with Autism Spectrum Disorder (ASD) during embryonic development of BTBR T+ Itpr3tf (BTBR) mice. Notably, our findings indicate a premature emergence of cortical projection neurons (CPNs) with an immature identity in ASD-affected cortices. These CPNs exhibit the highest degree of differential transcript usage (DTU), significantly overlapping with their cell type markers and being enriched in RNA splicing processes. Exon inclusion was significantly enriched in ASD and the related RNA binding proteins (RBPs) were extracted, nearly 60% of which have been reported as ASD risk genes. Lastly, we revealed a reduction in isoform diversity in ASD, potentially linked to H3K27ac dysregulation in the associated genes. Collectively, our study marks a substantial advancement in understanding the molecular basis of cortical development and function, paving the way for future studies on neurodevelopmental disorders.
