Single-cell Isoform Sequencing Reveals Transcriptional Dysregulation in ASD Mouse Cortex Development

RNA splicing is pivotal in neural development, yet the role of isoform diversity across cell types remains unclear. Here, we combined metabolic RNA labeling and single-cell full-length transcriptome sequencing to capture transcriptional dynamics in developing mouse cortices. We observed predetermined cell states supported by nascent RNAs and characterized the driving isoforms of transcription factors that regulated the development of deep- and upper-layer neurons. Additionally, we investigated isoform regulation associated with autism spectrum disorder (ASD) during the embryonic development of BTBR T  +  Itpr3tf mice. Our findings indicated premature emergence of callosal projection neurons (CPNs) with an immature identity in ASD-affected cortices. These CPNs exhibited abnormal transcript usage, and the related RNA binding proteins included nearly 60% that have been reported to be ASD risk genes. We identified isoform switching events modulating neurogenesis and ASD development. Finally, we observed reduced isoform diversity in ASD potentially linked to dysregulated H3K27ac levels. Collectively, our study represents a significant advancement in understanding the molecular basis of cortical development and functions.