Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model

The trigeminal ganglion (TG) plays a key role in allergic rhinitis (AR), mediating symptoms like nasal itching and sneezing via sensory neuron activation. Yet, the underlying transcriptomic mechanisms remain unclear. While short-read RNA-seq struggles to accurately capture complex transcript isoforms, long-read sequencing offers full-length coverage but limited quantitation. Here, we combine both technologies to comprehensively profile the TG transcriptome in an AR mouse model. We identify 25,988 high-confidence full-length isoforms from 13,011 known and 237 novel genes, including 7,543 (29.02%) novel isoforms absent from reference databases. These are enriched in RNA splicing and processing genes. Alternative first exons are the most common splicing event and are especially frequent among novel isoforms. AR induces shifts in gene expression, splicing dynamics, and promoter activity, suggesting neuro-immune crosstalk. Single-cell RNA-seq integration further reveals that while some genes lack cell type-specific expression, their alternative splicing patterns are highly cell type-specific, suggesting that AS may play a crucial role in diversifying gene function across different cell types. The findings provide a comprehensive full-length transcriptome dataset, facilitating in-depth exploration of the interplay between sensory alterations and AR in trigeminal ganglion.