Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain

Single-cell sequencing technology reveals unique splicing patterns in developing and adult mouse and human brains

In the nervous system, the splicing patterns of messenger RNA (mRNA) play a critical role in establishing cellular identity and regulating cellular functions. However, a comprehensive atlas depicting the mRNA splicing patterns across brain regions has been lacking. Recently, a research team from New York has systematically studied the full-length mRNA splicing patterns in mouse and human brain regions using an enhanced single-cell long-read sequencing technique (scIsoR-seq2), and compared them across different brain regions, developmental stages, and cell types.

The study was led by Dr. Hagen U. Tilgner and Dr. M. Elizabeth Ross’s research groups from Weill Cornell Medicine and published in the journal Nature Neuroscience. The researchers obtained single-cell transcriptomic data from different developmental stages (postnatal days 14, 21, 28, and 56) and brain regions (hippocampus, visual cortex, striatum, thalamus, and cerebellum) of the mouse brain, and performed in-depth analyses.

During the study, the researchers found that for 72% of genes, the expression of their mRNA splicing isoforms varied significantly across developmental stages, cell types, or brain regions. The selection of splicing sites, transcription start sites, and polyadenylation sites differed significantly between cell types, affecting the encoded protein structures and being associated with disease-related mutations. Additionally, genes related to neurotransmitter transport and synaptic turnover exhibited variable splicing patterns across different cell types and brain regions.

Notably, during the mouse adolescent period (postnatal days 21-28), splicing variations across major cell types peaked, particularly in brain regions such as the hippocampus and cortex. During this critical period, neuronal subtypes exhibited the most pronounced splicing variations across brain hemispheres.

Furthermore, the researchers found that the cell type-specific splicing patterns observed in mice were conserved in the human hippocampus, suggesting that the findings can be extrapolated to the human brain. At the same time, the human brain acquired some novel cell type-specific splicing isoforms, hinting at the existence of potentially gained functional splicing isoforms.

This comprehensive single-cell full-length splicing atlas revealed a high degree of splicing variation across development, anatomical structures, and species, providing new insights into our understanding of transcriptional regulation in the brain. The research findings are publicly available at www.isoformatlas.com.