A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types
Genome-wide spatial long-read approaches often lack single-cell resolution and yield limited read lengths. Here, we introduce spatial ISOform sequencing (Spl-ISO-Seq), which reveals exons and polyadenylation sites with near-single-cell resolution. Spl-ISO-Seq selects long cDNAs and doubles to triples read lengths compared to standard preparations. Adding a highly specific software tool (Spl-ISOquant) and comparing human post-mortem pre-puberty (8-11 years) to post-puberty (16-19 years) visual cortex samples, we find that cortex harbors stronger splicing and poly(A)-site regulation than white matter. However, oligodendrocyte regulation is stronger in white matter. Among cortical layers, layer 4 has the most developmentally-regulated splicing changes in excitatory neurons and in poly(A) sites. We also find repeat elements downstream of developmentally-regulated layer 4 exons. Overall, alternative splicing changes are linked to post-synaptic structure and function. These results root developmental splicing changes during puberty in specific layers and cell types. More generally, our technologies enable exciting observations for any complex tissue.
Authors
- Wen Hu (ORCID: https://orcid.org/0000-0002-0604-2119)
- Julien Jarroux (ORCID: https://orcid.org/0000-0002-7185-6960)
- Lieke Michielsen (ORCID: https://orcid.org/0000-0003-4615-1309)
- Andrey D. Prjibelski (ORCID: https://orcid.org/0000-0003-2816-4608)
- Dmitry Korkin (ORCID: https://orcid.org/0000-0002-3875-9085)
- Oleksandr Narykov (ORCID: https://orcid.org/0000-0002-3336-0534)
- Gian Gaetano Tartaglia
- Yi He (ORCID: https://orcid.org/0000-0002-6641-5618)
- Brian Evans (ORCID: https://orcid.org/0000-0002-9345-4778)
- Andrea Vandelli (ORCID: https://orcid.org/0000-0002-8879-0144)
- Alexandru I. Tomescu (ORCID: https://orcid.org/0000-0002-5747-8350)
- Careen Foord (ORCID: https://orcid.org/0000-0003-2984-834X)
- M. Elizabeth Ross (ORCID: https://orcid.org/0000-0001-6440-8089)
- Iman Hajirasouliha (ORCID: https://orcid.org/0000-0002-0600-3371)
- Hagen Tilgner (ORCID: https://orcid.org/0000-0002-7058-3606)
- Justine Hsu (ORCID: https://orcid.org/0000-0003-2713-5119)
- Natan Belchikov (ORCID: https://orcid.org/0000-0002-3816-7055)
Institutions
- Worcester Polytechnic Institute (US)
- University of Helsinki (FI)
- Cornell University (US)
- Italian Institute of Technology (IT)
- Lander Institute (IL)
- MIND Research Institute (US)
- Center for Neuro-Oncology (US)
- Weill Cornell Medicine (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-08-29
- DOI
- https://doi.org/10.1038/s41467-025-63301-9
- Citations
- 4
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 3.22
Funders
- National Science Foundation
- European Commission
- National Institutes of Health
- Weill Cornell Medical College
- National Institute on Drug Abuse
- National Institute of General Medical Sciences