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
Year: 2025
Type: article
Abstract: Genome-wide single-cell and spatial long-read approaches have gained traction, but mostly lack single-cell resolution - and yield limited read lengths. Here, we introduce spatial ISOform sequencing (Spl-ISO-Seq), which reveals exons and polyadenylation sites from long reads 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 samples of the visual cortex (8-11 years) to post-puberty samples (16-19 years), we find that cortical layers harbor stronger splicing and poly(A)-site regulation than the adjacent white matter, with enrichment of multiple protein-domain types. For oligodendrocytes however, developmental splicing changes are stronger in white matter. Among cortical layers, layer 4 has the most developmental changes in alternative-exon inclusion in excitatory neurons and in poly(A) sites. We also find many repeat elements, especially ERV1 long terminal repeats downstream of developmentally-regulated layer 4 exons. Overall, alternative splicing changes are linked to synapses - specifically at the post-synapse. Age-linked splicing changes in layers 1-3 and 4 are associated with autism spectrum disorder but not with schizophrenia, amyotrophic lateral sclerosis and Alzheimer's disease. These results root developmental splicing changes during puberty and the resulting protein changes in specific layers and cell types. More generally, our new technologies enable new observations for any complex tissue.
Source: Nature Communications
Language: English
Topic: RNA Research and Splicing
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $6,990
Funders: National Science Foundation, U.S. Department of Health and Human Services, European Commission, Academy of Finland, National Institutes of Health, Weill Cornell Medical College, McMaster Institute for Research on Aging, McMaster University, National Institute of Mental Health, National Institute on Drug Abuse, National Institute of General Medical Sciences, U.S. National Library of Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NextGenerationEU
Awards: Cross-species conservation of cell-type and single-cell specific isoform expression, G1724173427, G1779475623, G1984825719, G232756130, Enlarging the Limits of Practical Tractability for Graph Problems in Bioinformatics, G3068058667, Foundations of Safe and Complete Algorithms with Applications, G3218096046, G3458391363, G3460178181, Flow Decompositions: Algorithms and Bioinformatics Applications, G3693075473, G4283653072, G434337789, G4623149213, G4776263922, Genetic and Environmental Influences on Addiction, G5246018189, G544149491, G6224492464, G6478996275, Predicting the functional impact of alternative splicing on protein-protein interactions using an integrated approach, G6647055838, G7090951942, G7731361579, Multiome measurements connecting transcription start sites at single-nucleotide resolution, DNA methylation and open chromatin status to splicing outcome across single cells in health and disease, Graduate Research Fellowship Program (GRFP), G888419579, G8933570164, Understanding Genetic Complexity in Spina Bifida, Integrative Single Cell isoform and chromatin accessibility Mapping of Chronic Opioid Exposure in Cognitive Brain Areas in HIV
OpenAlex ID: W4413812072