Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes
Zachery Wolfe,
David Liska and
Adam Norris ()
Additional contact information
Zachery Wolfe: University of California, Riverside
David Liska: Southern Methodist University
Adam Norris: University of California, Riverside
Nature Communications, 2025, vol. 16, issue 1, 1-14
Abstract:
Abstract Profiling alternative splicing in single neurons using RNA-seq is challenging due to low capture efficiency and sensitivity. We therefore know much less about splicing patterns and regulation across neurons than we do about gene expression. Here we leverage unique attributes of C. elegans to investigate deep neuron-specific transcriptomes with biological replicates generated by the CeNGEN consortium, enabling high-confidence assessment of splicing across neuron types even for lowly-expressed genes. Global splicing maps reveal several striking observations, including pan-neuronal genes harboring cell-specific splice variants, and abundant differential intron retention across neuron types. We develop an algorithm to identify unique cell-specific expression patterns, which reveals both cell-specific isoforms and potential regulatory factors establishing these isoforms. Genetic interrogation of these factors in vivo identifies three distinct splicing factors employed to control splicing in a single neuron. Finally, we develop a user-friendly platform for spatial transcriptomic visualization of these splicing patterns with single-neuron resolution.
Date: 2025
References: Add references at CitEc
Citations:
Downloads: (external link)
https://www.nature.com/articles/s41467-025-58296-2 Abstract (text/html)
Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.
Export reference: BibTeX
RIS (EndNote, ProCite, RefMan)
HTML/Text
Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58296-2
Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/
DOI: 10.1038/s41467-025-58296-2
Access Statistics for this article
Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie
More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().