ArticleNature communications2025
Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Whole-organism spatial transcriptomics at single-cell resolution inbioRxiv : the preprint server for biology · 2026Article
- Pervasive non-triplet alternative splicing drives functional isoform diversity.Nature communications · 2026Article
- Local Protein Synthesis at Synapses: A Driver for Synapse Diversification.Journal of neurochemistry · 2025Review
- Identity and functions of monoaminergic neurons in the predatory nematodebioRxiv : the preprint server for biology · 2025Article
- Conserved Calcineurin A splice variants regulate both constitutive and experience-dependent behaviors through tissue-specific signaling.PLoS genetics · 2025Article
- Regulated microexon alternative splicing in single neurons tunes synaptic function.EMBO reports · 2025Article
- Alternative splicing across the C. elegans nervous system.Nature communications · 2025Article
- Neuron-specific repression of alternative splicing by the conserved CELF protein UNC-75 in Caenorhabditis elegans.Genetics · 2025Article
- Detecting gene expression in Caenorhabditis elegans.Genetics · 2025Review
- Conserved role for spliceosomal component PRPF40A in microexon splicing.RNA (New York, N.Y.) · 2024Article
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3 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.