Dynamic alternative splicing programs drive tissue specification and organismal development. Here, we present the most comprehensive, tissue-resolved alternative splicing dataset in Caenorhabditis elegans to date, spanning three major tissue types from early embryogenesis to adulthood. We uncovered broad developmental and tissue-regulated alternative splicing trends and identified putative RNA-binding proteins (RBPs) coordinating co-regulated splicing networks governing tissue identity. Among the network of regulated splice variants, we uncovered additional, unannotated microexons for further study in C. elegans. Through a forward genetic screen, we identified RBM-25, a U1 snRNP-associated regulatory protein, as a key regulator that preferentially enhances the inclusion of short exons and microexons alongside its binding partner PRP-40. Phenotypic profiling of rbm-25 mutants demonstrated significant defects in behviour, reproductive fitness, lifespan, and synaptic signalling, indicating a key role for RBM-25-regulated target transcripts in normal physiology and behaviour. Together, these findings expand our appreciation for spatiotemporal isoform diversity during animal development, and provide mechanistic insights into how microexon splicing is regulated.
Bina Koterniak, Ernest Liang, Michael Zoberman et al.· bioRxiv· 0 citations
RNA splicing shapes neuronal identity and disease risk, yet current maps lack the developmental resolution and depth to resolve this complexity. Here, we integrate deep long-read RNA sequencing and proteomics in induced pluripotent stem cell-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half previously unknown) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences. Population genetics demonstrates that variants affecting novel exons and splice sites are under negative selection, underscoring the potential significance of these isoforms. During neuronal maturation, we observe that autism risk genes undergo dynamic isoform switching, including microexon inclusion and intron retention, that remodel key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between alternative transcript processing events, including transcription start sites, exon splicing, and polyadenylation. Finally, our atlas enables variant reinterpretation in autism, highlighting the value of an isoform-centric view for interpreting pathogenic variation in neurodevelopment. Alternative splicing expands neuronal diversity, but many brain RNA isoforms remain uncharacterized. Here, the authors generate a high‑resolution proteogenomic atlas of human neuron development, uncovering thousands of novel isoforms and revealing dynamic splicing changes in autism risk genes.
N. Xu, Katherine M. Rynard, E. Radley et al.· Nature Communications· 1 citation
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