Regulated unproductive splicing in animal development

The National Institute of General Medical Sciences awarded $433,233 to Northwestern University on September 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to investigate regulated unproductive splicing in animal development.

The research examines how genes couple alternative splicing with nonsense-mediated decay (NMD) to regulate gene expression post-transcriptionally. The project focuses on poison exons—exons that, when spliced into transcripts, introduce premature termination codons that trigger NMD-mediated transcript degradation. The investigator will determine the full complement of poison exons alternatively spliced through development, characterize their regulatory mechanisms, and assess their roles in health and disease, particularly given evidence that variants affecting poison exon splicing produce disease phenotypes.

Northwestern University's Sponsored Research Division is the recipient. Performance occurs in Chicago, Illinois, with a period of performance through May 31, 2031.

Abstract

Alternative splicing (as) of genes is widely understood as a mechanism to create protein diversity. Nearly all protein-coding genes use as to generate multiple protein isoforms. Curiously, a significant proportion of as events do not result in functional protein isoforms and are instead targeted for degradation through the nonsense mediated decay (NMD) pathway. Surveillance by the NMD pathway has been well-documented to remove MIS- spliced transcripts and transcripts containing deleterious mutations that result in a premature termination codon (PTC). However, unlike unregulated MIS-splicing and random nonsense mutations, several evidence points to certain genes 'purposely' coupling as with NMD to regulate gene expression. Many of these genes contain exons, termed poison exons (PES), which when spliced into a transcript, 'poisons' the transcript by introducing a PTC resulting in its NMD-mediated degradation. My research program investigates the mechanism of PE- mediated post-transcriptional gene regulation and its role in animal development. Multiple lines of evidence point to PES being critical players in post-transcriptional gene regulation. Many known PES are highly conserved and are enriched in specific gene classes such as splicing factors and other RNA binding proteins where they autoregulate the gene's expression using a negative feedback loop. Recent advances in sequencing technologies have revealed PES being developmentally regulated and cell-type specific suggestive of a broader regulatory function. Finally, deep intronic sequencing of patient samples have revealed gene variants that alter PE splicing resulting in disease phenotypes; demonstrating that PE-mediated gene regulation is critical in health and diseases. However, despite the gaining importance of PES, the full complement of PES that are alternatively spliced throughput development are not known. Moreover, a systematic functional interrogation of PES and the mechanism through which they regulate developmental phenotypes has also not been investigated. Through this mira award, my research program will 1) leverage long-read sequencing to identify and annotate PES critical in vertebrate development, 2) systematically perturb PES in zebrafish and perform phenotyping using the tools my lab has developed to understand PE function, and finally 3) mechanistically investigate how PE-mediated gene regulation interplays with canonical transcriptional gene regulation. Overall, this research program will establish PES as critical regulators of post-transcriptional gene regulation, opening the doors to PE-modulating targeted therapies such as antisense oligos for treating developmental disorders.