# The role of poison exons in neurodevelopment

> **NIH NIH R21** · NORTHWESTERN UNIVERSITY · 2021 · $440,000

## Abstract

Project summary
Exons in the genome that lead to the introduction of premature truncation (stop) codon (PTC) and mark these
transcripts as targets for nonsense-mediated decay (NMD) are called poison exons (PEs). These PEs have
recently been shown to be used throughout mouse and human neurodevelopment where they are alternatively
spliced over the course of development. Moreover, genetic variants that perturb the splicing of PEs have been
associated with neurodevelopmental disorders, including epilepsy and malformations of cortical development.
However, the full complement of PEs that are alternatively spliced throughout human development are not
known. Therefore, in Aim 1 of this study we will use long-read sequencing in induced pluripotent stem cell
(iPSC)-derived neuronal progenitor cells (NPCs) and neurons, treated with cycloheximide to inhibit NMD, to
identify PEs. Moreover, while recent efforts have elucidated the use of PEs during neurodevelopment, we have
very limited understanding of their function. In Aim 2 we will adapt the recently described paired guide RNAs
for alternative exon removal (pgFARM) approach to delete candidate PEs in iPSC-derived neuronal progenitor
cells (NPCs) and determine the effects on proliferation of these cells. Our preliminary analysis suggests that
many PEs that are included in transcripts in NPCs (NPC-PEs), encode for genes required for mature neuronal
function, including ion transport and synaptic vesicle assembly and release. We hypothesize that deletion of
NPC-PEs will lead to the ectopic expression of these genes, exit of the cell-cycle and premature neuronal
differentiation of NPCs. This exploratory, high-risk, high-reward study is not intended to identify all PEs that are
alternatively spliced throughout development, rather we aim to determine the efficacy of using long-read
sequencing where NMD is inhibited to identify PEs. Moreover, we aim to develop a high-throughput assay for
determining the role of these PEs in early stages of neurodevelopment. Collectively, the outcomes of this study
will provide the platforms and experimental paradigms for (1) identifying PEs used in human
neurodevelopment (2) provide a framework for the interpretation of intronic genetic variants identified by
genome sequencing in individuals with neurodevelopmental and neuropsychiatric disorders (3) determining the
function of these PEs in development. We intend that this data will be used to pursue future individual or
program level funding applications.

## Key facts

- **NIH application ID:** 10373264
- **Project number:** 1R21NS121572-01A1
- **Recipient organization:** NORTHWESTERN UNIVERSITY
- **Principal Investigator:** Gemma Louise Carvill
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $440,000
- **Award type:** 1
- **Project period:** 2021-09-15 → 2024-03-14

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10373264

## Citation

> US National Institutes of Health, RePORTER application 10373264, The role of poison exons in neurodevelopment (1R21NS121572-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10373264. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*