Decoding Mechanisms of Nonsense-mediated mRNA Decay through Alternative Splicing

SUMMARY The human genome preserves a strict regulation of gene expression to maintain physiological integrity. RNA processing plays a key central role in this regulation and has drawn significant attention in recent times due to its implications for a wide breadth of diseases. Alternative splicing (AS) can encode different protein isoforms from the same gene to support rapidly changing biological processes. AS often generates erroneous mRNAs with a premature translation termination codon, which are selectively degraded by nonsense-mediated mRNA decay (NMD) to safeguard the generation of defective proteins. This coordinated action is termed as AS-NMD. In humans, ~95% of genes undergo AS, among which ~33% are targets of AS-NMD, suggesting that it is not merely noise. Substantial evidence demonstrated that AS-NMD evolved as a powerful mechanism to regulate gene expression in normal physiology and is often fine-tuned in a developmental stage-specific or tissue-specific manner. Growing evidence suggests that AS-NMD is frequently dysregulated (induced or suppressed) and is the root of many human maladies. Why certain genes in certain tissues or diseases are susceptible to differential or aberrant AS-NMD regulation remains an unresolved mystery. Therefore, elucidating the regulation of AS- NMD is crucial to understanding this vital mechanism in normal physiology and diseases, which will redefine therapeutic strategy and significantly impact clinical outcomes. We recently showed that AS-NMD is induced in splicing factor mutated hematopoietic defects. In contrast, AS-NMD is suppressed in splicing factor overexpressed diseases (such as cardiac and liver dysfunction, brain and developmental abnormalities, diabetes, lupus, and neoplasia). These provide excellent model systems to systematically identify positive and negative effectors and underlying mechanisms of differential AS-NMD regulation. We will characterize the AS- NMD regulation in normal cells and its misregulation (induction and suppression) in disease-specific model cells. We will define cis-acting RNA codes that regulate AS-NMD, characterize trans-acting protein networks and their dynamic interactions with RNA in the AS-NMD pathway, and delineate tissue-specific or disease-specific mechanisms. Finally, we will develop tools to manipulate AS-NMD errors using oligonucleotide-based pharmacology as a therapeutic approach. Completion of these studies will connect the missing puzzles in the AS-NMD regulation, answer how an evolutionarily conserved surveillance mechanism can be exploited to turn on pathological maladies, and develop a commonly approached innovative molecular technology to correct AS- NMD errors applicable to a range of human diseases.