Alternative splicing is a genetic process in which different parts of genes are cut out and the remaining segments are combined during transcription into messenger RNA (mRNA). This method enhances the variety of proteins that can be crafted from genes by arranging sections of genetic material in various ways. It is thought to contribute to biological complexity by allowing genes to create diverse versions of proteins, known as protein isoforms, for a multitude of functions.
Recent research from the University of Chicago indicates that alternative splicing might have an even more significant role in biology beyond merely generating new protein isoforms. The study, published this week in Nature Genetics, suggests that the most profound effect of alternative splicing may stem from its ability to regulate gene expression levels.
The research team, chaired by Yang Li, PhD, Benjamin Fair, PhD, and Carlos Buen Abad Najar, PhD, examined extensive genomic data, spanning different stages from initial transcription to the degradation of RNA transcripts in the cell. They discovered that cells produced three times more “unproductive” transcripts (RNA molecules with errors or unusual structures) compared to their analysis of finished RNA.
Unproductive transcripts are swiftly eliminated by a cellular mechanism called nonsense-mediated decay (NMD). Li’s team estimated that, on average, around 15% of transcripts initiated are immediately degraded by NMD; notably, this figure escalated to 50% for genes exhibiting low expression levels.
“This was a major breakthrough,” remarked Li, an Associate Professor of Medicine and Human Genetics. “It’s already seen as wasteful to discard 15% of mRNA transcripts, but no one expected the cell to be generating so much and discarding the errors right away, seemingly without a reason.”
Why would a cell activate its genetic production machinery only to immediately discard 15 to 50% of what it produces? And why would transcription produce so many errors initially?
“We believe it’s because NMD is so effective,” Li explained. “The cell can afford to make errors without causing harm, so there’s no pressure to minimize mistakes.”
Nonetheless, Li was curious if there might also be an intentional reason behind this prevalent occurrence. His team conducted a genome-wide association study (GWAS) to compare gene expression levels across various cell lines. They identified a number of variations at genetic sites known to influence the amount of unproductive splicing. These sites were frequently linked with changes in gene expression due to NMD as well as variations in the production of multiple protein isoforms.
Li posits that cells may intentionally choose to eliminate transcripts that are likely to be targeted by NMD to lower expression levels. If the emerging RNA is destroyed before it is fully achieved, it will fail to generate proteins to perform biological functions, effectively silencing the genes, much like deleting an email before sending it.
“We determined that genetic variations which enhance unproductive splicing frequently lead to reduced gene expression levels,” Li noted. “This indicates that this mechanism must influence expression significantly, given its widespread nature.”
The team also discovered that numerous variants associated with complex diseases correlate with higher unproductive splicing and lower gene expression. Hence, they believe that a deeper understanding of its effects could facilitate the creation of new treatments that capitalize on the alternative splicing-NMD process. Drug compounds could be designed to lessen unproductive splicing, thereby boosting gene expression. One already approved treatment for spinal muscular atrophy utilizes this strategy to restore proteins that are being suppressed. Another method might involve enhancing the NMD process to lower expression, as seen in aggressive cancer genes.
“We believe we can target many genes now that we know how prevalent this process is,” said Li. “Previously, it was thought that alternative splicing primarily served to add complexity to organisms by producing various protein versions. We are now demonstrating that this might not be its primary function after all; it could be mainly for regulating gene expression.”
The study, titled “Global impact of unproductive splicing on human gene expression levels and traits,” was funded by the National Institutes of Health (grants R01GM130738, R01HG011067, and R35GM147498), a GREGoR Consortium Grant, and the W. M. Keck Foundation.
Other contributors include Junxing Zhao, Austin Reilly, Gabriela Mossian, Jonathan P Staley, and Jingxin Wang from the University of Chicago, along with Stephanie Lozano from the University of California, Davis.
