Alternative Splicing Shapes Biological Complexity through Gene Expression Modulation

A genetic process known as “alternative splicing” involves cutting out specific gene segments and joining the remaining segments to form messenger RNA (mRNA) during transcription. By putting diverse genetic code segments together, this process broadens the range of proteins that can be produced from genes.

This process is thought to increase biological complexity by enabling genes to produce multiple protein variants, or isoforms, each serving different functions.

Beyond merely producing novel protein isoforms, alternative splicing may have an even bigger impact on biology, according to a recent study from the University of Chicago. The research, which was published in the journal Nature Genetics, suggests that alternative splicing may have the greatest effect via controlling the levels of gene expression.

Under the direction of Yang Li, PhD, Benjamin Fair, PhD, and Carlos Buen Abad Najar, PhD, the research team examined extensive genomic data sets spanning early transcription to the point at which RNA transcripts are eliminated by the cell. When they examined steady-state, completed RNA alone, they discovered that cells created three times as many “unproductive” transcripts RNA molecules with errors or unusual structures.

Null-mediated decay (NMD) is a biological process that rapidly eliminates unproductive transcripts. According to Li's team's calculations, NMD degrades approximately 15% of transcripts on average the moment they are initiated; when examining genes with low expression levels, that figure increased to 50%.

We thought that was a huge breakthrough. It already seems wasteful to degrade 15% of mRNA transcripts, but no one would have thought that the cell is transcribing so much and getting rid of the errors immediately, seemingly without any purpose.”

Yang Li, Associate Professor, Medicine and Human Genetics, University of Chicago

Why would the cell activate its machinery for producing genetic material only to discard 15–50% of what it produced right away? And why would there be so many errors in the transcribing to begin with?

Li said, “We think it is because NMD is so efficient. The cell can afford to make mistakes without damaging things, so there is no selective pressure to make fewer mistakes.”

However, Li surmised that there had to be a reason for such a prevalent occurrence. Using a genome-wide association study (GWAS), his group was able to compare the levels of gene expression in various cell lines.

Numerous differences were discovered at genomic sites known to influence the amount of fruitless splicing. These loci were linked to variations in multiple protein isoform synthesis and variations in genetic expression brought on by NMD.

According to Li, cells occasionally deliberately choose transcripts destined for NMD to lower expression levels. The nascent RNA cannot form proteins to carry out biological tasks if it is destroyed before it is fully transcribed. This silences the genes effectively, much as when someone deletes a draft email before they can send it.

We found that genetic variations that increase unproductive splicing often decreased gene expression levels. This shows that there this mechanism must have some effect on expression because it is so widespread."

Yang Li, Associate Professor, Medicine and Human Genetics, University of Chicago

The group discovered that a large number of variations connected to intricate illnesses are also linked to reduced gene expression and more ineffective splicing. Thus, they think that gaining a deeper comprehension of its effects could aid in the creation of novel therapies that take advantage of the alternative splicing-NMD process.

It is possible to engineer drug molecules that improve gene expression by reducing the amount of unproductive splicing. This method of restoring shut-off proteins is already used in one licensed medication for spinal muscular atrophy. Another strategy is to increase the NMD process to reduce expression, for instance, in genes associated with cancer that are overexpressed.

We think we can target a lot of genes because now we know how much this process is going on. People used to think that alternative splicing was mainly a way to make an organism more complex by generating different versions of proteins. Now we are showing that it might not be its most important function. It could be simply to control gene expression.”

Yang Li, Associate Professor, Medicine and Human Genetics, University of Chicago