Cells use alternative splicing to regulate gene expression, study finds

Alternative splicing is a genetic process in which different segments of genes are deleted and the remaining pieces are joined together during transcription into messenger RNA (mRNA). This mechanism increases the diversity of proteins that can be generated from genes, by assembling sections of genetic code into different combinations. This is thought to increase biological complexity by allowing genes to produce different versions of proteins, or protein isoforms, for many different uses.

New research from the University of Chicago suggests that alternative splicing may have an even greater influence on biology than simply creating new protein isoforms. The study, published this week in Genetics of natureshows that the most important impact of alternative splicing may come from its role in regulating gene expression levels.

The research team, led by Yang Li, Benjamin Fair and Carlos Buen Abad Najar, analyzed large genomic datasets, covering various stages, from early transcription to the destruction of RNA transcripts by the cell. They found that cells produced three times more “unproductive” transcripts (RNA molecules with errors or unexpected configurations) than when they analyzed only the finished RNA in a steady state.

Unproductive transcripts are quickly destroyed by a cellular process called nonsense-mediated degradation (NMD). Li’s team calculated that on average, about 15% of initiated transcripts are almost immediately degraded by NMD; when they looked at genes with low expression levels, that figure jumped to 50%.

“We thought this was a major breakthrough,” said Li, associate professor of medicine and human genetics. “It already seems pointless to degrade 15 percent of mRNA transcripts, but no one would have imagined that the cell would transcribe so much and immediately eliminate errors, seemingly for no purpose.”

Why would the cell activate its gene production machinery to immediately destroy 15 to 50% of its output? And why would transcription make so many mistakes?

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

But Li suspected there must be a reason for such a widespread phenomenon. His team conducted a genome-wide association study (GWAS) to compare gene expression levels across different cell lines. They found many variations at genetic locations that are known to affect the level of unproductive splicing. These loci were just as often associated with differences in gene expression caused by NMD as they were with differences in the production of multiple protein isoforms.

Li says cells sometimes deliberately select NMD-determined transcripts to decrease their expression levels. If nascent RNA is destroyed before it is fully transcribed, it will never produce proteins to perform biological functions. This effectively silences genes, like deleting a draft of an email before its author can press “send.”

“We found that genetic variations that increase unproductive splicing often decrease gene expression levels,” Li said. “This shows that this mechanism must have an effect on expression, because it is so widespread.”

The team found that many variants linked to complex diseases are also associated with less productive splicing and reduced gene expression, so they believe that a better understanding of its impact could help develop new treatments that exploit the alternative splicing process—NMD.

Drug molecules could be designed to decrease the amount of unproductive splicing and thus increase gene expression. A drug approved for spinal muscular atrophy already takes this approach to restore proteins that are stuck. Another approach might be to increase the NMD process to decrease expression, for example in rampant cancer genes.

“We think we can target a lot of genes because we now know how complex this process is,” Li said. “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 show that this may not be its most important function. It may simply be to control gene expression.”