There are approximately 20,000 genes that can be translated into protein in a human cell. Due to redundancies in the genetic code, changes in the DNA sequence of genes can either preserve or alter the protein product. Interestingly, scientists have found that around 100 genes per individual have sequences that, if translated faithfully, code for a dysfunctional protein. Many of these nonsense variants are unique and rare in the overall population but some of them, around 20 per individual, are common and present in the homozygous state, meaning both copies of the gene, the one inherited from the father and the one inherited from the mother, have the same sequence. The high frequency of these variants suggests that the disruption they cause must be mild or that the gene product is non-essential. While there have been several studies which lend support to those explanations, another possibility remains—that the nonsense variants in the DNA sequence do not actually prevent the production of the functional protein product. Indeed, there are many cases where the levels of functional protein appear normal despite the presence of sequence variation in the corresponding gene that is expected to alter the protein. In their recent study in Genome Research, scientists in the Bradley Lab (Public Health Sciences, Basic Sciences) investigated the possible mechanisms that could account for this discrepancy.
Genes are composed of regions of sequence that code for protein, called exons, and non-coding regions of sequence called introns. When genes are expressed, they are transcribed into messenger RNAs and a protein complex called the spliceosome removes introns from the mRNA. In genes with multiple exons, it is common for the spliceosome to cut out certain exons of some genes. This process, called alternative splicing, can generate multiple different protein products from a single gene, called isoforms. Scientists in the Bradley Lab hypothesized that common nonsense variants may occur more often in genes with multiple isoforms. They determined the frequency of having a nonsense mutation that would specifically affect one or more protein isoforms of alternatively spliced genes and found that lowly abundant and common nonsense variants are more common in alternatively spliced sequence that affects protein isoforms. In contrast, rare nonsense variants occur in isoform-specific sequence just as frequently as synonymous variants that do not change the protein sequence. Together, their data suggests that nonsense variants that are common and accumulate in the population frequently affect only specific isoforms of proteins and thus do not halt all protein production from those genes.
Another mechanism that could account for protein levels remaining high despite nonsense variants in the corresponding gene is called stop codon readthrough. The genetic code is written in base 3, such that a group of three DNA nucleotides called a codon corresponds to a specific amino acid or to a “stop” signal. Ribosomes “read” through mRNA sequences, starting at a specific “start” codon and translating each codon after that into amino acids that are linked together to form a protein. When the ribosome reaches a stop codon, it stops adding to the chain and falls off of the mRNA. Premature stop codons are one type of nonsense mutation, along with frameshift variants, which alter the reading frame and therefore sequence of the protein by removing or adding bases in factors other than 3. Scientists in the Bradley Lab hypothesized that in some cases ribosomes may actually translate premature stop codon variants into an amino acid and then continue translating the remaining sequence as normal. They analyzed whether ribosomes were associated with sequence downstream (ahead) of nonsense variants and were able to detect several mRNAs where that was the case. They identified 15 genes with nonsense variants from which it was possible to collect mRNA and ribosome profiles from individuals completely lacking (0/0) or having two copies (1/1) of the nonsense variant. Among those 15, they found that 2 had similar ribosome coverage across the entire mRNA in 0/0 and 1/1 individual despite the presence of the nonsense mutation in the 1/1 individuals. Furthermore, they were able to detect the full-length protein product in those individuals with two (1/1) copies of the nonsense mutation.
Overall, their research demonstrates how nonsense variants do not always completely prevent protein production, providing incentive to investigating and discovering the many mechanisms that control the way that DNA is translated into a functional protein.
Jagannathan S, Bradley RK. 2016. "Translational plasticity facilitates the accumulation of nonsense genetic variants in the human population." Genome Research.
This research was funded by the Ellison Medical Foundation and the FSH Society.