Within the instruction manual of our cells, the genes, not all information is used to build proteins. Genes are composed of two types of sequences: exons, which are the coding regions that get translated into proteins, and introns, which are non-coding segments that interrupt them. Introns are found in the genes of most complex organisms, including humans. The presence of these intervening sequences means that the initial genetic message is a rough draft that requires editing.
Removing Introns Through Splicing
The process of excising introns and joining exons is known as splicing. This editing occurs after a gene’s DNA sequence has been transcribed into a preliminary RNA molecule, called pre-messenger RNA (pre-mRNA). This pre-mRNA molecule is a direct copy of the gene, containing both exons and introns.
This molecular editing is performed by a machine called the spliceosome. The spliceosome is a complex made of small nuclear RNAs and numerous proteins. It assembles on the pre-mRNA and recognizes specific sequences at the boundaries of each intron. These boundary markers, known as splice sites, act as signals, telling the spliceosome where to cut.
Think of the spliceosome as a highly skilled film editor. The editor scans the raw footage, identifies the start and end points of scenes that need to be removed, and carefully cuts them out. Once the unwanted scenes are gone, the editor splices the remaining clips together. In the same way, the spliceosome snips the pre-mRNA at the intron-exon junctions, removes the intron, and then joins the two adjacent exons. The discarded intron is degraded, and the mature messenger RNA (mRNA) is now ready to be translated into a protein.
The Functional Roles of Introns
For many years, introns were dismissed as “junk DNA,” but this view is now outdated. These non-coding sequences have significant roles in the cell. Introns are integral to regulating gene activity and generating biological complexity. Their presence in a gene allows for alternative splicing, which expands the information capacity of the genome.
Alternative splicing allows a single gene to produce multiple, distinct proteins. During the splicing process, the cellular machinery can be directed to include or exclude certain exons along with the introns. By mixing and matching different exon segments, a cell can create a variety of different mRNA transcripts from one gene. It is estimated that over 90% of human genes undergo alternative splicing, which helps explain how around 20,000 protein-coding genes can generate a much larger number of unique proteins.
Beyond enabling protein diversity, introns can also contain regulatory sequences that influence gene expression. Some introns harbor enhancers or silencers, which are stretches of DNA that can increase or decrease the rate at which a gene is transcribed. The physical length of introns can also be a factor, as longer introns can create more space between exons, increasing the chances for genetic recombination—a process called exon shuffling—which can lead to the evolution of new genes and proteins over time. Some introns even contain the code for functional RNA molecules that have their own jobs in the cell after being spliced out.
Splicing Errors and Disease
The precision of the splicing process is important for cellular health. When this molecular editing goes awry, it can have serious consequences, leading to the production of faulty proteins or no protein at all. A substantial portion of disease-causing mutations affect splicing. These errors can occur if there is a mutation in the DNA sequence of a splice site, which prevents the spliceosome from recognizing where to cut.
Such mistakes can lead to several problematic outcomes. An intron might be incorrectly left in the final mRNA, or an exon might be mistakenly removed along with the introns. Either scenario alters the genetic recipe, resulting in a non-functional or even harmful protein. The reading frame of the genetic code can be shifted, leading to a completely different and usually truncated protein product.
Specific human diseases have been directly linked to splicing errors. For example, certain mutations that cause cystic fibrosis interfere with the proper splicing of the CFTR gene, leading to a defective protein. Similarly, spinal muscular atrophy is often caused by a splicing defect in the SMN2 gene, which prevents the production of enough functional survival motor neuron protein. Some forms of cancer and neurodegenerative disorders, like frontotemporal dementia, have also been traced back to mutations that disrupt the normal splicing patterns of specific genes.