A single gene in your DNA can be thought of as a recipe for building a specific protein. The cell, however, can modify this recipe to create different versions of that protein, each with a unique role. This process is known as alternative splicing. It functions like a film editor creating multiple movie trailers (proteins) from the same raw footage (the gene), with each trailer telling a slightly different story.
This molecular editing allows an organism to produce a vast array of proteins from a limited number of genes. The human genome, for example, has about 20,000 protein-coding genes but can generate a much larger number of unique proteins through this process. Alternative splicing occurs constantly within our cells, tailoring proteins to the needs of different tissues and developmental stages.
Gene Structure and the Splicing Process
To understand how the cell edits its protein recipes, we first need to look at the structure of a gene. Genes are segments of DNA, but not all the information within a gene is used to build a protein. The coding sequences containing the instructions are called exons, and these are interrupted by non-coding sequences called introns. In humans, a gene has about eight or nine exons interspersed with a similar number of introns.
Before a protein can be built, the gene’s information is transcribed into a molecule called precursor messenger RNA (pre-mRNA). This transcript is a direct copy of the gene, including both exons and introns. The introns must then be removed and the exons joined together to create a final, mature messenger RNA (mRNA) molecule. This “cut-and-paste” editing is known as splicing.
This task is performed by a molecular machine called the spliceosome. The spliceosome, composed of proteins and small RNA molecules, recognizes specific sequences at the beginning and end of each intron. It cuts out the introns and stitches the remaining exons together in their original order. This standard, or constitutive, splicing process creates a single mRNA blueprint that is then translated into a protein.
Mechanisms of Alternative Splicing
Alternative splicing adds a layer of regulation to this process, allowing the cell to deviate from the standard script. The spliceosome can be directed to include or exclude certain exons, creating multiple different mRNA transcripts from a single pre-mRNA molecule. There are several primary ways this is achieved.
The most common mechanism in mammals is exon skipping. In this scenario, an entire exon is bypassed and spliced out along with the surrounding introns. The resulting mRNA is shorter and will produce a protein lacking the amino acid sequence encoded by the skipped exon. This modification can significantly alter the protein’s final structure and function.
Another mechanism is intron retention, where an intron is kept in the final mRNA sequence. Retaining an intron can introduce a stop signal that halts protein production prematurely or insert a new functional segment into the protein.
Cells can also utilize alternative splice sites. The spliceosome normally recognizes specific sequences that mark the start and end of an intron. By recognizing a slightly different sequence near the usual cut site, the spliceosome can make an exon longer or shorter. This fine-tuning alters the protein-coding message and leads to a different product.
Functional Importance in Biology
In the human nervous system, alternative splicing generates the array of proteins needed for neuronal development, synaptic function, and cell-to-cell communication. Different cell types can produce unique versions of structural proteins, ion channels, and receptors from the same set of genes. This contributes to the brain’s complexity.
The process also plays a role in development. As an organism develops, the patterns of alternative splicing change, switching from fetal protein versions to adult versions. For instance, the muscle protein titin exists in different forms due to this process. Fetal heart tissue produces longer, more elastic versions of the protein, while adult hearts produce shorter, stiffer forms better suited for mature cardiac function.
Link to Human Disease
Since alternative splicing is integral to normal biological function, errors in this process can have health consequences. Dysregulation of splicing, often caused by genetic mutations, can lead to the production of faulty or non-functional proteins. A significant percentage of human hereditary diseases have been linked to such errors.
Spinal Muscular Atrophy (SMA) is a clear example of a disease caused by a splicing defect. This severe neurodegenerative disorder results from insufficient levels of the Survival Motor Neuron (SMN) protein. Humans have two genes that produce this protein, SMN1 and SMN2. While SMN1 produces the functional protein, a difference in the SMN2 gene causes an exon to be skipped most of the time, leading to an unstable protein. In individuals with SMA, the SMN1 gene is non-functional, and the SMN2 gene cannot produce enough SMN protein to support motor neurons.
Certain forms of muscular dystrophy are also linked to splicing errors. In Duchenne muscular dystrophy (DMD), mutations disrupt the production of the dystrophin protein. In some cases, therapeutic strategies use molecules called antisense oligonucleotides to intentionally skip an additional exon. This can restore the proper reading frame of the gene, allowing for the production of a shorter but still partially functional dystrophin protein. Misregulation of splicing is also a feature of many cancers, where altered protein isoforms can contribute to tumor growth and resistance to therapy.