The genetic information in our cells provides instructions for building our bodies. These instructions, held within genes, must undergo a precise editing process before they can be used to create proteins. At the heart of this process are markers known as splice junctions, which signal where the genetic script needs to be cut and pasted. Understanding these junctions is important for comprehending how a single gene can create various proteins and how errors in this system can cause disease.
Genes, RNA, and the Blueprint for Proteins
A gene is a segment of DNA that holds the blueprint for a specific protein. To use this blueprint, the cell creates a temporary copy of the gene as a molecule called ribonucleic acid, or RNA. This initial copy, known as pre-messenger RNA (pre-mRNA), is a direct transcript of the gene’s sequence but contains more information than is needed for the final protein.
The pre-mRNA molecule is composed of alternating segments called exons and introns. Exons are the sequences that code for parts of the final protein, while introns are non-coding sequences interspersed between them. Think of introns as extra material in a rough draft that must be removed to produce a clean final version.
Because of introns, the pre-mRNA must be processed to remove these non-coding regions and stitch the coding exons together. This creates a mature messenger RNA (mRNA) molecule that contains a continuous set of instructions. This mature mRNA is then transported out of the cell’s nucleus to the protein-building machinery.
What Are Splice Junctions?
Splice junctions are the specific locations on pre-mRNA that mark the boundaries between introns and exons. They act as precise signals, indicating where the cellular machinery should cut the RNA to remove an intron and join the two adjacent exons. These junctions are defined by short, recognizable sequences of nucleotides, the building blocks of RNA.
At the beginning of an intron is a donor site, while at the end is an acceptor site. In most human genes, a “GU-AG rule” is followed. This means the donor site consists of the nucleotides guanine (G) and uracil (U), and the acceptor site has adenine (A) and guanine (G). These conserved sequences are the primary signals that guide the splicing process.
The function of these junctions is to ensure that introns are removed perfectly. If the cut is made even one nucleotide off, it can shift the entire reading frame of the genetic code. This would result in a completely different and likely non-functional protein being produced.
The Spliceosome: Precision Machinery for RNA Editing
The task of recognizing splice junctions and performing the cutting and pasting of RNA is carried out by a large molecular machine called the spliceosome. The spliceosome is composed of several small nuclear RNAs (snRNAs) and a large number of proteins. Together, these components form small nuclear ribonucleoproteins, or snRNPs (pronounced “snurps”), which are the functional units of the spliceosome.
The process begins when different snRNPs recognize and bind to the donor and acceptor splice sites, as well as to another sequence within the intron known as the branch point. This assembly brings the two ends of the intron together, forming a loop structure. The spliceosome then acts like a pair of molecular scissors, cleaving the RNA at the donor and acceptor sites to release the intron.
Once the intron is removed, the spliceosome ligates, or pastes, the two exons together, creating a continuous coding sequence. This action completes the formation of a mature mRNA molecule, ready for the next steps in protein production.
Alternative Splicing: One Gene, Many Proteins
The system of exons and introns allows for a process known as alternative splicing. This mechanism enables a single gene to produce multiple different proteins by selectively including or excluding certain exons from the final mRNA. By using different combinations of splice junctions, the cell can create a variety of protein isoforms, each with a unique function, from the same gene.
This process vastly increases the coding capacity of the genome. While humans have an estimated 20,000 protein-coding genes, the number of different proteins in the body is far greater, largely thanks to alternative splicing. For example, one version of a protein might be produced in muscle tissue, while a different version with an altered function is produced in the brain, both originating from the same gene.
The selection of which splice junctions to use is a regulated process, influenced by various protein factors that can enhance or suppress the recognition of specific sites. This regulation allows cells to fine-tune gene expression in response to developmental cues, environmental signals, or specific cellular needs.
Splice Junction Defects and Human Disease
Given the precision required for splicing, errors in this process can have severe consequences for human health. Mutations that alter the nucleotide sequence of a splice junction can disrupt the ability of the spliceosome to recognize it correctly. This can lead to the inactivation of a splice site, causing an entire exon to be skipped from the final mRNA, a phenomenon known as exon skipping.
Alternatively, a mutation can weaken a splice site, causing it to be used less efficiently, or activate a “cryptic” splice site that is normally ignored. This can result in the inclusion of parts of an intron or the incorrect trimming of an exon. Both of these outcomes can lead to the production of a defective protein, which is the underlying cause of many genetic disorders.
Many inherited diseases are linked to splicing mutations. For instance, certain mutations causing cystic fibrosis and spinal muscular atrophy disrupt the normal splicing of genes. Similarly, alterations in splicing patterns are a common feature in many types of cancer, where the production of different protein isoforms can contribute to tumor growth and progression.