Exons And Introns: Functions and Types

A gene is not one continuous instruction. In most plants, animals, and other complex organisms, the coding message is broken into pieces, and between those pieces sit long stretches that do not code for anything. The coding pieces are called exons. The non-coding pieces in between are called introns.

This raises an obvious question: why would a gene be built with its message interrupted like this? The answer turns out to be one of the most elegant parts of molecular biology. Before the message is used, the cell cuts out the introns and stitches the exons together, in a step called splicing. And because the exons can be stitched together in different combinations, a single gene can produce several different proteins. This article explains what exons and introns are, how splicing works, what each does, their types, and how they differ.

Figure: Gene structure with exons and introns

Exons play a crucial role in determining the structure and function of proteins. Mutations within exons can lead to various genetic disorders or diseases, depending on how they affect the resulting protein’s structure or function. Additionally, alternative splicing, where different combinations of exons join together, can produce multiple protein isoforms from a single gene. This increases the diversity of proteins generated from the genome.

While introns do not encode protein sequences, they can play critical regulatory roles in gene expression. For example, introns may contain regulatory elements such as enhancers or silencers that influence transcriptional activity. Some introns also contain sequences involved in alternative splicing regulation or other post-transcriptional processes.

The presence of introns in genes is a common feature in eukaryotic genomes. This feature distinguishes them from prokaryotic genomes, which typically lack introns. Introns’ evolutionary origins and functions are still areas of active research in molecular biology and genetics.

Figure: Gene with Introns and Exons

What are exons and introns?

A gene in a eukaryote (an organism whose cells have a nucleus, such as plants, animals, and fungi) is usually made of two kinds of segment that alternate along its length.

1. Exons are the coding segments. They carry the instructions that are kept and used to build the protein. The word is a memory aid: exons are EXpressed.
2. Introns are the non-coding segments that sit between the exons. They are transcribed at first but are then cut out and not used to build the protein. The memory aid: introns are INtervening (and they stay IN the nucleus).

When a gene is first transcribed, the RNA copy (called pre-mRNA) contains both exons and introns, in the same order as in the gene. This copy cannot be used yet. It has to be processed first.

How splicing works

Splicing is the step that turns the raw pre-mRNA into a usable, mature mRNA. During splicing, the introns are cut out and the exons are joined together in order. The result is a continuous coding message with no interruptions, ready to be translated into protein.

In most eukaryotic genes, splicing is carried out by a large molecular machine called the spliceosome, made of proteins and small RNA molecules. The spliceosome recognizes short signal sequences that mark the start and end of each intron (commonly a GU at the start of the intron and an AG at the end), cuts the intron out at those points, and joins the neighboring exons.

Here is the key consequence, and the reason introns matter so much: the exons do not always have to be joined in the same way. By including some exons and leaving out others, one gene can produce several different mRNAs, and therefore several different proteins. This is called alternative splicing, and it is how the roughly 20,000 human genes can make a far larger number of proteins.

Functions of Exons

Exons are essential components of genes that encode the information necessary for protein synthesis and function. They not only determine the structure and function of proteins but also play roles in gene regulation, mRNA processing, genetic integrity, and evolutionary innovation.

1. Encoding Protein Sequences: The primary function of exons is to encode the amino acid sequences that make up proteins. Each exon corresponds to a specific segment of the protein sequence. The combination of exons determines the final protein’s structure and function.
2. Determining Protein Structure and Function: The sequence of exons within a gene directly influences the structure and function of the resulting protein. Different combinations of exons, through processes such as alternative splicing, can produce protein isoforms with distinct properties, allowing for functional diversity.
3. Carrying splicing signals: The edges of exons carry short sequences that the splicing machinery recognizes. These signals help ensure the introns are removed cleanly and the exons are joined in the right order.
4. Recognition of Splicing Signals: Exons contain specific sequences, such as splice sites, that the splicing machinery recognizes during mRNA processing. These sequences help ensure that the exons are joined correctly and the introns are removed, producing mature mRNA.
5. Maintenance of Genetic Integrity: Exons are often more conserved across species than introns, indicating their importance in maintaining the integrity of genetic information. Mutations within exons can significantly affect protein structure and function, leading to various genetic disorders or diseases.
6. Evolutionary Conservation and Innovation: Exons play a crucial role in evolutionary processes. Conserved exons often encode essential protein domains or functional motifs preserved throughout evolutionary history. Conversely, the emergence of new exons through processes such as exon shuffling or gene duplication can contribute to the evolution of novel protein functions.

Functions of Introns

Introns were once thought to be “junk DNA” with no particular function, but research over the years has revealed several essential functions that introns can serve:

1. Regulation of Gene Expression: Introns can contain regulatory elements such as enhancers or silencers and binding sites for transcription factors. These elements can influence the transcriptional activity of the gene, affecting the rate of mRNA production.
2. Alternative Splicing: Introns are crucial for alternative splicing, a process where different combinations of exons join together to generate multiple mRNA isoforms from a single gene. This process can significantly increase the diversity of proteins produced from a single gene, allowing for tissue-specific or developmental stage-specific protein variants.
3. Facilitation of Evolutionary Adaptation: Introns can provide genomic flexibility and facilitate evolutionary changes. For example, introns can accumulate mutations without necessarily affecting the coding regions of the gene, allowing for the exploration of new genetic variations over evolutionary time scales.
4. Regulation of mRNA Stability and Transport: Some introns contain sequences that regulate mRNA stability or transport. These sequences can influence how long mRNA molecules persist in the cell before their degradation, or they can affect mRNA localization within the cell.
5. Creation of MicroRNAs: Some introns can give rise to microRNAs (miRNAs) through intronic miRNA biogenesis. These miRNAs can regulate gene expression by binding to target mRNA molecules and promoting their degradation or inhibiting translation.
6. Protection against transposon insertions: Introns can act as a buffer zone against the insertion of transposable elements or other DNA sequences that could disrupt gene function if inserted into exonic regions.

Difference Between Exons and Introns

The simplest way to hold the difference: exons are kept and expressed, introns are removed. Everything else follows from that. Exons carry the protein code and end up in the mature mRNA. Introns interrupt the code, are spliced out, and do their work (mostly regulatory) before they are removed. Exons tend to be conserved across species because changing them changes the protein; introns tolerate more change because they are not translated.

Types of Exons

Exons can be classified into different types based on their functional characteristics and contribution to gene expression and protein synthesis. Here are some common types of exons:

1. Constitutive Exons: These exons are present in the mature mRNA of a gene under normal conditions and are constitutively included in the transcript. They are essential for the primary structure and the protein’s function.
2. Alternative Exons: Inclusion and exclusion of alternative exons from the mature mRNA can occur through alternative splicing. The inclusion or exclusion of alternative exons can give rise to different mRNA isoforms, leading to protein variants with distinct structures and functions.
3. Cassette Exons: Cassette exons are an alternative exon that can be included or skipped as a unit in the mature mRNA transcript. The inclusion or exclusion of cassette exons can generate different protein isoforms.
4. Mutually Exclusive Exons: These are a subset of cassette exons where there is inclusion of only one exon from a set of exons in the mature mRNA transcript. The selection of which exon is included is mutually exclusive with the inclusion of the others.
5. Internal Exons: Internal exons are exons located within the coding region of a gene, as opposed to exons at the beginning (5′ end) or end (3′ end) of the gene. They contribute to the coding sequence of the mature mRNA transcript.
6. Terminal Exons: Terminal exons are exons located at the ends of a gene, either at the 5′ end (5′ terminal exons) or the 3′ end (3′ terminal exons). They are typically involved in the mRNA’s untranslated regions (UTRs) and may contain regulatory elements essential for mRNA stability, localization, or translation.

The presence of alternative exons and alternative splicing significantly increases the diversity of protein isoforms produced from a single gene.

Types of Introns

Introns are non-coding regions of genes that are transcribed into mRNA but are removed during mRNA splicing. While they are often categorized based on their lengths or positions within a gene, introns can also be classified based on their functions or splicing mechanisms.

For most purposes, the important distinction is between the common spliceosomal introns (removed by the spliceosome) and the rarer self-splicing introns (which remove themselves). The main types are below.

1. Canonical or U2-type Introns: These are the most common introns present in eukaryotic genes. They are characterized by consensus sequences at their splice sites, including the 5′ splice site (GU), the branch site (A nucleotide), and the 3′ splice site (AG). Splicing of these introns is carried out by the major spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs) and other proteins.
2. Minor or U12-type Introns: These are less common than canonical introns but are present in some eukaryotic organisms, including humans. They have distinct consensus sequences at their splice sites compared to canonical introns and are spliced out by a minor spliceosome containing different snRNPs. U12-type introns are generally shorter and less frequent than U2-type introns.
3. Group I and Group II Introns: These types of introns are present in organellar genomes (e.g., mitochondria and chloroplasts) and some bacteria and archaea. These introns can self-splice, meaning they can catalyze their removal from precursor RNA molecules without the aid of spliceosomes. Group I introns typically fold into complex secondary structures and use guanosine as a cofactor for splicing, while Group II introns have a conserved secondary structure resembling the spliceosomal snRNAs.
4. tRNA Introns: Transfer RNA (tRNA) genes often contain one or more introns that are removed during tRNA processing. These introns are usually spliced out by enzymes called tRNA splicing endonucleases and are not typically processed by the spliceosome.
5. Mobile Element Insertions: Some introns are derived from mobile genetic elements, such as retrotransposons or DNA transposons, which insert themselves into genes. These introns may contain sequences related to the transposable element and can sometimes disrupt gene function if not correctly spliced.

How to Remember

Exon versus intron, by the letters. Exons are EXpressed (kept in the final mRNA and used to build protein). Introns are INtervening and stay IN the nucleus (cut out, never reach the protein). The first two letters of each word carry the meaning.

Splicing in one image. Think of the pre-mRNA as a filmstrip with unwanted scenes (introns) between the good scenes (exons). Splicing is the editor cutting out the unwanted scenes and taping the good ones together into the final film. Alternative splicing is the editor making different cuts to produce different films from the same footage.

The splice-site signals. Most introns begin with GU and end with AG. A memory phrase: "GU at the start, AG at the end," marks where the spliceosome cuts.

Why exons are more conserved. Change an exon and you change the protein, which is often harmful, so evolution keeps exons stable. Change an intron and usually nothing happens to the protein, so introns drift more freely. "Exons are guarded, introns are free."

Alternative splicing = more proteins than genes. One gene, several exon combinations, several proteins. This is how about 20,000 human genes make many more proteins. "One gene, many proteins, thanks to splicing."

Key exam facts

Where Students Get Confused

Exons are expressed; introns are removed. The names are easy to swap. Exons are EXpressed and kept; introns INtervene and are spliced out. If you remember only one thing, remember which one ends up in the protein: the exon.

Both are transcribed at first. A common mistake is to think only exons are transcribed. In fact the first RNA copy (pre-mRNA) contains both. The introns are removed afterward, during splicing. The difference is not in transcription but in what happens after.

Introns are not "junk." They were once dismissed as junk DNA, but they carry regulatory elements, enable alternative splicing, and can give rise to microRNAs. Non-coding does not mean useless.

Alternative splicing does not create new exons. It selects which existing exons to include or skip. The gene already contains the exons; alternative splicing chooses different combinations of them.

Prokaryotes usually lack introns. Introns are mainly a eukaryotic feature. Most bacterial genes are continuous, which is one reason bacterial genes can be transcribed and translated at the same time.

References

1. Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. Molecular Biology of the Gene. 7th ed. Pearson; 2013.
2. Alberts B, Heald R, Johnson A, et al. Molecular Biology of the Cell. 7th ed. W.W. Norton; 2022.
3. Nelson DL, Cox MM. Lehninger Principles of Biochemistry. 8th ed. W.H. Freeman; 2021.