Exons And Introns: Functions and Types

Exons are regions of a gene that contain coding information for the synthesis of proteins. During the process of gene expression exons are transcribed into mRNA and eventually translated into proteins. 

Exons are interspersed with introns. Introns are non-coding regions of a gene that interrupt the coding sequences, or exons, within the gene. During the process of gene expression, introns are transcribed into mRNA along with exons. However, unlike exons, introns are typically removed from the pre-mRNA through splicing before the mRNA is translated into protein.

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 distinguishing them from prokaryotic genomes, which typically lack introns in their genes. Introns’ evolutionary origins and functions are still areas of active research in molecular biology and genetics.

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. Regulation of Gene Expression: Exons can contain regulatory elements influencing gene expression. For example, specific sequences within exons may serve as binding sites for transcription factors or other regulatory proteins, modulating the gene’s transcription rate.
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 splicing together of exons are correct and 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.

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 generating 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. 

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 occur typically 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.
6. Intergenic Introns: These are located between genes and are part of the non-coding regions of the genome. While they do not interrupt coding sequences, they can contain regulatory elements that can impact gene expression or chromatin structure.

Difference Between Exons and Introns

This table concisely overviews the main distinctions between exons and introns, including their location, function, and evolutionary significance.

References

1. Blake, C. Molecular biology: Exons — present from the beginning?. Nature 306, 535–537 (1983). https://doi.org/10.1038/306535a0 
2. Patthy, L. (1987, April). Intron-dependent evolution: Preferred types of exons and introns – core. CORE. https://core.ac.uk/download/pdf/81939996.pdf 
3. Forsdyke, D. (2006). Exons and introns. Springer. https://link.springer.com/content/pdf/10.1007/978-0-387-33419-6_10.pdf