Alternative Splicing of Genes: Definition, Mechanism & Regulation

Instructor: Erika Steele

Erika has taught college Biology, Microbiology, and Environmental Science. She has a PhD in Science Education.

The traits you see in living beings, including humans, are determined by complex genetic controls. This lesson will discuss how alternative splicing of genes contributes to the diversity of traits seen in organisms. After the lesson there will be a brief quiz to see how much you have learned.


Figure 1: Alternative splicing allows cells to piece together segments of DNA to create multiple proteins from one gene.
Alternative splicing

Have you ever read that humans are 44% genetically similar to a fruit fly? I'm sure when you saw that, you probably wondered, 'How the heck can an insect be almost 50% similar to me?' Well, it's the truth! Humans have about five times the number of proteins (or traits) as fruit flies but only twice the number of genes.

Cells have to make a lot of proteins in order to function right. For organisms with more complex cells, they need to have slightly different proteins to perform similar functions in different organelles. In multicellular organisms, different proteins with the same function have to be made for different organs in the body. Instead of having dozens of genes to make separate proteins for each location, cells will use alternative gene splicing in order to generate different forms of the protein from one gene as shown in Figure 1.

Gene Structure

Figure 2: Genes are found on chromosomes and contain the directions to make the proteins that make a cell function.
Genes are found on chromosomes.

Before getting started, let's do a brief review of some things that you need to understand before discussing alternative gene splicing. First, what's a gene? Well, a gene is basically a stretch of DNA that codes for a protein. Genes are found on chromosomes in the nuclei of the cells that make up an organisms as shown in Figure 2. Genes contain the sequences that tell the cell how to make the proteins it needs to function. The coding region is the part of the gene that contains DNA sequence that tells the cell how to make a trait.

Figure 3: The coding region contains sequences that belong in the gene (exons) and sequences that must be removed (introns)
exons and introns

If you look more closely at the coding region, you will see that it's made of things called exons and introns (Figure 3). Like any set of instructions, genes have extra words in them that you can just skip over. Introns are intervening sequences that will be removed and usually don't show up in the protein; they are like the annoying parts of instructions that nobody reads. Exons are the expressed region of the gene; the exon sequences will be a part of the final mRNA that encodes the protein. The exons are critical for building the gene.


Figure 4: RNA must be processed before it can leave the nucleus.
transcription of RNA

We're discussing alternative splicing, but what's splicing? Splicing normally happens as genes are converted from DNA into a protein in eukaryotic cells (any cell that has a nucleus). Before the RNA can leave the nucleus to be converted to a protein, the introns are cut out and the exons are pasted together. Splicing can be compared to Cliff's notes for making a protein in that it prepares an RNA with only the necessary information to make protein.

Figure 5: Alternative splicing allows one gene to make multiple slightly differing versions of a protein.
alternative splicing

For some genes, splicing generates one gene product or protein, the exons can only be put together in one way. Alternative splicing allows the exons to be put together in different ways to generate multiple proteins with slightly different functions, called isoforms.

Going back to the instructions analogy, alternative splicing can be compared to an instruction book for convertible furniture. The instruction book for my son's crib had instructions to make a crib, a toddler bed, and a full size bed from the same parts. This is exactly how alternative splicing works. The same exons, or parts can be put together in different ways to make similar proteins with slightly different functions.

Types of Alternative Splicing

Exon Skipping

Figure 6: Exon skipping creates smaller versions of a protein by removing exons.
exon skipping

The most common method of alternative splicing is exon skipping which is exactly what it sounds like; some exons are left out of final mRNA. When translated, the shorter mRNA will create a smaller protein.

Mutually Exclusive Exons

Figure 7: Mutually exclusive exons cannot be together in the final mRNA use to encode a gene.
mutually exclusive exons

Mutually exclusive exons are exons that cannot be on the same transcript. If the final mRNA includes one exon, the other cannot be in the mRNA as shown in Figure 7.

Intron Retention

Figure 8: Alternative versions of a protein can be created by including sequences from introns.
intron retention

Alternative mRNAs from a gene can be generated by including introns in the mRNA instead of removing them. In Figure 8, a larger mRNA is created by including the intron.

Deciding Which Protein to Make

Figure 9: Splicing occurs on the splicesome which is a collection of enzymes that cut out the introns and ligate (or paste) the exons together.
spliceosome formation

Spliceosomes regulate and control splicing in cells. They're made of enzymes called small nuclear ribonucleoproteins (snRNPs pronounced). The way snRNPs work is by recognizing conserved sequences in splice sites, removing the introns, and then pasting the exons together.

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