It is Sunday, the supermarket is closed and I’m hungry. After looking through the kitchen I’ve found some pasta, rinsed meat, a zucchini, some mushrooms, a jar of Bolognese sauce and a package of lasagna sheets. So what shall I eat, pasta or lasagna?

Just as it is possible to make different dishes by using some ingredients but leaving out others, it is also possible to make different proteins by including or leaving out certain “ingredients” of genes. This process is called alternative splicing and it makes it possible to produce different proteins from the same gene (these different protein versions from the same gene are called isoforms). In this way, our bodies can produce over 100.000 proteins from only 20.000 genes.

Gene structure

A gene is a segment of DNA which is transcribed into messenger RNA (mRNA) and then translated into a protein (read about transcription and translation here). Genes consist of different regions, of which only exons will end up in the final protein. Genes consist of untranslated regions (UTRs) on both ends (5’-end and the 3’-end), exons and introns (see the figure below). The UTRs are, as the name indicates, not translated into protein. These regions are however involved in determining the activity of the gene. The exons are the parts of the gene that are translated into protein, the introns are spliced out of the mRNA before it leaves the nucleus. But what is splicing?


pre-mRNA and splicing


When a gene is “transcribed”, it means that the sequence of A,T,G and C’s are being copied into a RNA molecule with the same sequence but a U instead of a T (read more here). This process doesn’t discriminate between the different regions (UTR, exon and intron) of the gene, it simply copies. After copying a gene, the resulting RNA sequence is called a pre-mRNA. This is because it still contains the introns, which are not used to make protein. These are removed before the mRNA leaves the nucleus in a process called splicing (see the figure below). Splicing is performed by a complex of different RNA molecules (small nuclear RNA or snRNA) and several proteins. This complex of RNA molecules and proteins is called the spliceosome.  What it does is simple, it recognizes the boundaries of exons and introns, folds up the intron, cuts it out and connects the 2 exons together. Next, a 5’ cap is added to the 5’ end of the mRNA, this increases the stability of the molecule once it leaves the nucleus. Finally, a string of A’s is added to the 3’ end of the mRNA, which is called the poly-A tail and also increases the stability of the mRNA and it increases the readability of the molecule once it is to be translated to protein.


Alternative splicing


So far so good. But what about alternative splicing? The principle is the same, a pre-mRNA is produced and spliced, a 5’ cap is added and a poly-A tail is added. The only difference is, that instead of just splicing the introns out, some exons might be spliced out too. This leads to different proteins, one in which all 3 exons are used and one in which only exon 1 and 3 are used. So one gene for two proteins (see figure below).

The example discussed here concerns a gene with only 3 exons. Although this keeps the explanation simple, it does not provide the potential of many different isoforms. If we would have more exons that would mean more flexibility in the number of proteins that can be formed from a single gene. The gene Dscam from the fruitfly (Drosophila melanogaster) has 95 exons and can form 38.016 different proteins. So this one fly gene can form more different proteins than the number of genes we humans have in total! This Dscam gene with its extraordinary high number of isoforms is an exception, most genes do not make so many different isoforms. As mentioned earlier in this post, with about 20.000 genes and more than 100.000 proteins, the average number of isoforms from each gene should be about 5.


All in all, alternative splicing is an essential part of complex animals like us. The use of alternative splicing makes it possible to have many different proteins to fulfil all the different tasks necessary in our lives without the need of a gigantic genome. Isn’t it nice to know that we are not carrying all that redundant information around?