If I cast my mind back to studying biology at school, the message was very clear: DNA contains genes, and genes make proteins. Simple enough right? Well, scientists of the 20th Century thought much the same until 1977 when everything changed. The pieces we once thought of as ‘junk’ have become a hub of incredible insight. In this piece, we are going to dive into the discovery of introns and their role within the genome.
Discovery of introns
You might be able to imagine the shock to my adolescent mind when I discovered that non-coding introns make up a whopping 25% of the human genome, 4 to 5 times higher than protein coding DNA.
Introns were first described by Richard Roberts’ and Phil Sharp’s lab in 1977. When mRNA was allowed to pair with the DNA it derived from, intervening DNA ‘looped out’ as it had nothing to pair with. The sizes of the DNA segments were deduced using restriction enzymes, and it was confirmed that eukaryotic mRNA molecules were significantly shorter than their corresponding genes.
One reason that this discovery wasn’t successfully made until relatively late in the study of gene regulation is that gene regulation was mostly studied in relatively simple bacterial systems. Unfortunately, most bacterial transcription is co-linear, where there is an exact correspondence with the mRNA and the DNA encoding it.
While introns, for some time, were considered ‘junk DNA’ that were simply removed before mRNA translation, researchers began to realise that they actually played several vital roles in genomic regulation.
The removal of introns from a pre-mRNA, or the primary transcript, to create an mRNA molecule is known as splicing. The process of splicing is now well characterised. It occurs within a complex known as the spliceosome, which is a huge ribonucleoprotein found in the nucleus. The spliceosome folds the primary transcript at introns and cleaves them at particular sequences called splice sites. Amazingly, some RNA molecules have exhibited the ability to ‘self-splice’, without the need for the spliceosome.
While it’s not immediately obvious what the purpose of splicing is alone, its true power is revealed through alternative splicing. One gene may contain many introns. When the introns are removed, the remaining RNA material (exons) can be arranged in a variety of orders, allowing for one gene to code for multiple proteins. It’s like swapping the words around in a sentence. It’s a sentence like the words in swapping around. Sorry, I couldn’t resist.
Alternative splicing not only vastly increases the number of proteins the genome is able to produce, but it also adds a new layer of transcriptional regulation outside of transcription factors and epigenetic changes. Depending on which splice sites are used, the proportions of the different gene transcripts created through alternative splicing can be altered.
Introns may also provide some level of mutation protection. Genome-wide analyses in both yeast and humans have revealed that intron-containing genes have decreased DNA damage compared to intron-less genes of similar expression.
It’s not always hunky-dory though. Abnormal variations in splicing are also implicated in disease. A large proportion of human genetic disorders result from splicing variants. In fact, RNA splicing errors have been estimated to occur in a third of genetic diseases. Abnormal splicing variants are also thought to contribute to the development of cancer. Splicing factor genes are frequently mutated in different types of cancer.
Evolutionary history of the intron
After the discovery of introns in the eukaryotic nucleus there was significant debate as to whether introns in modern-day organisms were inherited from a common ancient ancestor (termed the introns-early hypothesis), or whether they appeared in genes rather recently in the evolutionary process (termed the introns-late hypothesis). Another theory is that the spliceosome and the intron-exon structure of genes is a relic of the RNA world hypothesis, which suggests that all life started out as self-replicating RNA molecules on primordial Earth.
The most popular current theory is that introns arose within eukaryotes as “selfish genetic elements”, genetic segments that can enhance their own transmission at the expense of other genes in the genome, even if this has no positive effect on the organism.
While introns evolved slowly, science certainly isn’t! It’s going to be exciting to continue to see what other secrets are hidden away in the mysterious intragenic parts of the genome.
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