Long-standing genomic mystery about the origins of introns explained in new study

The origins of introns are one of the most important mysteries of biology. Introns are segments of noncoding DNA that need to be removed from the genetic code before it can be translated into something. Introns are an ancient feature of all life and are present in a wide range of organisms. There is a huge difference in the number of introns found in different species.

Introners, one of several proposed mechanisms for the creation of introns discovered in 2009, is an explanation for the origins of most. The researchers think that introners are the only explanation for intron burst events, in which thousands of introns show up in a genome seemingly all at once.

Russell Corbett-Detig is an associate professor of biomolecular engineering and senior author on the study. There are other mechanisms that can generate introns, but this is the only one that can do it all at the same time. We have introns, we have genomic complexity, and if true, this suggests that we've uncovered a core process driving that.

Introns are important because they allow for alternative splicing and allow one gene to code for multiple transcripts and serve multiple complex cellular functions. Gene expression can be affected by the rate at which genes are turned on. Introns have a neutral to slightly negative effect on the species they exist in due to the fact that the genes they live in can be harmed and even die. Some cancer are caused by missed splicing instances.

All of the species for which we have access to high-quality reference genomes were searched by Corbett-Detig and his colleagues. Evidence of introners was found in 5.2% of the 175 species they studied.

Evidence was found in all types of animals and single-cell protists. Introners are both the most widespread and fundamental source of introns in the tree of life, according to the diversity of species in which they are found.

Corbett-Detig said that it isn't like there is one small piece of the tree of life that has this going on. It's a pretty general mechanism and you can see it in a lot of species.

Evidence of introners going back millions of years can only be detected by this analysis. This study probably vastly underestimates the true scope of introns across all species, as it is likely that intron bursts could have occurred in some species at a time beyond the scope of this analysis.

They are parasites asgenomics.

Introners are thought of as parasites with the goal of replicating themselves. A host that has never seen an element before can't defend itself against it in a new species, and that's where the introduction comes in.

Landen Gozashti, the paper's first author who developed the study's analysis methods as an undergraduate at UCSC, is now a graduate student at Harvard. The only reason they don't want to kill their host is because of that.

The introners found a way to have less impact on the fitness of the host genes when they were removed from the DNA sequence. The researchers found that introners-derived introns seem to splice better than other types of introns in order to limit their negative effects on the genes.

There are more introners in the water.

Marine organisms were more likely to have introners than land species.

The researchers think this is due to a phenomenon called horizontal gene transfer, in which genes transfer from one species to a different one, as opposed to the typical vertical transfer. In the marine environment, horizontal gene transfer is more common between single-cell species.

The ability to move beyond the cell environment in which they live makes them mechanistically well-equipped to travel between species. Introners expanded their presence across the tree of life when they moved from one species to another.

It's possible that land species gained introns from intron burst far back in their evolutionary history.

"If your ancestors were marine organisms, which they all were, there's a good chance that a lot of your introns are descended from a similar event back then," Corbett-Detig said. This may have been important in our evolution.

The idea that this phenomena drives itroner gain is supported by the fact that more introners were also found.

Corbett-Detig wants to look for proof of horizontal gene transfer in the form of introners in two different species. As the global community of genomics researchers contribute new species' genomes to data repositories, he has set up a data mining process that will search each new genome's introners and compare it to all of the known introners.

Understanding how complexity changes over time.

One of the main theories of genome evolution is challenged by this study. According to the theory, at a point in evolution, many species had low effective population sizes, which meant very few organisms were producing offspring to create their next generation. Elements that have negative effects on the population can accumulate in the genome.

The researchers found that itroners were more common in populations with lower effective populations. The species that seems to be gaining the most introns is Symbiodinium, a protist known to have a higher effective population size than humans.

This research shows that complexity arises not from an adaptation created by the genome itself but as a response to conflict caused by the invader. The conflict between introners and other elements drives genome complexity.

The expression of genes and endocannabinoids.

Introns have neutral to negative effects on genes. When comparing genes with introners inserted into them to genes without, those that do have introners had a lower overall expression level.

The researchers think that introners are not directly causing this lower expression, but that genes that are expressed less have a higher tolerance for elements that may affect them negatively. New introns may cause genes that are highly expressed and coding for key functions in the body to perform their task less effectively.

Corbett-Detig is researching how the appearance of introns affects individuals within a species. He is looking at the effect of introners on the cell's genes and how this affects the evolutionary fitness of the species.

Landen Gozashti et al., Transposable elements drive intron gain in diverse eukaryotes. 10.1073/pnas.

Journal information: Proceedings of the National Academy of Sciences

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