New model describes the enormous range of DNA in nature

Why neutral sequences, frequently referred to as “junk DNA,” are not removed from the genomes of living things in nature and persist there even millions of years later is a scientific mystery that could have a possible answer according to a new model created at Tel Aviv University.

The reason, according to the researchers, is that functional DNA frequently coexists with junk DNA. Evolution rejects the functional areas because deletion events along the boundaries between junk and functional DNA are likely to harm them. The model aids in comprehending the enormous range of genome sizes found in nature.

The research team referred to the process that the new model depicted as “border induced selection.” It was created at Prof. Tal Pupko’s lab at the Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, under the direction of PhD student Gil Loewenthal, in conjunction with Prof. Itay Mayrose (Faculty of Life Sciences, Tel Aviv University). The study was published in Open Biology.

The amount of the genome in living things in nature fluctuates during evolution, according to the experts. For instance, certain species of salamander have genomes that are 10 times larger than those of humans.

The rate of deletions and short insertions, which are termed in short as 'indels', is usually measured by examining pseudogenes. Pseudogenes are genes that have lost their function, and in which there are frequent mutations, including deletions and insertions of DNA segments.”

Tal Pupko, Professor, Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University

Pupko added, “In previous studies that characterized the indels, it was found that the rate of deletions is greater than the rate of additions in a variety of creatures including bacteria, insects, and even mammals such as humans. The question we tried to answer is how the genomes are not deleted when the probability of DNA deletion events is significantly greater than DNA addition events.”

PhD student Loewenthal added, “We have provided a different view to the dynamics of evolution at the DNA level. As mentioned, when measuring the rate of indels there will be more deletions, but the measurements are carried out in pseudogenes which are quite long sequences. We claim that in shorter neutral segments, deletions are likely to delete adjacent functional segments which are essential for the functioning of the organism, and therefore will be rejected. We call this phenomenon “border-induced selection.”

He further stated, “If so, when the segment is short, there will be a reverse bias so that there will be more insertions than deletions, and therefore short neutral segments usually are retained. In our study, we simulated the dynamics of indels, while taking into account the effect of "border-induced selection” and compared the simulation results to the distribution of human intron lengths (introns are DNA segments in the middle of a protein-coding gene, which themselves do not code for a protein).”

He concluded, “A good match was obtained between the results of the simulations and the distribution of lengths observed in nature, and we were able to explain peculiar phenomena in the length distribution of introns, such as the large variation in intron lengths, as well as the complex shape of the distribution which does not look like a standard bell curve.”