Of the approximately three billion base pairs that make up the human genome, only about 2% code for proteins, while the remaining 98% perform less clear functions.
It is dismissed by some as “junk DNA,” and its origins, implications, and potential purpose in the evolution of life have captured the attention of biologists ever since the disruption of our chromosomes was first noticed in the 1960s.
Researchers at Tel Aviv University in Israel have now added some important insights into why non-coding DNA persists, which could help us better understand the rich diversity of genome sizes in the living world.
In 1977, scientists Richard Roberts and Phil Sharp independently noticed that much of the chaos of DNA is not only scattered throughout our genes, but often interrupts them mid-sequence—a discovery that would later earn them a Nobel Prize.
They are known as introns, and they seem to overload complex cells like ours while leaving simpler cells like bacteria cells untouched. It also added a lot of effort to the process of translating DNA into matter.
Each time a new protein is added, these breaks must be cut out of the genetic template, requiring the coding instructions to be reconnected before they can be interpreted as a protein. It may take a daily comparison to remove thousands of irrational characters just to read a sentence.
This seemingly wasteful way of working is needed by all of nature, except for those lucky bacteria and other prokaryotes.
It so happens that the number of introns varies greatly from species to species; Humans have about 140,000 introns, rats about 33,000, common fruit flies about 38,000, brewer’s yeast (or brewer’s yeast, Saccharomyces cerevisiae, Saccharomyces cerevisiae) only about 286, and the single-celled fungus Encephalitozoon cuniculi only 15.
Why didn’t evolution eliminate this mess through natural selection to make us more efficient beings? fail even after millions of years of development?
“Interestingly, the opposite happened because eukaryotes have larger genomes, longer proteins, and much larger genomic regions compared to prokaryotes,” the scientists involved in this latest intron study wrote in their recently published report.
The researchers hypothesized that the removal of any interfering DNA segments around the coding regions would likely be detrimental to the survival of the animal, as the coding regions could also be excised at the same time.
“Lots that develop near the boundary sometimes protrude into the protected area and are therefore subject to strong antiseptic selection,” the researchers write.
This “edge-induced selection” when there is a neutral sequence between coding regions can create insertion bias for short non-coding DNA sequences.
Essentially, “junk DNA” acts as a mutation buffer, protecting regions containing the most sensitive sequences needed to encode proteins.
The researchers created a mathematical model to show this dynamic in action.
It has previously been suggested that “deletion bias leads to genome shortening over evolutionary age,” the team explained.
The counterintuitive conclusion that long-range neutral sequences can appear even with a strong deletion propensity is due to the rejection of deletions that invade the highly conserved boundaries of neutral sequences.
While their model provides a plausible explanation for intraspecies variation in intron lengths, it fails to explain why they differ between species.
“One explanation is that the same model parameters evolve. Thus, different species have different ratios of insertions and deletions, and possibly a different propensity for the appearance of conserved regions within introns,” they write.
Knowing that bias exists could help explain the diversity of introns we see in nature and why some organisms seem to be genetically more “random” than others.
And, in the end, it may not be coded, but endowed with functions that we do not yet know about. In recent years, science has increasingly moved away from describing all introns as “junk DNA” as more possible functions have been discovered, including the transcription of introns into RNA strands that control protein production.
What we think of as garbage can eventually become a genetic treasure. This may seem like a complicated way to create an organism, but with several billion years of evolution behind it, nature seems to know what it’s doing.
This article was published in Open Biology.
Source: Science Alert