“Junk DNA” - A Hidden Treasure
By William Huang
You may think that the human genome is an efficient and thorough entity that has been carefully optimized through evolution. After all, we humans have been on this Earth for over 7 million years! However, this is far from the truth. In fact, only 1.5 percent of our DNA actually codes for proteins, which are biological molecules that perform actions for our cells and help with the structure and regulation of tissues and organs. The other 98.5 percent is called “junk”, nucleotides that have been thought to be useless until recent research..
Where does this “junk DNA” come from?
The script of DNA only contains four letters: A (adenine), G (guanine), C (cytosine), and T (thymine). Together, these letters create the fundamental structure of our genes, which are responsible for coding proteins. However, the making of proteins is not a straightforward process from genes to proteins. Instead, DNA is first transcribed into RNA (think of it as single-stranded DNA), which is then sliced and reassembled. The pieces that are sliced are the “junk, portions of DNA never used to make proteins. Yet again, we are left pondering why our body produces this “junk”, and why it spends so much energy on it.
What is the value in “junk DNA”?
This question was explored by the Encyclopedia of DNA Elements, or ENCODE team. This international team of over 400 scientists investigated the mystery behind “junk DNA” and looked at the function of every letter of the genome.
Prior to ENCODE’s research, scientists believed that this DNA was truly useless. In 2008, a study was published in
Molecular Biology of the Cell that found that when introns (the non-coding portions of the DNA) were removed from genes, there was no significant effect on the cell . However, ENCODE’s publication in
Nature
in 2012 finally shed light on functions of “junk DNA.” The work had uncovered previously unknown elements of "junk" DNA, such as several regulatory elements. While regulatory elements do not produce proteins, they instruct the 1.5 percent of genes to produce more or less of these molecules, hence having an indirect effect on protein synthesis.
Scientists also made an intriguing discovery through this research. In addition to controlling the amount of protein translated, “junk DNA” also helps maintain genetic structure. These pieces of DNA, called satellite DNA, do not have regulatory functions. Instead, they provide structure. Satellite DNA is located in the middle of the chromosome, where the two halves are joined. It also can be found at the tips of chromosomes where it protects DNA from breaking down.
Some “junk DNA” is truly junk.
Despite the discoveries in the functions of “junk DNA”, some researchers still believe it is useless. Dan Graur, an evolutionary biologist at the University of Houston, believes that 75 percent of “junk DNA” is useless. Graur used mathematical modeling to determine how much DNA could possibly be useful. He considered the frequency of deleterious mutations our genome acquires over time, along with fertility rates. Because those mutations can be lethal, Graur estimates in a 2017 paper in Genome Biology and Evolution that no more than a quarter of our genetic code can be functional.
Elements known as transposons are believed to make up to 40 percent of the human genome. These transposons, also known as “selfish” genetic elements, are sequences of DNA that are able to “copy and paste” themselves, often causing mutations when they insert themselves in the middle of a gene. Viral DNA is also considered harmful, as DNA from viruses forcefully inserts itself into the human genome, which can code for harmful proteins that can cause cancer or other diseases.
Citations:
https://www.discovermagazine.com/health/our-cells-are-filled-with-junk-dna-heres-why-we-need-it
