DNA: Dark matter junk? Nope, it’s Actually useful

By Olivia Kutlesa

Since its’ colossal discovery in 1953, DNA has been of immense interest to the scientific world. This hereditary molecule is present in all life forms, transferred from parent to offspring, and confers all behavioural and morphological traits coded by genes. But until recently 99 percent of DNA was dismissed as ‘dark matter’ or even, as the media put it, ‘junk.’ These vast sections of DNA were named ‘junk’ because they lacked genes, stripping them of their ability to code for proteins.

Evidently, this “acclaimed” fact was difficult to grasp for scientists and on Sept. 5, 2012 the Encyclopedia of DNA Elements (ENCODE) project counterclaimed this fact by providing the first comprehensive view of how the human genome actually functions.

ENCODE has proved that over 80% of ‘useless’ DNA is involved in vital biochemical processes, specifically the regulating of protein-coding genes and determining where they are produced. Without it the human genome operating system could not function; hence these bits of DNA have been conserved throughout our evolution.

This is perhaps the largest discovery concerning the human genome since it was first fully sequenced in 2003. At this time, scientists identified each individual “building-block” nucleotide inside the DNA that comprises the collective human genome. Ultimately, they discovered the ingredients, but the world of science was rocked with a surprise; only 2% of human DNA is involved in protein generation.

Imagine the human genome as a toolbox: the 21,000 genes that a human being has (as discovered in 2003) are the functioning tools. ENCODE has now revealed that the 10,000 non-coding regions of DNA actually regulate our genes and control their functionality with vast versatility.

Dr. Ewan Birney is one of the leaders at the ENCODE consortium. “Our genome is simply alive with switches: millions of places that determine whether a gene is switched on or off,” he said. Essentially, these large non-coding regions provide the duct-tape and weights necessary to turn a screwdriver into a hammer.

About 18% of this “junk” DNA regulates gene action by synthesizing a type of single-stranded RNA molecule (ssRNA). These molecules act as DNA regulators by binding to certain sites along the DNA, which in turn may activate or deactivate a gene.  Depending on the type of gene, the ssRNA molecules can even control the amplitude of gene expression (how much or how little of the gene’s protein is synthesized). Such molecular differences establish disease aggressions, human height and whether your body will form parts of a liver or parts of a fingernail.

Additionally, the project’s findings help to clarify why it is that humans only have about 21,000 genes while simple organisms such as mice, tomatoes and apples have more. The answer, as it appears, is extreme versatility; even though we may not have a larger quantity of genes, we know how to manipulate them in complex ways through the use of non-coding regions that produce ssRNA molecules.

Though approximately 8% of the human genome still remains unmapped, this project has been acclaimed as a major achievement. In total, the raw data that ENCODE has mustered exceeds 15 trillion bytes — all based on their 1600 sets of experiments utilizing over 147 types of tissue. The institution invested $123 million dollars into the project, $43 million into the pilot project with an additional $125 million spent on a technology development and model organism research. As research continues, more will be invested.

The international ENCODE project is one comprised of over 500 scientists, in 32 labs, worldwide. Canada is not a part of the list of participating countries, which includes the United States and the United Kingdom. Their collaborative sets of 30 papers have been published in many scientific journals including Nature, Genome Research and Genome Biology.

Ultimately, this newfound information will aid scientists in forming a better comprehension of the gene operating systems, including how our bodies are able to compose organs on such macro-scale levels and what abnormal actions occur that cause a disease to begin and then spread. Albeit, the project has revealed that genome complexity is so extensive that perhaps the 21st century may very well pass without ever truly understanding it.




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