"Junk" DNA: Trash or Treasure?

By Andrew Gao

A Mystery in Our Genes

Many people think of the human genome as being an elegant, efficient entity, carefully refined throughout the years by the guiding hand of evolution. The reality is far from this. In fact, scientists estimate that around 98.5 percent of the billions of nucleotides of our DNA is “junk.” The vast majority of our DNA does not lead to the creation of proteins, which are the workhorses that carry out actions such as metabolism and movement. Only a mere 1.5 percent of our genome actually codes for proteins. From an evolutionary standpoint, this makes little sense.

The process of DNA replication, which is necessary for growth and reproduction, is energy-intensive and error-prone. Why would cells bother to produce and assemble six billion nucleotides (the building blocks of DNA) every time they needed to divide—when ninety million would suffice?

Even some of the world’s top minds have been stumped by this curiosity. Francis Crick, who famously won the Nobel Prize for co-discovering the structure of DNA, commented that most of the genome seemed to be “little better than "junk"” for no apparent reason. Until recently, many biologists were of the opinion that "junk" DNA is nothing more than trash, floating around our genome.

Is There Value in “Junk” DNA?

As biotechnology and our understanding of DNA has improved, scientists have begun to unravel the mysteries of "junk" DNA. In fact, recent findings are causing a major paradigm shift in the field of biology. Emerging evidence indicates that "junk" DNA may not be "junk" after all, thanks to the efforts of the ENCODE group. The ENCODE group is a team of over 400 researchers who have been painstakingly deciphering the human genome for years. Their experiments have focused on discovering the functions of the 98.5 percent of our genome that is supposedly "junk."

In 2012, the ENCODE team published papers in several journals, including the prestigious Nature, that caused a buzz in the scientific community. 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.

According to Evan Binkley, the leader of the ENCODE effort and a researcher at the European Bioinformatics Institute, at least 9 percent of the genome is involved in this regulatory function, but he notes that “9 percent can’t be the whole story.” What about the other ninety?

It turns out that there is even more to this mystery. In addition to controlling the amount of proteins that are being produced, “junk” DNA can also serve another role: maintaining genetic structure. Unlike regulatory elements, satellite DNA are not involved in changing the expression of protein-coding genes. Instead, they provide structure for DNA. For example, satellite DNA comprises 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, like how the plastic caps on shoelaces keep the fibers from fraying.

Not All “Junk” is Good

Although research has demonstrated that "junk" DNA can play helpful roles, this isn’t always true — it can also be harmful. For example, 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. They spread copies of themselves around the genome without serving much beneficial purpose to the organism. Transposons often cause mutations when they insert themselves in the middle of a gene.

Another detrimental type of "junk" DNA is viral DNA. Over the course of hundreds of thousands of years, many viruses have inserted their genetic material into our DNA, resulting in nearly six times more viral DNA in the human genome than protein-coding DNA. Around 8 percent of our genome is calculated to be from viruses that infected our ancestors. This viral DNA can sometimes produce harmful proteins that trigger cancer or other diseases.

A Plan for the Future

Bing Ren, PhD, is a Professor of Cellular and Molecular Medicine at the University of California, San Diego. He was one of the original researchers in the ENCODE project, along with Binkley. Today, Ren conducts large scale experiments to identify and catalogue regulatory elements. He compiles these elements into comprehensive genetic charts, like Google Maps, for the genome. According to him, these resources allow scientists to “design new strategies for diagnosis, prevention [and] treatment” for complex diseases such as schizophrenia. Ren’s research has brought up new questions. For example, some regulatory elements are isolated in the genome, far away from any protein-coding gene, yet they still affect protein production. Ren proposes that this could be due to the flexible 3D structure of DNA; while a regulatory element may be distant from another gene, DNA can fold to bring them closer together.

A Name Upgrade for “Junk DNA”?

While our understanding of "junk" DNA has expanded greatly, there is still much to be learned. As Evan Binkley puts it, research has posed “many more questions than it directly answers” and scientists will be “studying it for 50 years, 100 years” into the future. Binkley also advocates for the retirement of the phrase “"junk" DNA” in favor of a new term: noncoding DNA. After all, as his work has shown, "junk" DNA is far from what its name suggests. Bing Ren too notes that the secrets stored within noncoding DNA are “critical for biomedical research and medicine.” Evidently, the 20th century biologist’s trash is, to the modern day scientist, a treasure trove of information.

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