Non-coding half of human genome unlocked with novel sequencing technique

The game-changing discovery was part of a study led by Texas A&M biology doctoral candidate John C. Aldrich and Dr. Keith A. Maggert, an associate professor in the Department of Biology, to measure variation in heterochromatin. This mysterious, tightly packed section of the vast, non-coding section of the human genome, widely dismissed by geneticists as "junk," previously was thought by scientists to have no discernable function at all.

In the course of his otherwise routine analysis of DNA in fruit flies, Aldrich was able to monitor dynamics of the heterochromatic sequence by modifying a technique called quantitative polymerase chain reaction (QPCR), a process used to amplify specific DNA sequences from a relatively small amount of starting material. He then added a fluorescent dye, allowing him to monitor the fruit-fly DNA changes and to observe any variations.

Aldrich's findings, published today in the online edition of the journal PLOS ONE, showed that differences in the heterochromatin exist, confirming that the junk DNA is not stagnant as researchers originally had believed and that mutations which could affect other parts of the genome are capable of occurring.

"We know that there is hidden variation there, like disease proclivities or things that are evolutionarily important, but we never knew how to study it," Maggert said. "We couldn't even do the simplest things because we didn't know if there was a little DNA or a lot of it.

"This work opens up the other non-coding half of the genome."

Maggert explains that chromosomes are located in the nuclei of all human cells, and the DNA material in these chromosomes is made up of coding and non-coding regions. The coding regions, known as genes, contain the information necessary for a cell to make proteins, but far less is known about the non-coding regions, beyond the fact that they are not directly related to making proteins.

"Believe it or not, people still get into arguments over the definition of a gene," Maggert said. "In my opinion, there are about 30,000 protein-coding genes. The rest of the DNA -- greater than 90 percent -- either controls those genes and therefore is technically part of them, or is within this mush that we study and, thanks to John, can now measure. The heterochromatin that we study definitely has effects, but it's not possible to think of it as discrete genes. So, we prefer to think of it as 30,000 protein-coding genes plus this one big, complex one that can orchestrate the other 30,000."

Although other methods of measuring DNA are technically available, Aldrich notes that, as of yet, none has proven to be as cost-effective nor time-efficient as his modified-QPCR-fluorescence technique.

"There's some sequencing technology that can also be used to do this, but it costs tens of thousands of dollars," Aldrich said. "This enables us to answer a very specific question right here in the lab."

The uncharted genome sequences have been a point of contention in scientific circles for more than a decade, according to Maggert, a Texas A&M faculty member since 2004. It had long been believed that the human genome -- the blueprint for humanity, individually and as a whole -- would be packed with complex genes with the potential to answer some of the most pressing questions in medical biology.

When human DNA was finally sequenced with the completion of the Human Genome Project in 2003, he says that perception changed. Based on those initial reports, researchers determined that only two percent of the genome (about 21,000 genes) represented coding DNA. Since then, numerous other studies have emerged debating the functionality, or lack thereof, of non-coding, so-called "junk DNA."

Now, thanks to Aldrich's and Maggert's investigation of heterochromatin, the groundwork has been laid to study the rest of the genome. Once all of it is understood, scientists may finally find the root causes and possibly treatments for many genetic ailments.

"There is so much talk about understanding the connection between genetics and disease and finding personalized therapies," Maggert said. "However, this topic is incomplete unless biologists can look at the entire genome. We still can't -- yet -- but at least now, we're a step closer."