A novel sequencing technique developed by two biologists and research colleagues at Texas A&M University‘s Maggert Laboratory has revealed that an obscure swatch of human DNA once thought to be nothing more than biological trash may actually be able to provide a treasure trove of insight into complex genetic-related diseases such as cancer and diabetes.
The landmark 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 TAMU Department of Biology, to measure variation in heterochromatin — a tightly packed form of DNA, which comes in different varieties. This mysterious constituent 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.
A TAMU release notes that in the course of his otherwise routine analysis of DNA in fruit flies, John 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.
Mr. Aldrich’s findings, published Monday 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.
The PLOS1 article, entitled “Simple Quantitative PCR Approach to Reveal Naturally Occurring and Mutation-Induced Repetitive Sequence Variation on the Drosophila Y Chromosome“ (Published: October 06, PLoS ONE 9(10): e109906. doi:10.1371/journal.pone.0109906) co-authored by Mr. Aldrich and Dr. Keith A. Maggert notes that Heterochromatin is a significant component of the human genome and the genomes of most model organisms. The researchers say that although heterochromatin is thought to be largely non-coding, they’ve shown that it plays an important role in chromosome structure and gene regulation.
“Despite a growing awareness of its functional significance, the repetitive sequences underlying some heterochromatin remain relatively uncharacterized,” the coauthors note. “We have developed a real-time quantitative PCR-based method for quantifying simple repetitive satellite sequences and have used this technique to characterize the heterochromatic Y chromosome of Drosophila melanogaster. In this report, we validate the approach, identify previously unknown satellite sequence copy number polymorphisms in Y chromosomes from different geographic sources, and show that a defect in heterochromatin formation can induce similar copy number polymorphisms in a laboratory strain. These findings provide a simple method to investigate the dynamic nature of repetitive sequences and characterize conditions which might give rise to long-lasting alterations in DNA sequence.”
“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,” Dr. Maggert says. “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.”
Dr. 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,” Dr. Maggert says. “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, John 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,” Mr. Aldrich says “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 Dr. 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.”
The TAMU release observes that 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,” Dr. Maggert says. “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.”
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