New techniques better determine how old viral DNA affects human genes – ScienceDaily

New laboratory techniques can determine which of our genes are affected by DNA chips that have been left behind by viruses in our genetic code, a new study finds.

Viruses have long been known to reproduce by using the genetic machinery of the cells they invade. As part of that process, these microorganisms have, over time, left thousands of DNA sequences, called transposons, by the genetic material (taken) in many life forms, including mice and humans, say the authors of the study. Studies have determined decades ago that a few of these viral insertions play a role in the action of genes.

However, determining which transposons regulate which genes has been challenged, because transposons can influence a nearby gene or one that is located far away in the DNA molecule chain.

Published online on December 13 in Genome Biology, the new study describes methods that gather more information about the location and influence of viral insertions in genomes, identifying genes that may be governed by active transposons (most are silenced by the defense mechanisms of our cells).

"One of the interesting results of our study is that a single transposon can regulate more than one gene and that one gene can be regulated by more than one transposon, increasing the complexity of the potential impact of transposons on health and disease," senior study author Jane Skok, PhD, the Sandra and Edward H. Meyer Professor of Radiation Oncology at the Perlmutter Cancer Center of NYU Langone Health. "In addition, viral insertions of the same family prefer to interact with each other, potentially enhancing their impact on genetic activity."

Display of genetic reality

Decades after the discovery of DNA, researchers mainly thought of genetics in terms of genes, the pieces or sequences of DNA that code for instructions for building proteins in cells. Then scientists discovered that genes make up only 2 percent of our DNA and that most of the genetic complexity comes from the extensive non-gene code that affects when genes are turned on or off. Furthermore, half of that non-gene code was derived from insertions of viral DNA. That is why the authors say genetic variation and the potential for pathogenic errors, both in transposons and in genes.

The current results are based on the discovery that pieces of DNA, called enhancers, control gene activity. These amplifiers can be separated over a long distance from their target genes on a linear DNA chain but can crawl around in the 3D space to interact with another part of the chain by forming loops. Evidence was then found that some of these loop amplifiers may be parts of viral transposon sequences.

But those who tried to understand the role of these amplifiers had to deal with a problem.

Transposon insertions occur in many places and are therefore repetitions of the same DNA code (not unique). However, popular genome-wide association studies rely on finding a link between a single, unique piece of DNA and the risk of a disease. Repeating sequences are thus typically ignored because it is not clear which of these multiple insertion sites interact with a particular disease-related gene.

Experimental evidence supports the idea that amplifiers, by exercising influence, must make physical contact with their target genes through loop formation. The identification of such interactions between different pieces of DNA became possible in 2002 with the development of a technique called chromosome conformation.

The current study describes two variations on this technology, collectively referred to as 4TRAN, that use the repetitive nature of transposons to record their interactions. The techniques provide direct evidence that some transposons exert long-range control of genes through loops.

One of the new techniques, 4TRAN-PCR, was able to find all interactions involving members of a transposon family containing a certain DNA sequence, allowing the researchers to count the hundreds or thousands of sites where such transposons occur. The method showed that transposons more likely interact with DNA in local neighborhoods (topologically associating domains), but also that they participate in long-term interactions that are determined by the activation status of the compartments in which they are located.

The second technique, Capture 4TRAN, confirmed probes for each member of a viral family that, in combination with other tricks, enabled the team to determine the influence of a single transposon copy on a specific gene or specific genes. For example, the study showed that some of the 7,200 copies of repetitive DNA left by the viral MER41 family, which infected our primate ancestors 60 million years ago, now serve as enhancers that activate immune system genes through long-running DNA contacts through loops. Ironically, target genes work in this case to fight viruses.

For the future, the team has already started experimenting with the search for networks of interactions between transposons and genes that are different in cancer cells than in healthy cells.

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