It takes antisense to make sense of herpes infections

The Landthaler lab at the MDC and their collaborators discover that a herpes virus triggers the production of over 1,000 “antisense” transcripts in the genomes of cells it infects – hinting at a new mechanism by which viruses overcome cellular defenses.

It only takes a few lines of code to corrupt a computer’s files and the vast network of machines it is attached to. Herpes and other viruses that infect human cells also contain a very small amount of information, but this suffices to hijack a cell’s biology and turn it into a factory for their own reproduction. Scientists are only beginning to understand how viruses accomplish this. A completely new form of viral action has just been found in herpes simplex 1 (HSV-1), through a project from Markus Landthaler’s lab at the Berlin Institute of Medical Systems Biology (BIMSB) of the MDC. Collaborating with the Institute of Virology of the Saarland Medical School and other European partners, the team has discovered that HSV-1 causes causes its host cell to garble over a thousand specific pieces of information by producing it “backwards”. The work appears in the new “RNA and Gene Regulation” issue of Genome Biology.

HSV-1 is thought to infect about two-thirds of the population world-wide. It usually lies dormant, emerging for short periods to reproduce and spread. It rarely does more than cause cold sores, but the virus has features that make it a good laboratory model to study seven other forms of herpes that infect humans – some much more dangerous.

“A hallmark of HSV-1’s active phase is that it triggers a massive shutdown of the genome of cells it has infected,” Landthaler says. “We started the project hoping to get a clearer picture of the steps in that process. Along the way we discovered something that had never been observed in a viral infection.”

Reading backwards

Shutting down the host genome means preventing the cell from transcribing DNA sequences into RNA molecules. Some of these contain the chemical recipes for building proteins; the rest are noncoding RNAs that may play other important roles in the cell.

Lead authors Emanuel Wyler (Landthaler lab) and Vedran Franke (lab of Altuna Akalin), working with Jennifer Menegatti of the lab of Friedrich Grässer’s lab at the Saarland medical school, captured complete sets of RNAs that cells produced at different time points of an infection. By matching the molecules to corresponding sequences in the cell’s DNA, they could compare the RNAs made before and during an infection. This would help them track how the virus progressively shut down specific regions of the genome.

In the process they noticed that many RNAs started and ended at unusual places, often integrating information that healthy cells didn’t include. “RNA transcription usually begins when a molecular machine binds to a DNA sequence called a promoter,” Wyler says. “This points the machine toward a nearby region of DNA that contains the chemical recipe for an RNA. As the machine travels in that direction, it reads the ‘letters’ of the DNA sequence and builds an RNA molecule based on them. At some point it reaches a code that tells it to stop.”

Somehow the infection was confusing the machine, making it unable to find the proper starting and ending points – thus creating “read-throughs” of genes. Other groups had already reported this phenomenon in the wake of HSV-1 infections, so it wasn’t much of a surprise.

But the scientists noticed something else that was: as the infection progressed, cells were accumulating copies of another type of molecule called “antisense” RNA. This meant that the machinery that was transcribing the RNAs was reading the DNA sequence backwards. Ultimately, the scientists identified over 1,000 such RNAs that seemed to have been produced directly in response to the infection.

Sense vs. antisense

To make sense in English, a word is read from left to right, while Arabic flows from right to left. Specific regions in the genome behave like distinct languages: some are usually transcribed in the “head-to-tail” direction on a chromosome, others in reverse. So while it’s possible to read any specific region both ways, one is usually considered to make sense; even so, the same sequence is sometimes used to produce two opposing transcripts.

An infection suddently triggers transcripts from both directions across large parts of the genome – as if it were forcing a person’s left and right eyes to read the same text simultaneously in opposite directions. Even if the eyes could be trained to do this, the brain probably couldn’t process what they were seeing. The cell might find it just as hard to read sequences in both directions at the same time and make sense of the transcripts.

“If this happened,” Vedran Franke says, “the transcription machines that were moving in opposite directions would collide and neither RNA would be produced.” This suggested a “sense” for all that viral antisense: it might serve as yet another method to block the production of cellular proteins when the virus entered its infectious phase.

A strategy for survival?

One of the newly discovered transcripts was particularly intriguing because it overlapped with a gene called BBC3. “If sense RNA is made from this gene, it goes on to produce BBC3 protein,” Landthaler says. “This molecule is known to help trigger apoptosis – a sort of cellular suicide that is one of the body’s normal defenses against viral infections. Cells infected by HSV-1 initially try to start an apoptosis program, which would limit its reproduction and spread, but the virus counteracts those measures.” In more experiments, the scientists confirmed that making an antisense transcript from the region could impair the production of BBC3 in the sense direction.

Antisense transcription begins almost immediately upon infection and builds as time passes. Initial evidence showed that viral factors play an active role in triggering this progression, which may go on to generally perturb the cellular transcription machinery.

A study of data previously obtained by other groups revealed that chicken pox – caused by another herpes virus called VZV – also appeared to stimulate the production of hundreds of antisense RNAs. The remaining five herpes strains didn’t seem to be doing so.

“What this suggests,” Landthaler says, “is a completely new and unexpected mechanism by which HSV-1 and possibly other viruses might disrupt cells while creating conditions that promote their own reproduction.”

Further information

Emanuel Wyler, et al. (2017): “Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.” Genome Biology 18: 209. (Open Access) doi:10.1186/s13059-017-1329-5

Featured illustration: Artistic impression of HSV-1 on the surface of a cell. Credit: Russ Hodge, MDC (CC-BY)

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