Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Where Broken DNA is Repaired

03.08.2007
Ionizing radiation, toxic chemicals, and other agents continually damage the body's DNA, threatening life and health: unrepaired DNA can lead to mutations, which in turn can lead to diseases like cancer. Intricate DNA repair mechanisms in the cells' nuclei are constantly working to fix what's broken, but whether the repair work happens "on the road" — right where the damage occurs — or "in the shop" — at specific regions of the nucleus — is an unanswered question.

That question may now be closer to an answer. By comparing computer models of damaged human DNA with microscopic images of human cells that reveal focal sites of radiation-induced damage, researchers in the Life Sciences Division (LSD) of the Department of Energy's Lawrence Berkeley National Laboratory, with colleagues at NASA and the Universities Space Research Association, have found evidence that indeed there are specific regions where broken DNA is concentrated for repair.

"NASA has long been interested in the radiation hazards in space," says LSD's Sylvain Costes, who led the study. "On a trip to Mars, astronauts will be exposed to cosmic rays for as long as three years, so NASA has been trying to come up with a mechanistic model of DNA repair to estimate the increased risk of cancer. We are helping to develop such a model."

Double-strand breaks and radiation-induced foci

In many NASA studies cells have been exposed to particles like those found in cosmic rays, such as energetic iron nuclei produced in accelerators at Brookhaven National Laboratory. The goal is to determine how many double-strand breaks (DSBs) — in which both strands of the DNA double helix are severed — occur per gray of radiation. (One gray is equivalent to 100 rads, an older unit signifying "radiation absorbed dose"; a gray equals one joule of energy absorbed per kilogram of matter.)

DSB yield can be measured by pulling apart a cell's radiation-severed DNA using gel electrophoresis: the shorter the fragments in the gel bands, the more frequent the breaks. Interpreting the band patterns thus leads to an estimate of the average number of breaks per cell for a given dose and time following exposure. NASA has developed a computer model based on these measured DSB yields to predict DSB formation in hypothetical human cell nuclei.

On the other hand, gel electrophoresis fails to indicate the severity of the damage, or where in the nucleus the double-strand breaks occur. The default assumption has been that DSBs occur randomly in a homogenous distribution of DNA in the nucleus.

Most gel electrophoresis studies indicate about 25 to 30 DSBs per gray of gamma rays. In microscopic images of real cells, however, the visible sites that might be assumed to correspond to double-strand breaks — sites called "radiation induced foci," or RIF — occur at a lower rate, only about 15 per gray, depending on the cell type.

"What we see through the microscope is not the broken DNA itself but a collection of proteins associated with breaks, which we have labeled with fluorescent stains. These include modified histones, which are part of the chromosomal material, and other proteins that seek out DNA breaks and recruit repair machinery to fix them," says Costes. "The first question we had to answer was how closely RIF are associated with DSBs."

Costes recognized that one way to test the association was to calculate how energy was deposited by different kinds of radiation. A high-energy particle, for example, moves through the nucleus in a straight line and may strike DNA at any point along the way; the pattern of hits along the track should be essentially random.

"Physicists understand very well how energy is deposited in the cell's DNA," says Costes, "but the challenge was to make a predictive model that was consistent with what a biologist sees through the microscope. To test what should be seen, given a specific radiation dose, I set out to turn NASA's high-resolution DNA damage simulator" — a model based on data from gel electrophoresis — "into artificial microscope images of a nucleus damaged by radiation."

To do this, says Costes, "I simulated the optical transformation when imaging events at the nanoscale are viewed with a fluorescent microscope." One optical transformation is blurring, with the result that, in a real microscope, two nearby radiation-induced foci may blend together and look like one.

When such factors were taken into account, Costes's initial model, following the NASA model, confirmed random distribution of double-strand breaks at the micron scale. The frequency of DSBs was radiation dependent, however: in the case of cosmic rays (NASA's main concern), which lead to complex double-strand breaks, there was good agreement with the RIF frequencies seen in the microscope. But in the case of gamma rays, which lead primarily to sparse and noncomplex DSBs, measured frequencies in real microscope images were lower.

This suggests that RIF correspond to sites of complex double-strand breaks in DNA. Moreover — focusing on cosmic rays for the NASA project — although the DSB frequency was the same as predicted by the models, the RIF in real microscope images were distributed very differently.

Model physics, real biology

"For one thing, there is a time effect," says Costes. "Just five minutes after cells are exposed to high-energy particles, microscope images already show a nonrandom distribution of RIF." The RIF occur along straight lines, as expected for a particle track, but are not randomly distributed along the lines. "Even though we have the right foci frequency along a track, many foci appear to repulse each other within the first 30 minutes after irradiation" — a suggestion that they might be moving to specific regions of the nucleus.

Costes and his colleagues applied the same kinds of models and measurements to gamma rays and found that whereas the model predicted that these breaks would occur in a random pattern in three dimensions throughout the nucleus (not along lines), in fact, under the microscope, radiation-induced foci caused by gamma rays were also distributed nonrandomly. There were fewer RIF due to gamma rays than the model predicted, and they appeared more gradually.

The researchers now used a novel technique, "relative DNA image measurements," and analyzed the images to show where the DNA was dense, where it was less dense, and where the two densities met. They wanted to see whether, where RIF occurred, there was an underlying difference in the nature of the DNA.

Indeed there was. By comparison to the random distribution that might have been expected, RIF were more frequent in the low-density regions. And a preponderance of RIF coincided with the interfaces between the two kinds of DNA.

"In terms of physics, there's no obvious explanation for this observation," says Costes. "In terms of biology, we have some pretty good guesses."

What's evident is that the organization of the cell nucleus plays an important role in response to DNA damage. The high-density regions likely are heterochromatin, the parts of the chromosomes where genes are (for the most part) silenced. The low-density regions likely correspond to euchromatin, the parts of the chromosomes where most genes are actively transcribed. While it's possible that damage in condensed regions causes the condensed chromatin to open up and appear less dense, it is more likely, Costes believes, that the damaged sections actually migrate toward the less-dense chromatin and concentrate at the high-density/low-density interface.

Researchers have previously proposed the existence of "repairosomes" in mammalian cells, similar to specific regions where DNA is repaired in yeast, although these have never been observed in mammals. The fact that RIF concentrate in specific regions of the human cell nucleus — and apparently tend to move toward shared sites — is highly suggestive of such repair centers, where activities like the necessary clamping and orientation of the broken strands take place.

"Our results raise a number of interesting possibilities," says Costes. "If less-dense regions of the nucleus are more susceptible to radiation damage, we may be able to use this knowledge to make tumor cells easier to kill. Repair centers in mammalian cells are probably an efficient way to repair the typically sparse and noncomplex DNA damages of daily cellular life."

But there's a downside, Costes says. "Humans didn't evolve with cosmic rays, and the existence of repair centers may not be good news for astronauts — cosmic rays primarily generate spatial clusters of complex DNA breaks. If these breaks are gathered in common locations in the nucleus, they will most likely lead to chromosomal translocation, a process thought to play an initiative role in cancer."

Thus the data obtained by Costes and his colleagues through image-based modeling suggests a wealth of new opportunities for research.

"Image-based modeling reveals dynamic redistribution of DNA damage into nuclear sub-domains," by Sylvain V. Costes, Artem Ponomarev, James L. Chen, David Nguyen, Francis A. Cucinotta, and Mary-Helen Barcellos-Hoff, appears online in the August 2007 PLoS Computational Biology, (volume 3, issue 8) and can be reached by visiting http://dx.doi.org/10.1371/journal.pcbi.0030155.

Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California. Visit our website at http://www.lbl.gov.

Paul Preuss | EurekAlert!
Further information:
http://www.lbl.gov
http://dx.doi.org/10.1371/journal.pcbi.0030155

Further reports about: Cosmic Costes DNA damage DSB Gamma NASA RIF Radiation cosmic ray dense double-strand electrophoresis foci radiation-induced

More articles from Life Sciences:

nachricht Cancer diagnosis: no more needles?
25.05.2018 | Christian-Albrechts-Universität zu Kiel

nachricht Less is more? Gene switch for healthy aging found
25.05.2018 | Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut e.V. (FLI)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Powerful IT security for the car of the future – research alliance develops new approaches

The more electronics steer, accelerate and brake cars, the more important it is to protect them against cyber-attacks. That is why 15 partners from industry and academia will work together over the next three years on new approaches to IT security in self-driving cars. The joint project goes by the name Security For Connected, Autonomous Cars (SecForCARs) and has funding of €7.2 million from the German Federal Ministry of Education and Research. Infineon is leading the project.

Vehicles already offer diverse communication interfaces and more and more automated functions, such as distance and lane-keeping assist systems. At the same...

Im Focus: Molecular switch will facilitate the development of pioneering electro-optical devices

A research team led by physicists at the Technical University of Munich (TUM) has developed molecular nanoswitches that can be toggled between two structurally different states using an applied voltage. They can serve as the basis for a pioneering class of devices that could replace silicon-based components with organic molecules.

The development of new electronic technologies drives the incessant reduction of functional component sizes. In the context of an international collaborative...

Im Focus: LZH showcases laser material processing of tomorrow at the LASYS 2018

At the LASYS 2018, from June 5th to 7th, the Laser Zentrum Hannover e.V. (LZH) will be showcasing processes for the laser material processing of tomorrow in hall 4 at stand 4E75. With blown bomb shells the LZH will present first results of a research project on civil security.

At this year's LASYS, the LZH will exhibit light-based processes such as cutting, welding, ablation and structuring as well as additive manufacturing for...

Im Focus: Self-illuminating pixels for a new display generation

There are videos on the internet that can make one marvel at technology. For example, a smartphone is casually bent around the arm or a thin-film display is rolled in all directions and with almost every diameter. From the user's point of view, this looks fantastic. From a professional point of view, however, the question arises: Is that already possible?

At Display Week 2018, scientists from the Fraunhofer Institute for Applied Polymer Research IAP will be demonstrating today’s technological possibilities and...

Im Focus: Explanation for puzzling quantum oscillations has been found

So-called quantum many-body scars allow quantum systems to stay out of equilibrium much longer, explaining experiment | Study published in Nature Physics

Recently, researchers from Harvard and MIT succeeded in trapping a record 53 atoms and individually controlling their quantum state, realizing what is called a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

In focus: Climate adapted plants

25.05.2018 | Event News

Save the date: Forum European Neuroscience – 07-11 July 2018 in Berlin, Germany

02.05.2018 | Event News

Invitation to the upcoming "Current Topics in Bioinformatics: Big Data in Genomics and Medicine"

13.04.2018 | Event News

 
Latest News

In focus: Climate adapted plants

25.05.2018 | Event News

Flow probes from the 3D printer

25.05.2018 | Machine Engineering

Less is more? Gene switch for healthy aging found

25.05.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>