Getting a fix on DNA

By | Science & Technology
Special enzymes are able to repair the millions DNA mutations caused by the environment over a person's lifetime. Credit@Tom Ellenberger/Washington University School of Medicine

A team of researchers at the Lomonosov Moscow State University, led by Professor Vasily M. Studitsky has found an entirely new mechanism of DNA repair that may open up new horizons for the treatment and prevention of neurogenetic conditions. The research paper was published in AAAS’ online open access journal Science Advances.

”In higher organisms DNA is bound with proteins in complexes called the nucleosome. Every ~200 base pairs are organised in nucleosomes, consisting of eight histone proteins, which, like the thread on the bobbin – the wrapped double helix of DNA – is coiled into two supercoiled loops,” Studitsky explained. “Part of the surface of the DNA helix is hidden, because it interacts with histones. Our entire genome is packed this way, except for the areas from which the information is being currently read.”

The efficient and dense packaging allows a two-metre-long molecule of DNA to fit inside a microscopically small cell nucleus. However, this arrangement also makes some important parts of the genome inaccessible to DNA repair enzymes (proteins that repair impairment to the genome). Geneticists are aiming to repair or prevent these mutations from accumulating, which, left untreated, may lead to the development of neurodegenerative conditions such as Alzheimer’s and Parkinson’s.

Vasily M. Studitsky and his team were studying how the human body detects single-stranded breaks in DNA where one strand of nucleotides escapes contact with the other in regions where the DNA is wrapped around histones.

The central dogma of genetics is that “DNA makes RNA makes protein”. Hence, when proteins need to be manufactured in the cell, small regions of DNA are gradually unraveled and the two strands of DNA become separated. The information to build the required protein is written onto each of the strands. A single strand is then transcribed into a single-stranded RNA molecule. This RNA then acts as the template from which proteins may be built.

Schema of nucleosome organisation - DNA is wrapped twice around each nucleosome, which is comprised of 8 core histone molecules. Credit@Darekk2/Wikimedia Commons

Schema of nucleosome organisation – DNA is wrapped twice around each nucleosome, which is comprised of 8 core histone molecules. Credit@Darekk2/Wikimedia Commons

During this process, an enzyme called RNA polymerase moves along the DNA chain. When it encounters a separation in the chain it stalls and much like a human proofreader of a text, the RNA polymerase triggers a cascade of events, which results in repair enzymes arriving at the scene to fix the impaired area. However, RNA polymerase remains unable to detect anything atypical in the other DNA strand.

“We have shown … in vitro, that the repair of breaks in the other DNA chain, which is ‘hidden’ in the nucleosome, is still possible. According to our hypothesis, it occurs due to the formation of special small DNA loops in the nucleosome, although normally DNA wound around the histone ‘spool’ very tightly,” according to Studitsky. ”The loops form when the DNA is coiled back on nucleosome together with polymerase. RNA polymerase [may] ‘crawl’ along the DNA loops nearly as well as on histone-free DNA regions, [however] when it [stalls] near locations of the DNA seperates, it … triggers the cascade of reactions to start DNA repair.”

To explore the hypothesis, the team used enzymes to create single-stranded seperations in DNA at precise locations using specific enzymes. When the impact of these openings were investigated, the researchers discovered that when it was in the ‘other’ strand, RNA polymerase only comes to a halt in nucleosomes, rather than histone-free DNA. Studitsky’s team therefore concluded that the stalling of RNA polymerase may be facilitated by the loops, which act to prevent RNA polymerase moving any further.

Studitsky explained that “In terms of applied science, discovery of a new mechanism of reparation promises new prospective methods of prevention and treatment of medical conditions. We have shown that the formation of loops, which [signal] the polymerase, depends on its contacts with histones. If you make them more robust, it [may] increase the efficiency of the formation of loops and the probability of repair, which in turn [might] reduce the [probability] of [developing certain conditions]. If these contacts are destabilised, then, by using special methods of drug delivery, you [may] programme the apoptosis of the affected cells.” The research may open up entirely new avenues for treating a number of genetic conditions.

What other natural housekeeping mechanisms found in the human body might be used to develop new medical treatments?

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