DNA-mantle repair happens in one rather than several steps

The repair of chromatin, the inner mantle protecting DNA in the cell nucleus, is done by one repair protein instead of several in a stepwise process. The responsible protein is flexible and can therefore repair several components at the same time. This was discovered by biochemists of UU and other Dutch research institutes, who published their results in the scientific journal Science Advances.

Preventing chaos and offering protection

In animals, plants and fungi, the nucleus of every body cell contains long strands of hereditary material in the form of DNA, in humans about 2 metres. This fits into the minuscule cell nucleus because the DNA is rolled up so tightly and in several directions that it is no longer than a few micrometres  - one micrometre is a thousandth of a millimetre. To this end, special histones are attached to the DNA, around which the DNA is wound. Together, the DNA and these histones form the so-called chromatin. Biomolecular researcher and expert in the field of NMR technology Hugo van Ingen from Utrecht University: "The inner chromatin mantle is of crucial importance to ensure that the genetic information is properly protected."

Histone proteins in chromatine indicate whether certain proteins should be transcribed. Mutations in histones play a role in a number of cancers and immune responses.

Chromatin is also responsible for regulating all the activity on the DNA: the different types of histone proteins contain important information that indicates whether certain genes should be transcribed. "Mutations in these proteins play a role in a number of types of cancer and immune responses," says Van Ingen. "With that, histones have an epigenetic function: they are not part of DNA themselves, but they do contain important hereditary information."

Removing and replacing histones

Despite the protective role of chromatin, DNA is regularly damaged, or can even break into pieces, and this poses major risks. It is therefore important to continuously repair not only DNA damage in the cell nucleus, but also the chromatin mantle. When DNA breaks, chromatin is temporarily broken locally to repair the DNA damage. Van Ingen: "The four different nucleus histones are captured and put back after the DNA has been repaired." That removal and reinsertion is done by yet another type of protein: chaperone proteins.

This chaperone protein is super flexible. It can capture all four nucleus histones perfectly at the same time and build them into the mantle in the right way.

Until now, it was thought that the reinsertion of the histones was a stepwise process involving two or even more chaperone proteins. But now PhD candidate Ivan Corbeski from Van Ingen's research group has discovered, using NMR technology among others, that a single chaperone protein can repair the chromatin. Van Ingen: "We noticed early on in our research that the responsible chaperone protein, called APLF, is super flexible. It does not have a uniform structure and therefore it can perfectly capture all four nucleus histones at the same time and build them into the mantle in the right way."

Paradigm-shifting

To prove the strong evidence for one-step chromatin repair, the UU biochemists set up several collaborations. The Hubrecht Institute carried out molecular biological tests, researchers from the Netherlands Cancer Institute (NKI) unravelled the crystal structure of APLF, and cell biologists from the Leiden University Medical Center investigated the function of the chaperone protein in living cells. Van Ingen: "This has enabled us to gather evidence from multiple molecular disciplines to support our paradigm-shifting hypothesis that DNA repair occurs via a single step in the cell nucleus. The next question for us is why the process happens so differently here than in the many processes in the body in which multiple chaperone proteins are always involved."