A chip developed by the researchers revealed that the ability of three repair enzymes to recognize genetic damage also depends on the letters and structure of the DNA around it. The preferences have been linked to mutation patterns in evolution and cancer, but the study does not prove a causal link to cancer.
A mutation – a permanent change in the genetic code – is sometimes the result of DNA damage that is not properly repaired. Mutations They can impair gene function, contribute to aging and the development of diseases, including cancer. At the same time, they create the genetic diversity on which natural selection operates, and are therefore also the raw material of evolution.
Although DNA repair systems are constantly working, they do not repair all damage with the same efficiency. New research from Dr. Ariel Afek בWeitzman Institution of Science points to one explanation for this: the repair enzymes do not respond only to the damaged base, but also to the sequence of letters and the structure of the DNA molecule around it.
The research, led by the doctoral student Nega Levy, Published in the journal Nature CommunicationsThe researchers mapped the binding preferences of three Glycosylases Humanity – UDG, TDG and-MBD4 – which help repair damage caused by chemical changes in the cytosine base.
Thousands of injuries in every cell every day
Thousands of chemical reactions occur every day in every cell that can damage the genome. DNA repair systems detect and repair most damage, but some remain unrepaired and can become mutations when the cell replicates its DNA.
Dr. Afek explains that the rate of mutation accumulation reflects a balance between the rate of damage formation and the efficiency of repair. The balance is not uniform: certain regions of the genome accumulate more mutations than others, and it is not always clear whether this is due to increased exposure to damage, less efficient repair, or a combination of the two.
Most studies are based on the mutations that already remain in the genome – a kind of scars indicating past damage. However, this approach does not allow us to see the damage that has been successfully repaired and left no trace. The researchers therefore wanted to examine the stage of damage identification itself.
A chip containing thousands of damaged DNA sequences
For the study, the team developed a chip with thousands of short DNA molecules on it. All of them had the same type of genetic damage inserted into them, but the sequence of bases surrounding the damage site was different in each molecule.
The researchers added to the chip Repair enzymes The intensity of the light at each spot allowed us to measure how strongly the enzyme bound to each sequence. This resulted in a systematic map of the binding preferences of the three enzymes.
According to Levy, the enzymes behave “like a good editor examining each word in context.” Even bases located up to five places on either side of the damage affected the chances that the enzyme would recognize the site and bind to it.
The effect wasn't limited to letter identity. Preferred sequences also shared structural features. One enzyme, for example, bound more strongly to sequences in which the minor groove of the double helix was particularly narrow.
It is important to note that the experiment mainly measured the binding of enzymes to DNA sequences. Binding is a crucial step in repair, but does not alone guarantee that all damage will be repaired as efficiently in a living cell, where proteins and other control mechanisms operate.
Amino acid that scans the helix
To find out why one of the enzymes prefers a particular structure, Weizmann Institute researchers collaborated with Prof. Brian P. Weiser's group at Rowan University in New Jersey.
Computer simulations revealed that one of the amino acids in the enzyme scans the area near the damage and is attracted to the negative electrical charge that characterizes narrow areas in the minor groove of the DNA helix.
The finding illustrates that identifying genetic damage is not based solely on a chemical match to the damaged base. The enzyme also “reads” the local shape of the molecule and how the sequence of letters changes the structure and electrical charge around the site of damage.
Did repair preferences shape the genome?
In the next step, the researchers examined whether enzyme preferences are related to mutations that have accumulated in the human genome during evolution.
One common damage to DNA occurs when the base cytosine undergoes a chemical change. Cytosine normally pairs with guanine, but after the change, a mismatch can occur. If the mistake is not corrected before DNA replication, it can become a permanent mutation.
The researchers hypothesized that in regions where the repair enzymes bind well, more cytosine bases would be conserved, while in sequences that the enzymes have difficulty recognizing, more changes would accumulate. For one enzyme, a correspondence was found between binding preferences and the ratio of cytosine to thymine in parallel sequences in the human genome.
According to Afek, before attributing genetic change to natural selection and adaptation to the environment, one must understand which changes tend to accumulate in the first place due to the uneven activity of the repair systems.
Relationship to mutation patterns in tumors
The researchers also compared the enzyme preferences to “mutational signatures” – characteristic patterns of mutations found in human tumors. Some of the binding preferences were found to match signatures related to chemical changes in cytosine.
One possibility is that damage to the repair system allows mutations to accumulate in previously protected areas. Another possibility is that repair enzymes have evolved to better recognize areas that are particularly vulnerable to damage in the first place.
However, this is a pattern match. The study does not prove that the enzyme preferences caused the tumors to develop, and does not yet present a cancer treatment. To do so, the process will need to be tested in living cells, tissues, and disease models.
From genetic evaluation to improved repair enzymes
Understanding how repair enzymes recognize their targets could help in the future to improve gene editing tools and engineer enzymes with more precise preferences. Such systems could, in principle, identify specific damage or sequences without increasing activity throughout the genome.
According to Afek, the knowledge may in the future allow the development of enzymes that provide improved genetic protection or more targeted treatments for diseases in which repair mechanisms have been damaged. This is still a long-term research direction, and not a ready-made medical application.
Also participating in the study were Dr. Vered Levin Salomon, Dr. Naama Kessler and Omer Erez from the Department of Structural and Chemical Biology at the Weizmann Institute; Sharon N. Greenwood and Dr. Matthew Wang from the University of Rowan.
Questions and Answers
Which repair enzymes were tested in the study?
The researchers examined the human glycosylases UDG, TDG, and MBD4. These enzymes recognize and remove damaged or mispaired bases resulting from chemical changes in cytosine.
Why does the sequence surrounding the damage affect the repair?
The sequence determines not only which bases are near the damage, but also the shape of the DNA helix, the width of the grooves, and the local electrical charge. These characteristics can make it easier or harder for the enzyme to recognize the damage and bind to it.
Does the study prove that failure of repair enzymes causes cancer?
No. Enzyme preferences have been associated with mutational signatures in human tumors, but this does not prove causation. Further studies in cells and tissues are needed.
Can the findings already be used for treatment?
Not yet. The research is basic research. In the future, the knowledge may help improve gene editing tools, engineer repair enzymes, and develop targeted approaches to diseases related to damage toDNA repair.
Source/Original article
- The scientific article in Nature Communications
- The official article of the Weizmann Institute of Science
- Registration of the research in the Weizmann Institute's publication database
More on the subject on the science website
- Nobel Prize in Chemistry for discoverers of DNA repair mechanisms
- Thomas Lindahl: Life exists – therefore DNA must be repairable
- Sometimes the "life aspiration" of a single cell endangers the life of the whole body
- Technion research paves the way for targeted treatment of lung cancer
- A Breakthrough in CRISPR: Epigenetic Editing Without Cutting DNA
For the scientific article: Opening the scientific article
