Broken strands of DNA can be a problem by destabilizing the genome and generating cancer and antibiotic resistance. Researchers have been able to make DNA breaks with extraneous procedures, however, it was not known how these breaks occur without any outside intervention. Dr. Philip Hastings and Dr. Susan Rosenberg at the Baylor College of Medicine (BCM) have been able to elucidate how these breaks occur under normal conditions. It is known that resting cells that are not replicating (not producing daughter cells) have fragmented DNA.
Hastings and Rosenberg have used resting forms of Escherichia coli to determine how spontaneous DNA fragmentation occurs. Their report is published in the journal Nature Communications.
Enzymes known as DNA helicases are responsible for unzipping the DNA molecule. The whole DNA molecule is not unzipped at one time, but rather in segments. These segments create what is called a “replication fork.” There are small proteins known as single strand binding proteins that temporarily bind to each side of the replication fork, effectively keeping the two strands of DNA separate. DNA polymerase moves down one side of the open DNA and adds new complementary nucleotides to replicate one DNA strand. The other strand is copied as well, generating two copies of the chromosome. The unzipping process allows for opportunities for DNA breakage.
One type of DNA breakage occurs when the RNA polymerase collides with the replication machinery. This can happen when the RNA polymerase “backtracks” on the DNA template, or when RNA and DNA polymerases collide, meaning the system is trying to replicate and transcribe at the same time. However, it is known that DNA breakage occurs in cells that are not replicating. So, the question is, how do breaks occur when the DNA is not replicating?
Researchers have previously studied what are called “R loops.” R loops are hybrid RNA-DNA structures that have demonstrated to be “precursors of mutagenesis.” According to Hastings, “The role of R loops is to produce double-strand breaks,” explaining that these kinds of loops that result from RNA-DNA hybrids are more widespread under stress conditions, such as starvation. “Under most circumstances, RNA from gene transcription is protected against being incorporated into the DNA. However, we are working in starving cells that might not be able to produce enough protein to ensure this kind of protection.”
Earlier studies done by Hastings and Rosenberg demonstrated that genomes in stressed cells have “hot spots” for mutation. They pose the question, do cells somehow control where a given mutation occurs by controlling where it makes a double-strand break? Currently, they don’t know, but this new study is telling them that breaks are more likely to be made in a transcribed region and are open for reading. They point out that the genes in use are the ones most likely to be mutagenized.