Deoxyribonucleic acid (DNA) is the biological instruction manual dictating an organism’s development, function, and survival. Damage to the DNA sequence can disrupt cellular processes, and one of the most severe forms is a double-strand break (DSB), where both strands of the DNA’s double helix are severed.
If left unrepaired, a DSB can cause the loss of genetic information and trigger cell death. Cells possess repair systems to mend these breaks, safeguarding the genome from damage caused by environmental factors or internal cellular processes.
Defining Microhomology Mediated End Joining
Microhomology Mediated End Joining (MMEJ) is a pathway cells use to repair a double-strand break in DNA. Its defining feature is the use of very short, identical sequences of DNA bases, known as microhomologies, to guide the repair. These sequences consist of 5 to 25 matching base pairs.
These matching sequences are found on single-stranded DNA tails that emerge after a break. The MMEJ pathway uses these regions as a bridge to bring the severed ends together. This reliance on small patches of sequence similarity is what distinguishes MMEJ from other DNA repair pathways.
This process, however, comes at a cost. The repair is imprecise and leads to changes in the DNA sequence, making MMEJ an inherently mutagenic, or error-prone, mechanism.
The MMEJ Repair Mechanism
The MMEJ process begins after a double-strand break leaves two exposed DNA ends. The first step is end resection, where enzymes chew back one DNA strand at each broken end. This action exposes single-stranded DNA tails, making the microhomology sequences available. The MRE11 nuclease is an enzyme that initiates this resection.
Once the single-stranded tails are exposed, annealing occurs. During this step, the identical microhomology sequences on the two opposing tails pair up. This pairing brings the two broken ends of the DNA molecule together and aligns them for repair.
This annealing often leaves overhanging flaps of single-stranded DNA that do not match. These flaps, which are now redundant, are trimmed away by specialized enzymes like FEN1. This removal creates a more stable structure for the next step.
After the flaps are removed, small gaps may remain in the DNA backbone. The final step is ligation, where an enzyme called DNA ligase seals these nicks. In humans, DNA Ligase III is often responsible for this final step, completing the repair and restoring the DNA strand’s continuity.
Consequences of MMEJ Repair
MMEJ is an error-prone repair process because its mechanism permanently deletes the DNA sequence located between the microhomologies used for alignment. This loss of genetic information at the repair site is what makes MMEJ a mutagenic pathway.
The size of these deletions corresponds to the amount of DNA between the microhomology sequences. The loss of even a small DNA segment can disrupt a gene’s function or a regulatory element. This imprecision is a primary reason MMEJ is considered a last-resort repair option.
MMEJ can also cause complex chromosomal rearrangements. If a cell has multiple DSBs on different chromosomes, the pathway can join the wrong ends together. This can lead to translocations, where part of one chromosome attaches to another, or inversions, where a chromosome segment is flipped. These large-scale changes are associated with genomic instability.
MMEJ’s Role Within the Cell
MMEJ serves as a secondary or backup DNA repair mechanism. Cells have more precise methods for fixing double-strand breaks, such as Homologous Recombination (HR) and classical Non-Homologous End Joining (NHEJ). HR is a highly accurate pathway using an undamaged sister chromatid as a template, while NHEJ directly ligates broken ends with minimal changes.
MMEJ becomes more active when these primary pathways are unavailable. For instance, the HR pathway is only active during specific cell cycle phases when a sister chromatid is present as a template. If HR or classical NHEJ pathway components are defective, the cell may rely more on MMEJ to resolve breaks.
The MMEJ pathway depends on a distinct set of proteins. A primary protein in this process is DNA Polymerase Theta (Polθ), encoded by the POLQ gene in humans. Polθ has multiple functions suited for MMEJ, including helping to align microhomology sequences and synthesizing short patches of DNA to fill gaps during repair.
Significance in Health and Technology
The error-prone nature of MMEJ has implications for human health, especially cancer. Its tendency to cause deletions and chromosomal rearrangements contributes to genomic instability, a hallmark of many cancers. By promoting mutations, MMEJ can inactivate tumor-suppressing genes or activate genes that drive uncontrolled cell growth.
The reliance of certain cancers on MMEJ can also be a vulnerability. For example, many ovarian cancers have defects in the HR repair pathway. These cancer cells become dependent on MMEJ, and the protein Polymerase Theta (Polθ), for survival. This dependency means that drugs inhibiting Polθ could selectively kill these cancer cells, a concept known as synthetic lethality.
The MMEJ pathway is also relevant to gene editing technologies like CRISPR-Cas9. These tools create a targeted DSB, and the cell’s natural machinery performs the repair. Understanding MMEJ’s role is important for predicting gene editing outcomes, as its use can lead to unintended deletions at the target site.