Microhomology-mediated end joining (MMEJ), also known as alternative nonhomologous end-joining (Alt-NHEJ) is one of the pathways for repairing double-strand breaks in DNA. As reviewed by McVey and Lee, the foremost distinguishing property of MMEJ is the use of 5–25 base pair (bp) microhomologous sequences during the alignment of broken ends before joining, thereby resulting in deletions flanking the original break. Thus, MMEJ is frequently associated with chromosome abnormalities such as deletions, translocations, inversions and other complex rearrangements.
Two other well-known means of double-strand breakage repair are non-homologous end joining and homologous recombination. MMEJ is distinguished from the other repair mechanisms by its use of 5–25 base pair microhomologous sequences to align the broken strands before joining. MMEJ uses a Ku protein and DNA-PK independent repair mechanism, and repair occurs during the S-phase of the cell cycle, as opposed to the G0/G1 and early S-phases in NHEJ and late S to G2-phase in HR.
MMEJ works by ligating the mismatched hanging strands of DNA, removing overhanging nucleotides, and filling in the missing base pairs. When a break occurs, a homology of 5 - 25 complementary base pairs on both strands is identified and used as a basis for which to align the strands with mismatched ends. Once aligned, any overhanging bases (flaps) and mismatched bases on the strands are removed and any missing nucleotides are inserted. As this method's only way of identifying if the two strands are related is based on microhomology down/upstream from the site of breakage, it does not identify any missing base pairs which may have been lost during the break, and even removes nucleotides (flaps) in order to ligate the strand. MMEJ ligates the DNA strands without checking for consistency and causes deletions, since it removes base pairs (flaps) in order to align the two pieces.
MMEJ is an error-prone method of repair and results in deletion mutations in the genetic code, which may initiate the creation of oncogenes that could lead to the development of cancer. In most cases a cell uses MMEJ only when the NHEJ method is unavailable or unsuitable, due to the disadvantage posed by introducing deletions into the genetic code.
A biochemical assay system shows that at least 6 genes are required for microhomology-mediated end joining: FEN1, Ligase III, MRE11, NBS1, PARP1 and XRCC1. All six of these genes are up-regulated in one or more cancers.
FEN1 is over-expressed in the majority of cancers of the breast, prostate, stomach, neuroblastomas, pancreatic, and lung.
Ligase III is upregulated in chronic myeloid leukemia, multiple myeloma, and breast cancer.
MRE11 is over-expressed in breast cancers.
NBS1 is over-expressed in some prostate cancers, in head and neck cancer, and in squamous cell carcinoma of the oral cavity.
PARP1 is over-expressed in tyrosine kinase-activated leukemias, in neuroblastoma, in testicular and other germ cell tumors, and in Ewing’s sarcoma,
XRCC1 is over-expressed in non-small-cell lung carcinoma (NSCLC), and at an even higher level in metastatic lymph nodes of NSCLC. Perhaps even more interesting, deficiency in XRCC1, due to being heterozygous for a mutated XRCC1 gene coding for a truncated XRCC1 protein, suppresses tumor growth in mice in three experimental conditions for inducing three types of cancer (colon cancer, melanoma or breast cancer).
MMEJ always involves at least a small deletion, so that it is a mutagenic pathway. Several other pathways can also repair double-strand breaks in DNA, including the less inaccurate pathway of non-homologous end joining (NHEJ) and accurate pathways using homologous recombinational repair (HRR). Various factors determine which pathway will be used for repair of double strand breaks in DNA. When FEN1, Ligase III, MRE11, NBS1, PARP1 or XRCC1 are over-expressed (this occurs with FEN1 when its promoter is hypomethylated) the highly inaccurate MMEJ pathway may be favored, causing a higher rate of mutation and increased risk of cancer.
Cancers are very often deficient in expression of one or more DNA repair genes, but over-expression of a DNA repair gene is less usual in cancer. For instance, at least 36 DNA repair enzymes, when mutationally defective in germ line cells, cause increased risk of cancer (hereditary cancer syndromes). (Also see DNA repair-deficiency disorder.) Similarly, at least 12 DNA repair genes have frequently been found to be epigenetically repressed in one or more cancers. (See also Epigenetically reduced DNA repair and cancer.) Ordinarily, deficient expression of a DNA repair enzyme results in increased un-repaired DNA damages which, through replication errors (translesion synthesis), lead to mutations and cancer. However, FEN1, Ligase III, MRE1, PARP1, NBS1 and XRCC1 mediated MMEJ repair is highly inaccurate, so in these cases, over-expression, rather than under-expression, leads to cancer. This is supported by the observation that reduction of mutagenic XRCC1 mediated MMEJ repair leads to reduced progression of cancer.