removal of covalent modifcations, reloading of replicative DNA polymerase, DNA synthesis continues repair. Ionizing radiation, replication errors, oxidizing agents, and other metabolites produced in the cell cause breaks of this type. If these lesions were left unrepaired, they would quickly lead to the breakdown of chromosomes into smaller fragments and to loss of genes when the cell divides. However, two distinct mechanisms have evolved to deal with this type of damage (Figure 5–45). The simplest to understand is nonhomologous end joining, in which the broken ends are simply brought together and rejoined by DNA ligation, generally with the loss of nucleotides at the site of joining (Figure 5–46). This end-joining mechanism, which can be seen as a “quick and dirty” solution to the repair of double-strand breaks, is common in mammalian somatic cells. Although a change in the DNA sequence (a mutation) results at the site of breakage, so little of the mammalian genome is essential for life that this mechanism is apparently an acceptable solution to the problem of rejoining broken chromosomes. By the time a human reaches the age of 70, the typical somatic cell contains over 2000 such “scars,” distributed throughout its genome, representing places where DNA has been inaccurately repaired by nonhomologous end joining. But nonhomologous end joining presents another danger: because there seems to be no mechanism to ensure that two ends being joined were originally next to each other in the genome, nonhomologous end joining can occasionally generate rearrangements in which one broken chromosome becomes covalently attached to another. This can result in chromosomes with two centromeres and chromosomes lacking centromeres altogether; both processing of processing of 5˜ endsDNA ends by nuclease deletion of DNA sequence damage repaired accurately using sister chromatid as the template types of aberrant chromosomes are missegregated during cell division. As previously discussed, the specialized structure of telomeres prevents the natural ends of chromosomes from being mistaken for broken DNA and “repaired” in this way.
A much more accurate type of double-strand break repair occurs in newly replicated DNA (Figure 5–45B). Here, the DNA is repaired using the sister chromatid as a template. This reaction is an example of homologous recombination, and we consider its mechanism later in this chapter. Most organisms employ both non-homologous end joining and homologous recombination to repair double-strand breaks in DNA. Nonhomologous end joining predominates in humans; homologous recombination is used only during and shortly after DNA replication (in S and G2 phases), when sister chromatids are available to serve as templates.
repaired DNA has generally suffered a deletion of nucleotides (A)
Figure 5–45 Two ways to repair double-strand breaks. (A) Nonhomologous end joining alters the original DNA sequence when repairing a broken chromosome. The initial degradation of the broken DNA ends is important because the nucleotides at the site of the initial break are often damaged and cannot be ligated. Nonhomologous end joining usually takes place when cells have not yet duplicated their DNA.
(B) Repairing double-strand breaks by homologous recombination is more difficult to accomplish but restores the original DNA sequence. It typically takes place after the DNA has been duplicated (when a duplex template is available) but before the cell has divided. Details of the homologous recombination pathway are presented in the following section (see Figure 5–48).