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DNA double-strand breaks

Wednesday 19 November 2003

DNA double strand breaks (DSB) represent the most threatening lesion to the integrity of the genome in cells exposed to ionizing radiation and radiomimetic chemicals. Those breaks are recognized, signaled to cell cycle checkpoints and repaired by protein complexes (See: DNA double-strand break repair).

Double-strand breaks (DSBs), in which both strands in the double helix are severed, are particularly hazardous to the cell because they can lead to genome rearrangements.

The DNA double-strand break (DSB) is the principle cytotoxic lesion for ionizing radiation and radio-mimetic chemicals but can also be caused by mechanical stress on chromosomes or when a replicative DNA polymerase encounters a DNA single-strand break or other type of DNA lesion.

DSBs also occur as intermediates in various biological events, such as V(D)J recombination in developing lymphoid cells.

See also

- Double stand break repair

Two mechanisms exist to repair DSBs: non-homologous end joining (NHEJ) and recombinational repair (also known as template-assisted repair or homologous recombination repair).[7]
DNA ligase, shown above repairing chromosomal damage, is an enzyme that joins broken nucleotides together by catalyzing the formation of an internucleotide ester bond between the phosphate backbone and the deoxyribose nucleotides.
DNA ligase, shown above repairing chromosomal damage, is an enzyme that joins broken nucleotides together by catalyzing the formation of an internucleotide ester bond between the phosphate backbone and the deoxyribose nucleotides.

In NHEJ, DNA Ligase IV, a specialized DNA Ligase that forms a complex with the cofactor XRCC4, directly joins the two ends.[9] To guide accurate repair, NHEJ relies on short homologous sequences called microhomologies present on the single-stranded tails of the DNA ends to be joined. If these overhangs are compatible, repair is usually accurate.[10][11][12][13] NHEJ can also introduce mutations during repair. Loss of damaged nucleotides at the break site can lead to deletions, and joining of nonmatching termini forms translocations. NHEJ is especially important before the cell has replicated its DNA, since there is no template available for repair by homologous recombination. There are "backup" NHEJ pathways in higher eukaryotes.[14] Besides its role as a genome caretaker, NHEJ is required for joining hairpin-capped double-strand breaks induced during V(D)J recombination, the process that generates diversity in B-cell and T-cell receptors in the vertebrate immune system.[15]

Recombinational repair requires the presence of an identical or nearly identical sequence to be used as a template for repair of the break. The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover during meiosis. This pathway allows a damaged chromosome to be repaired using a sister chromatid (available in G2 after DNA replication) or a homologous chromosome as a template. DSBs caused by the replication machinery attempting to synthesize across a single-strand break or unrepaired lesion cause collapse of the replication fork and are typically repaired by recombination.

Topoisomerases introduce both single- and double-strand breaks in the course of changing the DNA’s state of supercoiling, which is especially common in regions near an open replication fork. Such breaks are not considered DNA damage because they are a natural intermediate in the topoisomerase biochemical mechanism and are immediately repaired by the enzymes that created them.

A team of French researchers bombarded Deinococcus radiodurans to study the mechanism of double-strand break DNA repair in that organism. At least two copies of the genome, with random DNA breaks, can form DNA fragments through annealing. Partially overlapping fragments are then used for synthesis of homologous regions through a moving D-loop that can continue extension until they find complementary partner strands. In the final step there is crossover by means of RecA-dependent homologous recombination.[16]

Anomalies in DNA double strand breaks repair can cause several human diseases as ATM and Ataxia telangiectasia, Nijmegen breakage syndrome, Fanconi anemia.
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Pathogeny

- A particularly hazardous type of DNA damage to dividing cells is a break to both strands in the double helix.

Two mechanisms exist to repair this damage. They are generally known as Non-Homologous End-Joining and recombinational repair, template-assisted repair, or homologous recombination.

- Recombinational repair requires the presence of an identical or nearly identical sequence to be used as a template for repair of the break.

- The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover in germ cells during meiosis.

- The recombinational repair mechanism is predominantly used during the phases of the cell cycle when the DNA is replicating or has completed replicating its DNA.

- This allows a damaged chromosome to be repaired using the newly created sister chromatid as a template, i.e. an identical copy that is moreover orderly paired to the damaged region.

- Many genes in the human genome are present in multiple copies providing many possible sources of identical sequences.

- But recombinational repair that relies on these copies as templates for each other is problematic because it leads to chromosomal translocations and other types of chromosomal rearrangements.

- Non-Homologous End-Joining (NHEJ) rejoins the two ends of the break in absence of a template sequence. However there is often DNA sequence loss during this process and so this repair can be mutagenic.

NHEJ can occur at all stages of the cell cycle but in mammalian cells is the main repair mechanism until DNA replication makes it possible for recombinational repair to use the sister chromatid as a template.

Since the vast majority of the genome in humans and other multicellular organisms is made up of DNA that contains no genes, the so-called "junk DNA", mutagenic NHEJ is likely to be less harmful than template-assisted repair would be in presence of multiple template sequences, since in the latter case undesirable chromosomal rearrangements are generated.

The enzymatic machinery used for NHEJ is also utilized in B-cells to rejoin breaks created by the RAG proteins during VDJ recombination a crucial step in the generation of antibody diversity by the immune system.

Pathology

Inaccurate repair or lack of repair of a DSB can lead to mutations or to larger-scale genomic instability through the generation of dicentric or acentric chromosomal fragments.

Anomalies in DNA double strand breaks repair can cause several human diseases:

- ATM and Ataxia telangiectasia
- Nijmegen breakage syndrome
- Fanconi anemia

See also

- DNA double-strand break repair

  • by non-homologous end-joining
  • by homologous recombination

- DNA double-strand break and apoptosis
- DNA double-strand break and checkpoints
- DNA double-strand break and chromosomal instability
- DNA double-strand breaks

References

- O’Driscoll M, Jeggo PA. The role of double-strand break repair - insights from human genetics. Nat Rev Genet. 2006 Jan;7(1):45-54. PMID: 6369571

- Karagiannis TC, El-Osta A. Double-strand breaks: signaling pathways and repair mechanisms. Cell Mol Life Sci. 2004 Sep;61(17):2137-47. PMID: 15338043

- Kobayashi J, Antoccia A, Tauchi H, Matsuura S, Komatsu K. NBS1 and its functional role in the DNA damage response. DNA Repair (Amst). 2004 Aug-Sep;3(8-9):855-61. PMID: 15279770

- Matsuura S, Kobayashi J, Tauchi H, Komatsu K. Nijmegen breakage syndrome and DNA double strand break repair by NBS1 complex. Adv Biophys. 2004;38:65-80. PMID: 15493328

- Valerie K, Povirk LF. Regulation and mechanisms of mammalian double-strand break repair. Oncogene. 2003 Sep 1;22(37):5792-812. PMID: 12947387

- Petrini JH, Stracker TH. The cellular response to DNA double-strand breaks : defining the sensors and mediators. Trends Cell Biol. 2003 Sep ;13(9):458-62. PMID : 12946624

- Pierce AJ, Stark JM, Araujo FD, Moynahan ME, Berwick M, Jasin M. Double-strand breaks and tumorigenesis. Trends Cell Biol. 2001 Nov;11(11):S52-9. PMID: 11684443

- Aguilera A. Double-strand break repair: are Rad51/RecA—DNA joints barriers to DNA replication? Trends Genet. 2001 Jun;17(6):318-21. PMID: 11377793

- Haber JE. Partners and pathways repairing a double-strand break. Trends Genet. 2000 Jun;16(6):259-64. PMID: 10827453

- O’driscoll M, Jeggo PA. The role of double-strand break repair - insights from human genetics. Nat Rev Genet. 2006 Jan;7(1):45-54. PMID: 16369571

- Karagiannis TC, El-Osta A. Double-strand breaks: signaling pathways and repair mechanisms. Cell Mol Life Sci. 2004 Sep;61(17):2137-47. PMID: 15338043

- Petrini JH, Stracker TH. The cellular response to DNA double-strand breaks: defining the sensors and mediators. Trends Cell Biol. 2003 Sep;13(9):458-62. PMID: 12946624

- Rouse J, Jackson SP. Interfaces between the detection, signaling, and repair of DNA damage. Science. 2002 Jul 26;297(5581):547-51. PMID: 12142523

- Jackson SP. Sensing and repairing DNA double-strand breaks. Carcinogenesis. 2002 May;23(5):687-96. PMID: 12016139

- Pierce AJ, Stark JM, Araujo FD, Moynahan ME, Berwick M, Jasin M. Double-strand breaks and tumorigenesis. Trends Cell Biol. 2001 Nov;11(11):S52-9. PMID: 11684443

- van Gent DC, Hoeijmakers JH, Kanaar R. Chromosomal stability and the DNA double-stranded break connection. Nat Rev Genet. 2001 Mar;2(3):196-206. PMID: 11256071

- Haber JE. Partners and pathways repairing a double-strand break. Trends Genet. 2000 Jun;16(6):259-64. PMID: 10827453