Non-homologous end joining

Non-homologous end joining (NHEJ) is a pathway that can be used to repair double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homologous recombination, which requires a homologous sequence to guide repair. The term "non-homologous end joining" was coined in 1996 by Moore and Haber.^[1]

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NHEJ is evolutionarily conserved throughout all kingdoms of life and is the predominant double-strand break repair pathway in many organisms, including higher eukaryotes such as human and mouse^{[citation needed]}. In budding yeast (Saccharomyces cerevisiae), however, homologous recombination dominates when the organism is grown under common laboratory conditions. Some species of bacteria, such as Mycobacterium tuberculosis, have an end joining pathway, while it is absent in others, like Escherichia coli.

NHEJ typically utilizes short homologous DNA sequences, termed microhomologies, to guide repair. Microhomologies in the single-stranded overhangs that are often present on the ends of double-strand breaks are used to promote restorative repair. When these overhangs are compatible, NHEJ almost always repairs the break accurately, with no sequence loss.^[1][2][3][4] Imprecise repair leading to loss of nucleotides can also occur, but is much less common. Nevertheless, NHEJ is often somewhat misleadingly referred to as an "error-prone" repair mechanism. This is likely because NHEJ can lead to translocations when organisms are subjected to large doses of radiation that cause many breaks per cell. Additionally, the NHEJ pathway is responsible for fusing the ends of chromosomes that have undergone telomere failure.^[5] These translocations may result in incorrect gene regulation, and (ultimately) cancer.

Proteins involved in NHEJ

A number of proteins are involved in NHEJ. The Ku heterodimer, consisting of Ku70 and Ku80, forms a complex with the DNA dependent protein kinase catalytic subunit (DNA-PKcs), which is present in mammals but absent in yeast. Ku is also involved in telomere function.^[6] The DNA Ligase IV complex, consisting of the catalytic subunit DNA Ligase IV and its cofactor XRCC4, performs the ligation step of repair.^[7] The recently discovered protein XLF, also known as Cernunnos, is homologous to yeast Nej1 and is also required for NHEJ.^[8][9][10] In yeast, the Mre11-Rad50-Xrs2 (MRX) complex is required for NHEJ and is thought to promote bridging of the DNA ends,^[11] but the corresponding mammalian complex of Mre11-Rad50-Nbs1 does not seem to be necessary. Instead, DNA-PKcs is thought to mediate end bridging.^[12] The Pol X family DNA polymerases Pol λ and Pol μ (Pol4 in yeast) fill gaps during NHEJ,^[13][3][14] and the nuclease Artemis is required for hairpin opening and may also be involved in trimming damaged or non-homologous nucleotides.^[15] In yeast, Sir2 was originally identified as an NHEJ protein, but is now known to be required for NHEJ only because it is required for the transcription of Nej1.^[16]

V(D)J Recombination

NHEJ plays a critical role in V(D)J recombination, the process by which B-cell and T-cell receptor diversity is generated in the vertebrate immune system.^[17] In V(D)J recombination, hairpin-capped double-strand breaks are created by the enzymes RAG-1 and RAG-2, which cleave the DNA at recombination signal sequences.^[18] These hairpins are then opened by the Artemis nuclease and joined by NHEJ.^[15] A specialized DNA polymerase called terminal deoxynucleotidyl transferase (TdT), which is only expressed in lymph tissue, adds nontemplated nucleotides to the ends before the break is joined.^[19][20] This process couples "variable" (V), "diversity" (D), and "joining" (J) regions, which when assembled together create the variable region of a B-cell or T-cell receptor gene. Unlike typical cellular NHEJ, in which accurate repair is the most favorable outcome, error-prone repair in V(D)J recombination is beneficial in that it maximizes diversity in the coding sequence of these genes. This role of NHEJ has also contributed to its reputation as an error-prone DNA repair pathway. Patients with mutations in RAG-1, RAG-2, and Artemis are unable to produce functional B cells and T cells and suffer from severe combined immunodeficiency (SCID).

References

1. ^ ^{a b} Moore JK, Haber JE. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol. 1996 May;16(5):2164-73. PMID 8628283
2. ^ Boulton SJ, Jackson SP. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J. 1996 Sep 16;15(18):5093-103. PMID 8890183
3. ^ ^{a b} Wilson, T. E., and Lieber, M. R. Efficient processing of DNA ends during yeast nonhomologous end joining. Evidence for a DNA polymerase beta (Pol4)-dependent pathway. (1999) J. Biol. Chem. 274, 23599–23609. PMID 10438542
4. ^ Budman J, Chu G. Processing of DNA for nonhomologous end-joining by cell-free extract. EMBO J. 2005 Feb 23;24(4):849-60. PMID 15692565
5. ^ Espejel S, Franco S, Rodriguez-Perales S, Bouffler SD, Cigudosa JC, Blasco MA. Mammalian Ku86 mediates chromosomal fusions and apoptosis caused by critically short telomeres. EMBO J. 2002 May 1;21(9):2207-19. PMID 11980718
6. ^ Boulton SJ, Jackson SP. 1998. Components of the Ku-dependent non-homologous endjoining pathway are involved in telomeric length maintenance and telomeric silencing. EMBO J. 17:1819–28 PMID 9501103
7. ^ Wilson, T. E., Grawunder, U., and Lieber, M. R. Yeast DNA ligase IV mediates non-homologous DNA end joining. (1997) Nature 388, 495–498. PMID 9242411
8. ^ Ahnesorg P, Smith P, Jackson SP. XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. Cell. 2006 Jan 27;124(2):301-13. PMID 16439205
9. ^ Buck D, Malivert L, de Chasseval R, Barraud A, Fondaneche MC, Sanal O, Plebani A, Stephan JL, Hufnagel M, le Deist F, Fischer A, Durandy A, de Villartay JP, Revy P. Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly. Cell. 2006 Jan 27;124(2):287-99. PMID 16439204
10. ^ Callebaut I, Malivert L, Fischer A, Mornon JP, Revy P, de Villartay JP. Cernunnos Interacts with the XRCC4{middle dot}DNA-ligase IV Complex and Is Homologous to the Yeast Nonhomologous End-joining Factor Nej1. J Biol Chem. 2006 May 19;281(20):13857-60. Epub 2006 Mar 29. PMID 16571728
11. ^ Chen, L., Trujillo, K., Ramos, W., Sung, P., and Tomkinson, A. E. Promotion of Dnl4-catalyzed DNA end-joining by the Rad50/Mre11/Xrs2 and Hdf1/Hdf2 complexes. (2001) Mol. Cell 8, 1105–1115. PMID 11741545
12. ^ DeFazio LG, Stansel RM, Griffith JD, Chu G. Synapsis of DNA ends by DNA-dependent protein kinase. EMBO J. 2002 Jun 17;21(12):3192-200. PMID: 12065431
13. ^ Nick McElhinny, S. A., and Ramsden, D. A. Sibling rivalry: competition between Pol X family members in V(D)J recombination and general double strand break repair. (2004) Immunol. Rev. 200, 156–164. PMID 15242403
14. ^ Daley JM, Laan RL, Suresh A, Wilson TE. DNA joint dependence of pol X family polymerase action in nonhomologous end joining. J Biol Chem. 2005 Aug 12;280(32):29030-7. Epub 2005 Jun 17. PMID: 15964833
15. ^ ^{a b} Ma, Y., Pannicke, U., Schwarz, K., and Lieber, M. R. Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. (2002) Cell 108, 781–794. PMID 11955432
16. ^ Lee SE, Paques F, Sylvan J, Haber JE. Role of yeast SIR genes and mating type in directing DNA double-strand breaks to homologous and non-homologous repair paths. (1999) Curr. Biol. 9:767–70. PMID 10421582
17. ^ Jung D, Alt FW. Unraveling V(D)J recombination; insights into gene regulation. Cell. 2004 Jan 23;116(2):299-311. Review. PMID: 14744439
18. ^ Schatz DG, Baltimore D. Stable expression of immunoglobulin gene V(D)J recombinase activity by gene transfer into 3T3 fibroblasts. Cell. 1988 Apr 8;53(1):107-15. PMID 3349523
19. ^ Gilfillan S, Dierich A, Lemeur M, Benoist C, Mathis D. Mice lacking TdT: mature animals with an immature lymphocyte repertoire. Science. 1993 Aug 27;261(5125):1175-8. PMID 8356452
20. ^ Komori T, Okada A, Stewart V, Alt FW. Lack of N regions in antigen receptor variable region genes of TdT-deficient lymphocytes. Science. 1993 Aug 27;261(5125):1171-5. PMID 8356451