Alternative titles; symbols
HGNC Approved Gene Symbol: LIG4
SNOMEDCT: 724177005;
Cytogenetic location: 13q33.3 Genomic coordinates (GRCh38): 13:108,207,442-108,218,349 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 13q33.3 | {Multiple myeloma, resistance to} | 254500 | Somatic mutation | 3 |
| LIG4 syndrome | 606593 | Autosomal recessive | 3 |
Wei et al. (1995) purified and cloned a novel DNA ligase, termed LIG4, from HeLa cells. They found that the cDNA encodes a polypeptide of 844 amino acids with a predicted mass of 96 kD, consistent with the observed size of the purified enzyme.
Wei et al. (1995) used fluorescence in situ hybridization to map the LIG4 gene to chromosome 13q33-q34.
Robins and Lindahl (1996) purified and characterized LIG4. They found that the protein coeluted with the DNA ligase III-XRCC1 (194360) complex, indicating that LIG4 may also be part of a protein complex. In HeLa cells, LIG4 occurred in part as an enzyme-adenylate complex. LIG4 efficiently joined single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Robins and Lindahl (1996) also reported that LIG4 differed from ligases I and III in its substrate specificity.
Grawunder et al. (1998) showed that targeted disruption of both DNA ligase IV alleles in a human pre-B cell line rendered the cells sensitive to ionizing radiation and ablated V(D)J recombination. This phenotype could only be reversed by complementation with DNA ligase IV but not by expression of either of the remaining 2 ligases, DNA ligase I or III. Hence, DNA ligase IV is the activity responsible for the ligation step in nonhomologous DNA end joining and in V(D)J recombination.
Yan et al. (2007) assessed whether the classical nonhomologous end-joining (NHEJ) pathway is critical for class-switch recombination (CSR) by assaying CSR in Xrcc4 (194363)- or Lig4-deficient mouse B cells. Classical NHEJ indeed catalyzed CSR joins, because classical NHEJ-deficient B cells had decreased CSR and substantial levels of IgH locus (147100) chromosomal breaks. However, an alternative end-joining pathway, which is markedly biased towards microhomology joins, supports CSR at unexpectedly robust levels in classical NHEJ-deficient B cells. In the absence of classical NHEJ, this alternative end-joining pathway also frequently joins IgH locus breaks to other chromosomes to generate translocations.
LIG4 Syndrome
O'Driscoll et al. (2001) identified 4 patients with features including immunodeficiency and developmental and growth delay who had mutations in the LIG4 gene (R278H; 601837.0004). They termed this syndrome LIG4 syndrome (606593). The clinical phenotype closely resembled the DNA damage response disorder, Nijmegen breakage syndrome (NBS; 251260). Some of the mutations identified in the patients directly disrupted the ligase domain, while others impaired the interaction between LIG4 and XRCC4 (194363). Cell lines from the patients showed pronounced radiosensitivity. Unlike NBS cell lines, they showed normal cell cycle checkpoint responses but impaired DNA double-strand break rejoining. An unexpected V(D)J recombination phenotype was observed involving a small decrease in rejoining frequency coupled with elevated imprecision at signal junctions.
Girard et al. (2004) showed that the clinical severity among 5 patients with LIG4 syndrome correlated with the level of residual ligase activity. Two linked polymorphisms (A3V and T9I) were found to decrease the activity of DNA ligase IV by approximately 2-fold. When combined with the otherwise mild R278H mutation, ligase activity was reduced to a level similar to that of LIG4 patients with immunodeficiency and developmental delay.
Ben-Omran et al. (2005) reported a 4-year-old boy with acute T-cell leukemia and a facial gestalt reminiscent of Nijmegen breakage syndrome. Mutation screening of the NBS1 gene (602667) was negative; sequencing of the LIG4 gene revealed homozygosity for a truncating mutation (R814X; 601837.0002).
In a patient with LIG4 syndrome, van der Burg et al. (2006) identified a homozygous mutation in the LIG4 gene (601837.0007).
Multiple Myeloma, Resistance to
Roddam et al. (2002) investigated the potential impact of 2 LIG4 polymorphisms--ala3 to val (A3V; 601837.0005) and thr9 to ile (T9I; 601837.0006), both caused by C-to-T transitions--on predisposition to several lymphoproliferative disorders, including leukemia, lymphoma, and multiple myeloma (254500), a tumor characterized by aberrant immunoglobulin class switch recombination. The A3V CT and T9I CT and TT genotypes were significantly associated with reduction in risk of developing multiple myeloma. The polymorphisms were in linkage disequilibrium, and a protective effect associated with them was found to be the result of the inheritance of the A3V-T9I CT and A3V-T9I TT haplotypes. These data suggested that genetic variants of NHEJ LIG4 may modulate predisposition to multiple myeloma.
Associations Pending Confirmation
Kuschel et al. (2002) performed genetic association studies in a population-based breast cancer case-control study analyzing polymorphisms in 7 genes involved in DNA repair. Among genes evaluated in the nonhomologous end-joining (NHEJ) pathway, a polymorphism in LIG4 was associated with a decrease in breast cancer risk. In the excision repair gene XRCC3 (600675), 2 haplotypes, AGC and GGC, were associated with nonsignificant reductions in breast cancer risk, and the rare GAT haplotype was associated with a significantly increased risk. The authors hypothesized that variability in DNA repair efficiency may alter breast cancer risk.
In mice, complete Lig4 deficiency causes embryonic lethality, massive neuronal apoptosis, arrested lymphogenesis, and various cellular defects (Frank et al., 1998). Frank et al. (2000) assessed potential roles in this phenotype for INK4a/ARF (CDKN2A; 600160) and p53 (191170), 2 proteins implicated in apoptosis and senescence. Ink4a/Arf deficiency rescued proliferation/senescence defects of Lig4-deficient fibroblasts but not other phenotypic aspects. In contrast, p53 deficiency rescued embryonic lethality, neuronal apoptosis, and fibroblast proliferation/senescence defects but not lymphocyte development or radiosensitivity. Young Lig4/p53 double-null mice routinely died from pro-B lymphomas. Thus, in the context of Lig4 deficiency, embryonic lethality and neuronal apoptosis likely result from a p53-dependent response to unrepaired DNA damage, and neuronal apoptosis and lymphocyte developmental defects can be mechanistically dissociated.
Using a tumor-prone mouse strain (Ink4a/Arf -/-), Sharpless et al. (2001) examined the impact of haploinsufficiency of a nonhomologous end-joining (NHEJ) component, Lig4, on murine tumorigenesis. Lig4 heterozygosity promoted the development of soft-tissue sarcomas that possessed clonal amplifications, deletions, and translocations. That these genomic alterations were relevant in tumorigenesis was supported by the finding of frequent amplification of Mdm2 (164785), a known oncogene in human sarcoma. Together, these findings supported the view that loss of a single Lig4 allele results in NHEJ activity being sufficiently reduced to engender chromosomal aberrations that drive nonlymphoid tumorigenesis.
Lee et al. (2000) found that all apoptosis in the developing nervous system of Lig4 -/- mice required Atm (607585), a serine/threonine protein kinase that functions as a DNA damage sensor in response to DNA double-strand breaks. All Lig4 -/- embryos that also lacked Atm were completely devoid of aberrant apoptosis.
Mills et al. (2004) created Rad54 (604289)/Lig4 double-mutant mice and determined that these factors cooperate to support cellular proliferation, repair spontaneous double-strand breaks, and prevent chromosome and single chromatid aberrations.
Nijnik et al. (2007) discovered a unique mouse strain with a hypomorphic Lig4(Y288C) mutation. The Lig4(Y288C) mouse, identified by a mutagenesis screening program, is a mouse model for human LIG4 syndrome (606593), showing immunodeficiency and growth retardation. Diminished DNA double-strand break repair in the Lig4(Y288C) strain causes progressive loss of hematopoietic stem cells and bone marrow cellularity during aging and severely impairs stem cell function in tissue culture and transplantation. The sensitivity of hematopoietic stem cells to nonhomologous end-joining deficiency is therefore a key determinant of their ability to maintain themselves against physiologic stress over time and to withstand culture and transplantation.
Using flow cytometry, ELISA, and immunofluorescence microscopy, Nijnik et al. (2009) identified multiple defects in lymphocyte development and function, including impaired V(D)J recombination, peripheral lymphocyte survival and proliferation, and B-cell class switch recombination, in Lig4(Y288C) mice. Lig4(Y288C) mice also had a high incidence of thymic tumors. Nijnik et al. (2009) proposed that impaired class switching underlies the impaired immune function in LIG4 syndrome, that a hypomorphic LIG4 mutation may confer a predisposition to lymphoid malignancies, and that there are multiple NHEJ-dependent processes in immune system function,
Rucci et al. (2010) found that transgenic mice carrying a homozygous R278H Lig4 mutation (601837.0004) had growth retardation, decreased life span, decreased fertility, severe cellular sensitivity to ionizing radiation, and a severe, but incomplete, defect in V(D)J recombination in immune cells with an incomplete block in B- and T-cell development. The thymus and the spleen were small, with decreased numbers of T cells. Peripheral T lymphocytes showed an activated and anergic phenotype, reduced viability, and a restricted repertoire, whereas B cells produced low-affinity antibodies that include autoreactive specificities. However, mutant mice were unable to mount high-affinity antibody responses. The mice showed a high frequency of thymic tumors associated with genomic instability. The phenotype was reminiscent of leaky human severe combined immunodeficiency (SCID).
O'Driscoll et al. (2001) identified a 1738C-T transition of the LIG4 gene in 2 sibs (patients 2303 and 2304) with LIG4 syndrome (606593). The mutation resulted in an arg580-to-ter substitution (R580X). The patients were compound heterozygotes; the mutation in the other LIG4 allele was R814X (601837.0002). The phenotype of the 2 patients, who were 46 and 48 years old, respectively, included microcephaly, growth retardation, pancytopenia, myelodysplasia, chronic respiratory infections, photosensitivity, telangiectasia, hypothyroidism, type II diabetes, and hypogonadism.
O'Driscoll et al. (2001) identified a 2440C-T transition of the LIG4 gene in 2 sibs (patients 2303 and 2304) with LIG4 syndrome (606593). The mutation resulted in an arg814-to-ter substitution (R814X). The patients were compound heterozygotes; the other allele had the R580X mutation (601837.0001). O'Driscoll et al. (2001) also identified the arg814-to-ter mutation in another patient with LIG4 syndrome (patient 99P0149) who was a compound heterozygote; the other LIG4 mutation in this patient was gly469 to glu (601837.0003).
In a 4-year-old boy with acute T-cell leukemia and a facial gestalt reminiscent of Nijmegen breakage syndrome, Ben-Omran et al. (2005) identified homozygosity for R814X in the LIG4 gene.
O'Driscoll et al. (2001) identified a G-to-A transition at nucleotide 1406 of the LIG4 gene in patient 99P0149 with LIG4 syndrome (606593). The mutation resulted in a gly469-to-glu substitution (G469E) in LIG4. The patient was compound heterozygous; the mutation in the other LIG4 allele was R814X (601837.0002). The phenotype of this patient, who was 9 years old, included microcephaly, developmental and mental delay, pancytopenia, multiple psoriasiform erythrodermatic skin patches, and atypical bone maturation.
O'Driscoll et al. (2001) identified 3 amino acid substitutions in homozygosity in the LIG4 gene of patient 411BR with LIG4 syndrome (606593): ala3 to val, resulting from a C-to-T transition at nucleotide 8, thr9 to ile, resulting from a C-to-T transition at nucleotide 26, and arg278 to his, resulting from a G-to-A transition at nucleotide 833. The arg278-to-his mutation was identical to that identified in patient 180BR, who had leukemia and whose cell line was radiosensitive and defective in double-strand break repair, by Riballo et al. (1999). The arg278 residue lies within a highly conserved motif encompassing the active site, and the substitution was shown to significantly impair LIG4 function (Riballo et al., 2001). The other 2 amino acid substitutions in patient 411BR, ala3 to val (A3V; 601837.0005) and thr9 to ile (T9I; 601837.0006), were considered to be likely polymorphic variants that may have aggravated the resulting phenotype. Patient 411BR, who was 9 years old, had a phenotype that included microcephaly at birth, developmental and mental delay, pancytopenia, and extensive plantar warts.
Roddam et al. (2002) identified an A3V polymorphism in the LIG4 gene caused by an 8C-T transition. The CT genotype of this polymorphism was found to be associated with a 2-fold reduction in risk of developing multiple myeloma (254500). A second polymorphism, thr9 to ile (T9I; 601837.0006), also due to a C-to-T transition (at nucleotide 26), was also associated with a reduced risk of multiple myeloma; the CT and TT genotypes of the T9I polymorphism were associated with a 1.5-fold and 4-fold reduction, respectively, in risk of developing multiple myeloma, suggesting a gene dosage effect for this polymorphism. The 2 variant alleles were in linkage disequilibrium and the protective effect associated with these polymorphisms was found to be the result of inheritance of the A3V-T9I CT and A3V-T9I TT haplotypes.
See 601837.0005 and Roddam et al. (2002).
In a patient with T cell-negative, B cell-negative, NK cell-positive severe combined immunodeficiency with sensitivity to ionizing radiation (606593), van der Burg et al. (2006) identified a homozygous 3-bp deletion (5333delCAA) in the LIG4 gene, resulting in the deletion of a glutamine at position 433 (Gln433del) between 2 conserved stretches in the catalytic domain of the protein. The patient, born of consanguineous Turkish parents, developed severe recurrent infections and candidiasis in the second year of life. She had no dysmorphic features or neurologic abnormalities. Laboratory analysis showed decreased immunoglobulins, reduced numbers of B and T cells, normal levels of NK cells, and almost undetectable levels of the LIG4 protein. Further analysis of patient's cells showed a defect in V(D)J recombination with extensive nucleotide deletions apparently caused by prolonged exonuclease activity during a delayed ligation process.
Ben-Omran, T. I., Cerosaletti, K., Concannon, P., Weitzman, S., Nezarati, M. M. A patient with mutations in DNA ligase IV: clinical features and overlap with Nijmegen breakage syndrome. Am. J. Med. Genet. 137A: 283-287, 2005. [PubMed: 16088910] [Full Text: https://doi.org/10.1002/ajmg.a.30869]
Frank, K. M., Sekiguchi, J. M., Seidl, K. J., Swat, W., Rathbun, G. A., Cheng, H.-L., Davidson, L., Kangaloo, L., Alt, F. W. Late embryonic lethality and impaired V(D)J recombination in mice lacking DNA ligase IV. Nature 396: 173-177, 1998. [PubMed: 9823897] [Full Text: https://doi.org/10.1038/24172]
Frank, K. M., Sharpless, N. E., Gao, Y., Sekiguchi, J. M., Ferguson, D. O., Zhu, C., Manis, J. P., Horner, J., DePinho, R. A., Alt, F. W. DNA ligase IV deficiency in mice leads to defective neurogenesis and embryonic lethality via the p53 pathway. Molec. Cell 5: 993-1002, 2000. [PubMed: 10911993] [Full Text: https://doi.org/10.1016/s1097-2765(00)80264-6]
Girard, P.-M., Kysela, B., Harer, C. J., Doherty, A. J., Jeggo, P. A. Analysis of DNA ligase IV mutations found in LIG4 syndrome patients: the impact of two linked polymorphisms. Hum. Molec. Genet. 13: 2369-2376, 2004. [PubMed: 15333585] [Full Text: https://doi.org/10.1093/hmg/ddh274]
Grawunder, U., Zimmer, D., Fugmann, S., Schwarz, K., Lieber, M. R. DNA ligase IV is essential for V(D)J recombination and DNA double-strand break repair in human precursor lymphocytes. Molec. Cell 2: 477-484, 1998. [PubMed: 9809069] [Full Text: https://doi.org/10.1016/s1097-2765(00)80147-1]
Kuschel, B., Auranen, A., McBride, S., Novik, K. L., Antoniou, A., Lipscombe, J. M., Day, N. E., Easton, D. F., Ponder, B. A. J., Pharoah, P. D. P., Dunning, A. Variants in DNA double-strand break repair genes and breast cancer susceptibility. Hum. Molec. Genet. 11: 1399-1407, 2002. [PubMed: 12023982] [Full Text: https://doi.org/10.1093/hmg/11.12.1399]
Lee, Y., Barnes, D. E., Lindahl, T., McKinnon, P. J. Defective neurogenesis resulting from DNA ligase IV deficiency requires Atm. Genes Dev. 14: 2576-2580, 2000. [PubMed: 11040211] [Full Text: https://doi.org/10.1101/gad.837100]
Mills, K. D., Ferguson, D. O., Essers, J., Eckersdorff, M., Kanaar, R., Alt, F. W. Rad54 and DNA ligase IV cooperate to maintain mammalian chromatid stability. Genes Dev. 18: 1283-1292, 2004. [PubMed: 15175260] [Full Text: https://doi.org/10.1101/gad.1204304]
Nijnik, A., Dawson, S., Crockford, T. L., Woodbine, L., Visetnoi, S., Bennett, S., Jones, M., Turner, G. D., Jeggo, P. A., Goodnow, C. C., Cornall, R. J. Impaired lymphocyte development and antibody class switching and increased malignancy in a murine model of DNA ligase IV syndrome. J. Clin. Invest. 119: 1696-1705, 2009. [PubMed: 19451691] [Full Text: https://doi.org/10.1172/JCI32743]
Nijnik, A., Woodbine, L., Marchetti, C., Dawson, S., Lambe, T., Liu, C., Rodrigues, N. P., Crockford, T. L., Cabuy, E., Vindigni, A., Enver, T., Bell, J. I., Slijepcevic, P., Goodnow, C. C., Jeggo, P. A., Cornall, R. J. DNA repair is limiting for haematopoietic stem cells during ageing. Nature 447: 686-690, 2007. [PubMed: 17554302] [Full Text: https://doi.org/10.1038/nature05875]
O'Driscoll, M., Cerosaletti, K. M., Girard, P.-M., Dai, Y., Stumm, M., Kysela, B., Hirsch, B., Gennery, A., Palmer, S. E., Seidel, J., Gatti, R. A., Varon, R., Oettinger, M. A., Neitzel, H., Jeggo, P. A., Concannon, P. DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency. Molec. Cell 8: 1175-1185, 2001. [PubMed: 11779494] [Full Text: https://doi.org/10.1016/s1097-2765(01)00408-7]
Riballo, E., Critchlow, S. E., Teo, S.-H., Doherty, A. J., Priestley, A., Broughton, B., Kysela, B., Beamish, H., Plowman, N., Arlett, C. F., Lehmann, A. R., Jackson, S. P., Jeggo, P. A. Identification of a defect in DNA ligase IV in a radiosensitive leukaemia patient. Curr. Biol. 9: 699-702, 1999. [PubMed: 10395545] [Full Text: https://doi.org/10.1016/s0960-9822(99)80311-x]
Riballo, E., Doherty, A. J., Dai, Y., Stiff, T., Oettinger, M. A., Jeggo, P. A., Kysela, B. Cellular and biochemical impact of a mutation in DNA ligase IV conferring clinical radiosensitivity. J. Biol. Chem. 276: 31124-31132, 2001. [PubMed: 11349135] [Full Text: https://doi.org/10.1074/jbc.M103866200]
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Roddam, P. L., Rollinson, S., O'Driscoll, M., Jeggo, P. A., Jack, A., Morgan, G. J. Genetic variants of NHEJ DNA ligase IV can affect the risk of developing multiple myeloma, a tumour characterised by aberrant class switch recombination. J. Med. Genet. 39: 900-905, 2002. [PubMed: 12471202] [Full Text: https://doi.org/10.1136/jmg.39.12.900]
Rucci, F., Notarangelo, L. D., Fazeli, A., Patrizi, L., Hickernell, T., Paganini, T., Coakley, K. M., Detre, C., Keszei, M., Walter, J. E., Feldman, L., Cheng, H.-L., and 10 others. Homozygous DNA ligase IV R278H mutation in mice leads to leaky SCID and represents a model for human LIG4 syndrome. Proc. Nat. Acad. Sci. 107: 3024-3029, 2010. [PubMed: 20133615] [Full Text: https://doi.org/10.1073/pnas.0914865107]
Sharpless, N. E., Ferguson, D. O., O'Hagan, R. C., Castrillon, D. H., Lee, C., Farazi, P. A., Alson, S., Fleming, J., Morton, C. C., Frank, K., Chin, L., Alt, F. W., DePinho, R. A. Impaired nonhomologous end-joining provokes soft tissue sarcomas harboring chromosomal translocations, amplifications, and deletions. Molec. Cell 8: 1187-1196, 2001. [PubMed: 11779495] [Full Text: https://doi.org/10.1016/s1097-2765(01)00425-7]
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Yan, C. T., Boboila, C., Souza, E, K., Franco, S., Hickernell, T. R., Murphy, M., Gumaste, S., Geyer, M., Zarrin, A. A., Manis, J. P., Rajewsky, K., Alt, F. W. IgH class switching and translocations use a robust non-classical end-joining pathway. Nature 449: 478-482, 2007. [PubMed: 17713479] [Full Text: https://doi.org/10.1038/nature06020]