Affinage

LIG3

DNA ligase 3 · UniProt P49916

Length
1009 aa
Mass
112.9 kDa
Annotated
2026-06-10
25 papers in source corpus 14 papers cited in narrative 15 extracted findings
Cross-family judge vs UniProt: tie faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

LIG3 is a DNA ligase that operates in both the mitochondrion and nucleus to seal DNA breaks across multiple repair and replication contexts (PMID:24013086). As the sole mitochondrial DNA ligase, it is essential for mtDNA maintenance; biallelic loss-of-function variants cause mtDNA depletion and a neurogastrointestinal encephalomyopathy syndrome, with patient cells showing reduced ligase activity and zebrafish lig3 disruption reproducing brain and gut phenotypes (PMID:33855352). In the nucleus, DNA ligase IIIα partners with XRCC1 to perform nick-sealing in base excision repair and single-strand break repair (PMID:24013086), and serves as a backup for Okazaki fragment ligation when LIG1 is absent: PARP1-HPF1-dependent ADP-ribosylation of histone H3 recruits LIG3 to chromatin for this function (PMID:33872376). Independently of XRCC1, LIG3 acts in PARP1-dependent alternative end-joining of double-strand breaks, including at telomere-internal breaks (PMID:27806302), and can substitute for LIG4 catalytic activity in NHEJ provided LIG4 is present as a structural scaffold, as shown by the embryonic lethality of combining nuclear LIG3 loss with catalytically inactive LIG4 (PMID:39673806). LIG3 transcription and its alt-NHEJ activity are amplified in oncogene-driven leukemias through a c-MYC–miRNA axis (PMID:25828893). Its ligation outcome is substrate-dependent: LIG3α cannot seal certain error-free polβ insertion products opposite 8-oxoG yet ligates the mutagenic alternative, so the choice of ligase determines whether BER ends error-free or mutagenic (PMID:40286853).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2013 High

    Establishing that a single gene encodes both the essential mitochondrial DNA ligase and nuclear ligase IIIα defined LIG3 as a multifunctional ligase spanning organellar mtDNA maintenance and several nuclear repair pathways.

    Evidence Review synthesizing KO/knockdown, in vitro ligation, and complementation studies across labs

    PMID:24013086

    Open questions at the time
    • Does not resolve which pathways depend on the XRCC1 partnership versus XRCC1-independent activity in vivo
    • Relative contribution of LIG3 to alt-NHEJ versus other ligases unquantified
  2. 2016 Medium

    Demonstrating PARP1- and LIG3-dependent end-joining of telomere-internal breaks extended LIG3's alt-NHEJ role to a defined genomic context with microhomology signatures.

    Evidence FokI-induced DSBs at telomeres with genetic depletion of PARP1 and LIG3, FISH and microhomology analysis

    PMID:27806302

    Open questions at the time
    • Does not establish direct LIG3 recruitment mechanism to telomeric breaks
    • Overlap with HR pathway at the same lesions not fully separated
  3. 2021 High

    Identifying PARP1-HPF1-mediated histone H3 ADP-ribosylation as the recruitment signal explained how LIG3-XRCC1 is targeted to chromatin to back up LIG1 in Okazaki fragment ligation.

    Evidence Xenopus egg extract cell-free system with immunodepletion of LIG1/PARP1/HPF1/XRCC1, chromatin fractionation, ADP-ribosylation assays

    PMID:33872376

    Open questions at the time
    • Whether this backup operates in mammalian cells under physiological LIG1 levels untested
    • Does not address efficiency relative to canonical LIG1 ligation
  4. 2021 Medium

    Showing RAD52 antagonizes XRCC1-LIG3α focus formation positioned LIG3-dependent SSBR within a competing pathway choice regulated by ssDNA/PAR-binding factors.

    Evidence XRCC1/LIG3α focus imaging, RAD52 KO/knockdown, camptothecin treatment, ssDNA and PAR binding assays

    PMID:33440161

    Open questions at the time
    • Direct physical competition for PAR/ssDNA versus indirect effect not fully resolved
    • Single lab, imaging-based readout
  5. 2021 High

    Linking biallelic LIG3 loss-of-function to a mtDNA depletion neurogastrointestinal encephalomyopathy established LIG3 as a Mendelian disease gene and confirmed its non-redundant mitochondrial role in patients and animal models.

    Evidence Whole exome sequencing, patient-cell ligase activity assays, zebrafish lig3 disruption, mtDNA copy number quantification

    PMID:33855352

    Open questions at the time
    • Tissue-specific basis of the neurogastrointestinal phenotype not mechanistically dissected
    • Does not address whether nuclear LIG3 functions contribute to disease
  6. 2015 Medium

    Defining a c-MYC–miR-150/miR-22 axis that upregulates LIG3 and PARP1 connected LIG3-driven alt-NHEJ to genomic instability in oncogene-driven leukemias.

    Evidence c-MYC inhibition, miRNA overexpression, expression analysis in primary/cultured leukemia cells and patient samples, alt-NHEJ assays

    PMID:25828893

    Open questions at the time
    • Direct miRNA-LIG3 transcript targeting versus indirect regulation not fully separated
    • Therapeutic exploitability untested
  7. 2018 Medium

    Co-immunoprecipitation of MALAT1 lncRNA with PARP1 and LIG3 suggested an RNA scaffold within the alt-NHEJ complex in multiple myeloma.

    Evidence MALAT1-PARP1/LIG3 RNA-protein co-IP, antisense gapmer knockdown, xenograft functional assays

    PMID:29632340

    Open questions at the time
    • Direct versus bridged RNA-protein contacts not resolved
    • Generality beyond multiple myeloma unknown
  8. 2025 High

    Mouse genetic epistasis revealed that LIG3 substitutes for LIG4 catalytic activity in NHEJ only when LIG4 remains present as a structural scaffold, clarifying the functional interdependence of the two ligases.

    Evidence Nuclear Lig3 KO crossed to catalytic-dead Lig4 knock-in mice, embryo resorption and lymphocyte development analysis

    PMID:39673806

    Open questions at the time
    • Molecular basis of LIG3 recruitment to the LIG4 scaffold unresolved
    • Does not identify which NHEJ steps require the scaffold
  9. 2025 Medium

    In vitro substrate-specific ligation assays showed LIG3α cannot seal error-free polβ dCTP:8-oxoG products but seals the mutagenic dATP product, establishing the ligase identity as a determinant of BER fidelity.

    Evidence In vitro ligation with purified LIG1 and LIG3α on defined polβ-insertion nick substrates opposite 8-oxoG

    PMID:40286853

    Open questions at the time
    • Cellular consequence of this discrimination not demonstrated
    • Structural basis of the substrate block unknown
  10. 2025 Medium

    Single-molecule kinetic comparison distinguished LIG3α from LIG1 by binding frequency and complex lifetime on nick and gap substrates, refining the biophysical basis of their division of labor.

    Evidence Single-molecule TIRF microscopy and in vitro ligation with purified LIG1/LIG3α on defined substrates (preprint)

    PMID:40666977

    Open questions at the time
    • Preprint, not yet peer-reviewed
    • Behavior in the context of partner proteins (XRCC1) not tested
  11. 2025 Medium

    A YY1-Lig3-PARP1 complex was implicated in extrachromosomal DNA biogenesis via Lig3-catalyzed religation after YY1-mediated DNA looping, extending LIG3 ligation into a cancer genome-remodeling role.

    Evidence Modeling, imaging in cancer cells, clinical chip verification, PARP inhibitor functional assays

    PMID:40769147

    Open questions at the time
    • Direct Lig3-YY1 physical interaction versus complex co-occurrence not fully resolved
    • Z-DNA/acidic microenvironment mechanism mechanistically incomplete
  12. 2025 Medium

    Genetic disruption of FEN1/JMJD1B-dependent flap processing revealed a PARP1-dependent LIG3 alternative Okazaki fragment maturation route that ligates unprocessed flaps at the cost of duplications.

    Evidence JMJD1B disruption, FEN1 R192Q mutation, PARP1 inhibition, PCNA binding and mutagenesis/sequencing (preprint)

    PMID:41280084

    Open questions at the time
    • Preprint, not yet peer-reviewed
    • Frequency of this route under unperturbed replication unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • How LIG3 is mechanistically recruited and selected over LIG1/LIG4 in each context, and the structural basis of its substrate-specific ligation outcomes, remains unresolved.
  • No structural model linking substrate identity to ligation discrimination
  • Recruitment hierarchy across competing pathways not unified
  • Tissue-specific contributions of nuclear versus mitochondrial LIG3 unclear

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016874 ligase activity 5 GO:0003677 DNA binding 2 GO:0140097 catalytic activity, acting on DNA 2
Localization
GO:0005634 nucleus 2 GO:0005739 mitochondrion 2 GO:0005694 chromosome 1
Pathway
R-HSA-73894 DNA Repair 3 R-HSA-69306 DNA Replication 2 R-HSA-1640170 Cell Cycle 1
Partners
HPF1LIG4MALAT1PARP1RAD52XRCC1YY1
Complex memberships
PARP1-LIG3 alt-NHEJ complexXRCC1-LIG3 complexYY1-Lig3-PARP1 complex

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2013 The LIG3 gene encodes multiple DNA ligase polypeptides: the only mitochondrial DNA ligase (essential for that organelle), and nuclear DNA ligase IIIα which partners with XRCC1 in base excision repair (BER) and single-strand break repair. Nuclear LIG3α also functions in an alternative NHEJ (alt-NHEJ) pathway for DSB repair that is independent of its XRCC1 interaction, and can substitute for LIG1 in DNA replication when LIG1 is absent. Review synthesizing genetic, biochemical, and cell biological experiments across multiple studies Gene High 24013086
2021 LIG3-XRCC1 complex serves as a backup system for Okazaki fragment ligation when LIG1 is absent. PARP1-HPF1-dependent ADP-ribosylation of histone H3 is required to recruit LIG3 onto chromatin for this backup ligation; depletion of PARP1 or HPF1 prevents LIG3 chromatin recruitment and Okazaki fragment joining in the absence of LIG1. Cell-free system from Xenopus egg extracts with immunodepletion of LIG1, PARP1, HPF1, and XRCC1; chromatin fractionation; ADP-ribosylation assays Nucleic acids research High 33872376
2021 RAD52 inhibits single-strand break repair (SSBR) by reducing DNA-damage-promoted co-localization of XRCC1 and LIG3α at repair foci, via RAD52's high-affinity binding to single-stranded DNA (ssDNA) and poly(ADP-ribose) (PAR). Co-localization/imaging of XRCC1/LIG3α foci, RAD52 knockout/knockdown, camptothecin treatment, ssDNA and PAR binding assays, cell survival assays Cell reports Medium 33440161
2018 MALAT1 lncRNA physically binds PARP1 and LIG3 and is a component of the alternative NHEJ (A-NHEJ) protein complex in multiple myeloma cells; degradation of MALAT1 by antisense oligonucleotides disrupts this complex, increases poly-ADP-ribosylation of nuclear proteins, and defects the DNA repair pathway leading to apoptosis. RNA-protein binding (co-immunoprecipitation of MALAT1 with PARP1/LIG3), antisense gapmer knockdown, in vitro and in vivo (xenograft) functional assays Leukemia Medium 29632340
2015 c-MYC transcriptionally activates LIG3 and PARP1 expression in BCR-ABL1- and FLT3/ITD-driven leukemias. c-MYC negatively regulates miR-150 and miR-22, which in turn suppress LIG3 and PARP1, driving increased alt-NHEJ activity and genomic instability. c-MYC inhibition, miRNA overexpression (miR-150, miR-22), gene expression analysis in primary and cultured leukemia cells and patient samples, alt-NHEJ activity assays Molecular cancer research : MCR Medium 25828893
2016 Telomere-internal double-strand breaks are repaired by a PARP1- and LIG3-dependent end-joining reaction consistent with alt-NHEJ or single-strand break repair, in addition to homologous recombination. FokI-induced DSBs at telomeres, genetic depletion of PARP1 and LIG3, telomere FISH and imaging, microhomology analysis Cell reports Medium 27806302
2021 Biallelic loss-of-function variants in LIG3 cause mitochondrial DNA depletion (without multiple deletions), impair mtDNA maintenance, and result in mitochondrial dysfunction manifesting as a neurogastrointestinal encephalomyopathy syndrome. Patient-derived cells show reduced LIG3 protein and ligase activity; disruption of lig3 in zebrafish reproduces brain alterations and gut transit impairment. Whole exome sequencing, in vitro ligase activity assays in patient cells, zebrafish lig3 disruption model, mtDNA copy number quantification, muscle biopsy/COX staining Brain : a journal of neurology High 33855352
2019 Sirt3 deacetylates LIG3 protein (along with other BER enzymes NEIL1, NEIL2, OGG1, MUTYH, APE1) in mitochondria; LIG3 is a substrate for Sirt3-mediated deacetylation, which modulates LIG3 activity in the mitochondrial BER pathway. Deacetylation assay with Sirt3 and BER substrates including LIG3 in colorectal cancer cells Polski przeglad chirurgiczny Low 32312920
2025 Nuclear LIG3 is recruited to NHEJ complexes to facilitate end joining in the presence (but not catalytic activity) of LIG4. Mice lacking nuclear LIG3 and expressing catalytically inactive LIG4 die as embryos (lethal genetic interaction), whereas nuclear LIG3-deficient mice alone are viable, demonstrating that LIG3 substitutes for LIG4 catalytic activity in NHEJ when LIG4 is present as a structural scaffold. Mouse genetics: nuclear Lig3 knockout strain crossed to Lig4 catalytic-dead knock-in; timed mating/embryo resorption analysis; lymphocyte development assays Nucleic acids research High 39673806
2025 LIG3 (with PARP1) performs an alternative Okazaki fragment maturation (OFM) process: when FEN1 demethylation by JMJD1B and subsequent LIG1 recruitment is disrupted, unprocessed 5' flaps trigger PARP1-dependent LIG3 recruitment to join incompletely processed Okazaki fragments. LIG3 has flap ligation activity in this context, supporting cell survival but causing duplications and mutations. Cell-based genetic disruption of JMJD1B and FEN1 R192Q mutation; PARP1 inhibition; PCNA binding assays; mutagenesis/sequencing bioRxivpreprint Medium 41280084
2025 LIG3α exhibits an inability to ligate polβ dCTP:8-oxoG insertion products (error-free repair intermediates) at the final BER step, while it can seal nicks from polβ mutagenic dATP insertion opposite 8-oxoG. This demonstrates that the identity of the BER ligase critically determines repair outcome (mutagenic vs. error-free) at the ligation step. In vitro ligation assays with purified LIG1 and LIG3α on defined nick substrates containing polβ insertion products opposite 8-oxoG The Journal of biological chemistry Medium 40286853
2025 YY1-Lig3-PARP1 form a complex in which Lig3 catalyzes DNA religation after YY1-mediated DNA looping to drive extrachromosomal DNA (ecDNA) biogenesis. PARylation-dependent acidic microenvironments mediated by the Lig3-YY1 complex promote Z-DNA formation, facilitating the fusion-religation process. Multi-layer perceptron modeling, imaging strategies in human cancer cells, clinical chip verification, PARP inhibitor functional assays Molecular cell Medium 40769147
2018 M-LPH (Mpv17-like protein) knockout in human hepatoma cells reduces LIG3 protein levels in mitochondria (along with TFAM and OGG1), impairing mitochondrial BER capacity and increasing mtDNA damage. LIG3 protein stability in mitochondria is therefore dependent on M-LPH. CRISPR-Cas9 M-LPH knockout, Western blot and confocal immunofluorescence of mitochondrial LIG3 protein, mtDNA damage quantification by PCR and 8-OHdG measurement Oxidative medicine and cellular longevity Low 30310528
2025 LIG3α binds less frequently to nick substrates (canonical A:T, mismatch G:T, and damaged 8-oxoG:A) than LIG1 but forms longer-lived complexes. Both ligases can bind gap DNA substrates with efficiency comparable to nicks; LIG1 forms more stable long-lived complexes on 1-nucleotide gaps, while LIG3α forms shorter-lived gap complexes. Both discriminate against larger gaps. Single-molecule total internal reflection fluorescence (TIRF) microscopy; in vitro ligation assays with purified LIG1 and LIG3α on defined substrates bioRxivpreprint Medium 40666977
2025 LIG3 associates with telomeres in response to pyridostatin-induced G-quadruplex stabilization and participates in microhomology-mediated end joining (MMEJ) repair at telomeres. Depletion of MMEJ factors (including LIG3) enhances telomere loss in pyridostatin-treated cells. Telomeric protein composition analysis, MMEJ factor depletion, chemical inhibition, telomere loss assays in human cells treated with pyridostatin bioRxivpreprint Low 41280084

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2018 Targeting the MALAT1/PARP1/LIG3 complex induces DNA damage and apoptosis in multiple myeloma. Leukemia 130 29632340
2016 Telomere-Internal Double-Strand Breaks Are Repaired by Homologous Recombination and PARP1/Lig3-Dependent End-Joining. Cell reports 88 27806302
2015 c-MYC Generates Repair Errors via Increased Transcription of Alternative-NHEJ Factors, LIG3 and PARP1, in Tyrosine Kinase-Activated Leukemias. Molecular cancer research : MCR 57 25828893
2013 Structure and function of the DNA ligases encoded by the mammalian LIG3 gene. Gene 54 24013086
2021 HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation. Nucleic acids research 48 33872376
2021 Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy. Brain : a journal of neurology 39 33855352
2023 CircRNA Galntl6 sponges miR-335 to ameliorate stress-induced hypertension through upregulating Lig3 in rostral ventrolateral medulla. Redox biology 33 37315345
2016 Association between Single-Nucleotide Polymorphisms of the hOGG1,NEIL1,APEX1, FEN1,LIG1, and LIG3 Genes and Alzheimer's Disease Risk. Neuropsychobiology 20 27010693
2019 Sirt3 regulates the level of mitochondrial DNA repair activity through deacetylation of NEIL1, NEIL2, OGG1, MUTYH, APE1 and LIG3 in colorectal cancer. Polski przeglad chirurgiczny 17 32312920
2011 Association between single nucleotide polymorphisms in the DNA repair gene LIG3 and acute adverse skin reactions following radiotherapy. Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology 16 21620500
2021 RAD52 Adjusts Repair of Single-Strand Breaks via Reducing DNA-Damage-Promoted XRCC1/LIG3α Co-localization. Cell reports 12 33440161
2015 Polymorphism of the LIG3 gene in keratoconus and Fuchs endothelial corneal dystrophy. Cellular and molecular biology (Noisy-le-Grand, France) 12 25817347
2025 Extrachromosomal DNA biogenesis is dependent on DNA looping and religation by YY1-Lig3-PARylation complex. Molecular cell 8 40769147
2018 Knockout of Mpv17-Like Protein (M-LPH) Gene in Human Hepatoma Cells Results in Impairment of mtDNA Integrity through Reduction of TFAM, OGG1, and LIG3 at the Protein Levels. Oxidative medicine and cellular longevity 6 30310528
2019 LIG3 gene polymorphisms and risk of gastric cancer in a Southern Chinese population. Gene 5 31034940
2025 Lig3-dependent rescue of mouse viability and DNA double-strand break repair by catalytically inactive Lig4. Nucleic acids research 3 39673806
2025 Repair pathway coordination from gap filling by polβ and subsequent nick sealing by LIG1 or LIG3α governs BER efficiency at the downstream steps. DNA repair 3 40081282
2025 Nick sealing of polβ mismatch insertion products by LIG1 and LIG3α during 8-oxoG bypass leads to mutagenic or error-free base excision repair. The Journal of biological chemistry 2 40286853
2025 Computational investigation unveils pathogenic LIG3 non-synonymous mutations and therapeutic targets in acute myeloid leukemia. PloS one 2 40493574
2024 Glutamine Supplementation as a Novel Metabolic Therapeutic Strategy for LIG3-Dependent Chronic Intestinal Pseudo-Obstruction. Gastroenterology 2 39173721
2025 JMJD1B-mediated FEN1 demethylation allows timely switching of Okazaki fragment maturation core enzymes to avoid mutagenic flap ligation by PARP1-LIG3. bioRxiv : the preprint server for biology 1 41280084
2024 Mutagenic ligation of polβ mismatch insertion products during 8-oxoG bypass by LIG1 and LIG3α at the downstream steps of base excision repair pathway. bioRxiv : the preprint server for biology 1 39484546
2019 Lack of associations between LIG3 gene polymorphisms and neuroblastoma susceptibility in Chinese children. Journal of Cancer 1 31737108
2026 Novel Biallelic LIG3 Mutations Causing Lethal Phenotype With Immunodeficiency. American journal of medical genetics. Part A 0 41741356
2025 Single-molecule analysis of gap and nick binding by LIG1 and LIG3α at the final step of DNA repair. bioRxiv : the preprint server for biology 0 40666977

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