| 2007 |
APLF (C2orf13) accumulates at sites of chromosomal DNA damage via two mechanisms: (1) FHA domain-mediated interaction with XRCC1 (stimulated by CK2 phosphorylation) and (2) a C-terminal zinc finger motif-dependent, XRCC1-independent mechanism. APLF also interacts with XRCC4 and XRCC5 (Ku86) by yeast two-hybrid, and is phosphorylated in an ATM-dependent manner following DNA damage. |
In vivo co-immunoprecipitation, YFP-tagged localization at laser-induced DNA damage sites, yeast two-hybrid, siRNA knockdown with strand break repair assay, ATM-dependent phosphorylation mapping |
Molecular and cellular biology |
High |
17353262
|
| 2007 |
APLF (Xip1/C2orf13) is rapidly recruited to DNA break sites via its C-terminal zinc finger motif; its accumulation is delayed and sustained when PARP-1 is inhibited. APLF stably interacts with XRCC1 through recognition of CK2-phosphorylated FHA-binding motifs in XRCC1, and XRCC1 is required to maintain steady-state APLF levels. APLF is phosphorylated at Ser-116 by ATM in response to ionizing radiation. |
GFP-tagged recruitment kinetics, PARP-1 inhibition, co-immunoprecipitation, siRNA knockdown, clonogenic survival assay |
The Journal of biological chemistry |
High |
17507382
|
| 2008 |
The C-terminal tandem zinc finger (PBZ) domain of APLF binds tightly to poly(ADP-ribose) (PAR), enabling APLF accumulation at DNA strand breaks independently of its FHA domain. APLF negatively affects PAR levels in vitro, and overexpression of APLF or its zinc finger domain suppresses PAR appearance in cells in a zinc finger-dependent manner. |
PAR-binding assays, in vitro PAR modulation assay, overexpression in A549 cells with PAR immunodetection, domain deletion/mutation |
Molecular and cellular biology |
High |
18474613
|
| 2008 |
APLF interacts with both Ku and XRCC4-DNA ligase IV in human cells. The APLF-XRCC4-DNA ligase IV interaction is FHA domain-dependent and phospho-dependent, mediated by CK2 phosphorylation of XRCC4 in vitro. APLF associates with Ku independently of its FHA and zinc finger domains and complexes with Ku at DNA ends. ATM phosphorylates APLF at Ser-116 after ionizing radiation. siRNA depletion of APLF impairs NHEJ. |
Co-immunoprecipitation, in vitro CK2 phosphorylation assay, domain mutant analysis, siRNA knockdown, NHEJ assay |
DNA repair |
High |
18077224
|
| 2010 |
Solution NMR structures of the two PBZ domains of APLF were determined, revealing a novel zinc finger fold. NMR interaction studies with PAR fragments, combined with in vivo PAR-binding data, defined the structural basis for PBZ-PAR recognition. |
NMR solution structure determination, in vivo PAR-binding assays |
Nature structural & molecular biology |
High |
20098424
|
| 2010 |
Structural and biochemical analyses identified Y381/Y386 and Y423/Y428 residues in the conserved C(M/P)Y and CYR motifs within each APLF PBZ domain as critical for interaction with the adenine ring of ADP-ribose; basic residues R387 and R429 coordinate additional interactions with the phosphate backbone. These residues are required for APLF recruitment to sites of DNA damage in vivo. |
Crystal structure/NMR, biochemical binding assays, site-directed mutagenesis, in vivo recruitment assays |
Proceedings of the National Academy of Sciences of the United States of America |
High |
20439749
|
| 2011 |
PARP-3 is stimulated by DNA double-strand breaks in vitro and functions in the same pathway as APLF to accelerate NHEJ. PARP-3 promotes accumulation of APLF at DSBs, and APLF promotes retention of the XRCC4/DNA ligase IV complex in chromatin. Class switch recombination in Aplf-/- B cells is biased toward microhomology-mediated end-joining; overexpression of XRCC4/DNA ligase IV circumvents the requirement for PARP-3 and APLF. |
Genetic epistasis (Aplf-/- mouse cells), in vitro PARP-3 activation assay, chromatin fractionation, class switch recombination assay, overexpression rescue |
Molecular cell |
High |
21211721
|
| 2011 |
APLF functions as a DNA-damage-specific histone chaperone. It preferentially binds the histone H3/H4 tetramer via its C-terminal acidic motif (homologous to NAP1L family motif). APLF exhibits histone chaperone activities in an acidic domain-dependent manner, and the NAP1L motif is critical for its DNA repair capacity in vivo. |
Histone binding assays (pulldown with H3/H4 tetramer), histone chaperone assays in vitro, domain deletion mutagenesis, in vivo DNA repair assay |
Molecular cell |
High |
21211722
|
| 2012 |
The vWA domain of Ku80 recruits APLF into Ku-DNA complexes. APLF then acts as a scaffold promoting recruitment and/or retention of XRCC4-Lig4 and XLF, assembling multi-protein Ku complexes capable of efficient DNA ligation in vitro and in cells. Disruption of APLF interactions with Ku80 or XRCC4-Lig4 confers cellular hypersensitivity and reduced DSB repair. |
Co-immunoprecipitation, in vitro DNA ligation assay, domain mutagenesis, siRNA/gene knockout in avian and human cells, cellular survival assay |
The EMBO journal |
High |
23178593
|
| 2013 |
ATM phosphorylation of APLF at Ser-116 is dependent on PARP3 levels and the APLF PBZ domains. Depletion or chemical inhibition of ATM or PARP3 reduces APLF accumulation at laser-induced DNA damage sites. Ser-116 phosphorylation is required for efficient DSB repair kinetics and cell survival after ionizing radiation, placing PARP3 and ATM in a common signaling pathway upstream of APLF phosphorylation. |
Phosphospecific antibodies, siRNA depletion, chemical inhibitors, laser-induced DNA damage recruitment assay, DSB repair kinetics assay, cell survival assay |
Nucleic acids research |
High |
23449221
|
| 2013 |
An evolutionarily conserved Ku-binding motif (KBM) within APLF mediates the physical interaction between APLF and Ku heterodimer, with peptides derived from this region sufficient to reconstitute Ku binding in vitro. Disruption of this motif relocalizes APLF to the cytoplasm, reduces XRCC4 association, and impairs NHEJ and APLF retention at DNA damage sites; nuclear localization signal rescue restores these defects. |
In vitro peptide reconstitution of Ku interaction, mutagenesis, immunofluorescence localization, NHEJ reporter assay, laser damage recruitment assay |
The Journal of biological chemistry |
High |
23689425
|
| 2016 |
APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcs (DNA-PK), and XRCC4-DNA ligase IV within an extended flexible NHEJ core complex. SAXS analyses reveal the solution architecture of a six-protein complex where APLF stabilizes assembly of Ku, DNA-PKcs, and X4L4, providing geometric access for ligation and phosphorylation. |
Small angle X-ray scattering (SAXS), mutational analyses, in vitro complex reconstitution |
The Journal of biological chemistry |
High |
27875301
|
| 2017 |
Crystal structure of the APLF FHA domain bound to phosphorylated XRCC1 peptides revealed the structural basis of FHA-FBM interaction, including pH dependence due to atypical pK values of phosphoserine/phosphothreonine residues. Binding affinity is enhanced by flanking residues through non-specific electrostatic interactions, supporting XRCC1-mediated nuclear co-transport of APLF. |
X-ray crystallography, NMR, fluorescence polarization binding assay, mutagenesis |
Nucleic acids research |
High |
29059378
|
| 2018 |
Crystal structures of the Ku-binding motifs (KBMs) of APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex showed that both KBMs bind remote sites on the Ku80 α/β domain, with the X-KBM occupying a pocket formed by unprecedented outward rotation of Ku80. Mutation of A-KBM and X-KBM binding sites in Ku80 compromises end-joining efficiency, accuracy, and cellular radiosensitivity. |
X-ray crystallography, laser irradiation recruitment assay, mutagenesis, radiosensitivity assay |
Nature structural & molecular biology |
High |
30291363
|
| 2018 |
The acidic domain of APLF (APLFAD) is intrinsically disordered and binds histone complexes (H3-H4)2 and H2A-H2B specifically and with high affinity. APLFAD prevents unspecific H2A-H2B-DNA complex formation (chaperone activity). NMR and mutagenesis showed that two aromatic side chains in APLFAD anchor to α1-α2 patches on H2A and H2B, covering most of their DNA-interaction surface. |
NMR structural studies, histone binding assays, chaperone activity assay, mutagenesis |
Nucleic acids research |
High |
29905837
|
| 2016 |
Downregulation of APLF in mouse embryonic fibroblasts promotes reprogramming to iPSCs by augmenting E-cadherin (Cdh1) expression through expediting loss of repressive MacroH2A.1 from the Cdh1 promoter and enhancing incorporation of active H3me2K4 marks at pluripotency gene (Nanog, Klf4) promoters. |
shRNA knockdown, ChIP for histone modifications, iPSC reprogramming efficiency assay |
Journal of cell science |
Medium |
27875275
|
| 2022 |
The crystal structure of the APLFAD-histone octamer complex shows that APLFAD tethers histones in their nucleosomal conformation. APLF acidic domain can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. |
X-ray crystallography of APLFAD-histone octamer complex, nucleosome assembly assay, mutagenesis, cell-based assay |
Science advances |
High |
35895815
|
| 2022 |
APLF stabilizes DNA end bridging (synapsis) and, together with Ku70-Ku80, establishes a minimal complex that supports DNA synapsis under piconewton forces for several minutes. The C-terminal acidic region of APLF is critical for DNA end bridging. lncRNA NIHCOLE further increases synapsis dwell time in the presence of Ku70-Ku80 and APLF. |
Magnetic tweezers assay, domain deletion (C-terminal acidic region mutants), in vitro reconstitution with purified proteins |
Cell reports |
High |
36640344
|
| 2024 |
APLF is recruited to stalled replication forks via PARP1 activity (through its PBZ domain binding to PAR). APLF recruitment enables FANCD2 recruitment to stalled forks. APLF depletion impairs interstrand crosslink (ICL) repair, reduces FANCD2 at stalled forks, and causes nascent DNA degradation by MRE11, establishing a novel role for APLF in fork protection. |
siRNA depletion, proximity ligation assay/ChIP for fork association, ICL repair assay, nascent DNA degradation assay (DNA fiber), PARP inhibition |
Nucleic acids research |
Medium |
38520407
|
| 2024 |
Nuclear localization of APLF in breast cancer cells is facilitated by PARP1, which transports APLF from cytosol to nucleus. PARP1 inhibition (olaparib) abrogates nuclear APLF expression and reduces EMT gene expression. Nuclear APLF in non-metastatic MCF7 cells (via NLS tagging) confers increased migration, invasion, and metastatic potential. |
Stable NLS-tagged APLF expression, PARP1 inhibition with olaparib, immunofluorescence localization, migration/invasion assays, in vivo metastasis assay |
Biochimica et biophysica acta. Molecular basis of disease |
Medium |
39384105
|
| 2024 |
Mouse APLF possesses kinase activity (established by enzymatic analysis). APLF co-localizes with γ-tubulin at centrosomes in mouse embryonic stem cells and governs centrosome number and integrity via PLK4 phosphorylation. Mutagenesis of R37 in the FHA domain abolishes kinase activity and disrupts centrosome number regulation. |
Immunofluorescence co-localization, enzymatic kinase assay, docking studies, site-directed mutagenesis (R37A), domain deletion analysis |
European journal of cell biology |
Low |
38968704
|