DFFB

Summary: DFFB/CAD associates with chromatin as the apoptotic DNA-fragmentation nuclease.

Reason: DFF40-DFF45 can localize to chromatin in NB4 cells, and active CAD/DFFB cuts linker DNA after its release from the DFF complex.

Summary: A cytosolic pool of DFF40/CAD translocates to a chromatin-enriched fraction during apoptotic DNA laddering.

Reason: The cited full-text study showed that cytosolic CAD availability determines oligonucleosomal DNA degradation and that apoptotic stimulation permits DFF40/CAD movement to a chromatin-enriched fraction.

Summary: DFFB/CAD binds DNA as part of its nuclease mechanism.

Reason: DNA binding is a real separable subfunction of the CAD endonuclease, and the mouse-derived orthology transfer is consistent with human DFF binding DNA through the CAD/DFF40 nuclease subunit; the core molecular activity is nevertheless the DNA endonuclease activity that uses this binding to cleave apoptotic chromatin.

Summary: DFFB/CAD is a nuclease.

Reason: Nuclease activity is a true but too-general parent of the DNA endonuclease activity carried by CAD/DFF40 during apoptotic DNA degradation.

Proposed replacements: DNA endonuclease activity

Summary: InterPro DFF40-family membership supports DNA endonuclease activity.

Reason: DFFB is the DNA-specific endonuclease released from the ICAD/DFF45 complex during apoptotic execution, and PTHR13067/IPR039729 specifically marks caspase-activated DNases.

Summary: DFFB/CAD enables DNA nuclease activity inherited in the CAD/DFFB family.

Reason: The PAINT node is exactly the caspase-activated DNase family; the inherited DNA nuclease activity is core and experimentally demonstrated in human DFFB, but DNA endonuclease activity captures the catalytic specificity better than its broader DNA nuclease parent.

Proposed replacements: DNA endonuclease activity

Summary: DFF40/CAD nuclease activity is retained after DFF45 C-terminal deletion.

Reason: The DFF45 truncation study dissected ICAD chaperone and inhibitor functions but still assayed DFF40/CAD-mediated apoptotic DNA fragmentation, so the row should use the more specific DNA endonuclease activity term.

Proposed replacements: DNA endonuclease activity

Summary: Purified DFF40 has intrinsic DNase activity.

Reason: The DFF40 cloning and reconstitution paper established that DFF40 is the active component of DFF and that purified DFF40 directly cleaves DNA; the more specific DNA endonuclease activity term captures that activity better than the parent DNA nuclease term.

Proposed replacements: DNA endonuclease activity

Summary: The DFFA-DFFB partner edge does not need a generic protein-binding annotation on DFFB.

Reason: DFFB forms an inhibited DNA fragmentation factor complex with DFFA/ICAD, but generic protein binding adds no molecular function beyond the DFF complex and CAD nuclease rows. The high-throughput DFFA edges in particular only rediscover the known complex partner.

Summary: The DFFA-DFFB partner edge does not need a generic protein-binding annotation on DFFB.

Reason: DFFB forms an inhibited DNA fragmentation factor complex with DFFA/ICAD, but generic protein binding adds no molecular function beyond the DFF complex and CAD nuclease rows. The high-throughput DFFA edges in particular only rediscover the known complex partner.

Summary: The DFFA-DFFB partner edge does not need a generic protein-binding annotation on DFFB.

Reason: DFFB forms an inhibited DNA fragmentation factor complex with DFFA/ICAD, but generic protein binding adds no molecular function beyond the DFF complex and CAD nuclease rows. The high-throughput DFFA edges in particular only rediscover the known complex partner.

Summary: The DFFA-DFFB partner edge does not need a generic protein-binding annotation on DFFB.

Reason: DFFB forms an inhibited DNA fragmentation factor complex with DFFA/ICAD, but generic protein binding adds no molecular function beyond the DFF complex and CAD nuclease rows. The high-throughput DFFA edges in particular only rediscover the known complex partner.

Summary: The DFFA-DFFB partner edge does not need a generic protein-binding annotation on DFFB.

Reason: DFFB forms an inhibited DNA fragmentation factor complex with DFFA/ICAD, but generic protein binding adds no molecular function beyond the DFF complex and CAD nuclease rows. The high-throughput DFFA edges in particular only rediscover the known complex partner.

Summary: CAD/DFFB acts in nuclei during apoptotic chromatin condensation.

Reason: CAD acts on chromosomal DNA in nuclei during apoptotic execution and can induce chromatin condensation in isolated HeLa nuclei, supporting nuclear localization for the active nuclease.

Summary: DFF can associate with DNA/chromatin in the nucleus.

Reason: The DFF complex directly binds DNA through DFFB/CAD and transfected DFF can associate with chromatin, supporting a nuclear DFFB pool.

Summary: Both cytosolic and nuclear DFF40/CAD pools are detected in cells.

Reason: DFF40/CAD is cell-type-dependently present in nuclear fractions; the apoptotic nuclease ultimately has to reach chromatin to generate oligonucleosomal DNA fragments.

Summary: InterPro and UniProt mappings correctly place DFFB in the nucleus.

Reason: The active DFF40/CAD nuclease functions on nuclear chromatin, and experimental localization rows support both nuclear/chromatin and cytosolic pools.

Summary: Human Protein Atlas immunofluorescence supports nucleoplasmic DFFB localization.

Reason: A nucleoplasmic DFFB pool is compatible with the nuclear and chromatin-associated DFF40/CAD pool that executes apoptotic DNA fragmentation.

Summary: Reactome places DFFB/DFF40 in the nucleoplasm during DFF import, DFF45 cleavage, DFF40 release, homodimerization, chromatin binding, and DNA cleavage.

Reason: These Reactome rows follow CAD from the inactive DFF40:DFF45 complex into the nuclear, DFF40-active steps of apoptotic DNA fragmentation. The importin-dissociation step is inferred from the general Ran:GTP importin mechanism but is consistent with nuclear DFF import.

Summary: Reactome places DFFB/DFF40 in the nucleoplasm during DFF import, DFF45 cleavage, DFF40 release, homodimerization, chromatin binding, and DNA cleavage.

Reason: These Reactome rows follow CAD from the inactive DFF40:DFF45 complex into the nuclear, DFF40-active steps of apoptotic DNA fragmentation. The importin-dissociation step is inferred from the general Ran:GTP importin mechanism but is consistent with nuclear DFF import.

Summary: Reactome places DFFB/DFF40 in the nucleoplasm during DFF import, DFF45 cleavage, DFF40 release, homodimerization, chromatin binding, and DNA cleavage.

Reason: These Reactome rows follow CAD from the inactive DFF40:DFF45 complex into the nuclear, DFF40-active steps of apoptotic DNA fragmentation. The importin-dissociation step is inferred from the general Ran:GTP importin mechanism but is consistent with nuclear DFF import.

Summary: Reactome places DFFB/DFF40 in the nucleoplasm during DFF import, DFF45 cleavage, DFF40 release, homodimerization, chromatin binding, and DNA cleavage.

Reason: These Reactome rows follow CAD from the inactive DFF40:DFF45 complex into the nuclear, DFF40-active steps of apoptotic DNA fragmentation. The importin-dissociation step is inferred from the general Ran:GTP importin mechanism but is consistent with nuclear DFF import.

Summary: Reactome places DFFB/DFF40 in the nucleoplasm during DFF import, DFF45 cleavage, DFF40 release, homodimerization, chromatin binding, and DNA cleavage.

Reason: These Reactome rows follow CAD from the inactive DFF40:DFF45 complex into the nuclear, DFF40-active steps of apoptotic DNA fragmentation. The importin-dissociation step is inferred from the general Ran:GTP importin mechanism but is consistent with nuclear DFF import.

Summary: Reactome places DFFB/DFF40 in the nucleoplasm during DFF import, DFF45 cleavage, DFF40 release, homodimerization, chromatin binding, and DNA cleavage.

Reason: These Reactome rows follow CAD from the inactive DFF40:DFF45 complex into the nuclear, DFF40-active steps of apoptotic DNA fragmentation. The importin-dissociation step is inferred from the general Ran:GTP importin mechanism but is consistent with nuclear DFF import.

Summary: Reactome places DFFB/DFF40 in the nucleoplasm during DFF import, DFF45 cleavage, DFF40 release, homodimerization, chromatin binding, and DNA cleavage.

Reason: These Reactome rows follow CAD from the inactive DFF40:DFF45 complex into the nuclear, DFF40-active steps of apoptotic DNA fragmentation. The importin-dissociation step is inferred from the general Ran:GTP importin mechanism but is consistent with nuclear DFF import.

Summary: Reactome places DFFB/DFF40 in the nucleoplasm during DFF import, DFF45 cleavage, DFF40 release, homodimerization, chromatin binding, and DNA cleavage.

Reason: These Reactome rows follow CAD from the inactive DFF40:DFF45 complex into the nuclear, DFF40-active steps of apoptotic DNA fragmentation. The importin-dissociation step is inferred from the general Ran:GTP importin mechanism but is consistent with nuclear DFF import.

Summary: Human Protein Atlas detects a nucleolar DFFB pool.

Reason: The experimental localization row is not contradicted, but nucleolus is not established as the principal CAD site for linker-DNA cleavage during apoptotic execution.

Summary: The broad cytoplasmic location can be refined to cytosol.

Reason: A cytosolic DFFB pool was purified and directly tested in PMID:22253444. Cytosol is already represented here and is more precise than cytoplasm; nuclear/chromatin pools remain separately supported.

Proposed replacements: cytosol

Summary: A cytosolic DFF40/CAD pool can be limiting for apoptotic DNA laddering.

Reason: The cited full-text study directly tested DFF40/CAD localization and found that low cytosolic DFF40/CAD explains failure of SK-N-AS cells to make oligonucleosomal DNA ladders after staurosporine treatment.

Summary: DFF was originally purified from HeLa cytosol.

Reason: The original DFF purification supports a cytosolic DFF pool containing the 40 kDa DFFB subunit that becomes active after caspase-3 cleavage of DFF45.

Summary: Reactome places DFFB/DFF40 in the cytosolic DFF complex before nuclear import.

Reason: The cytosolic DFF40:DFF45 complex is the precursor to importin-mediated nuclear import and later CAD activation by DFF45 cleavage.

Summary: Reactome places DFFB/DFF40 in the cytosolic DFF complex before nuclear import.

Reason: The cytosolic DFF40:DFF45 complex is the precursor to importin-mediated nuclear import and later CAD activation by DFF45 cleavage.

Summary: Reactome places DFFB/DFF40 in the cytosolic DFF complex before nuclear import.

Reason: The cytosolic DFF40:DFF45 complex is the precursor to importin-mediated nuclear import and later CAD activation by DFF45 cleavage.

Summary: DFF40/CAD degrades DNA as part of apoptotic oligonucleosomal fragmentation.

Reason: DNA catabolic process is a broad but correct parent for CAD cleavage of chromosomal DNA; DFF40/DFF45 is the apoptotic oligonucleosomal-fragmentation module, so the annotation should use the apoptotic DNA fragmentation child term.

Proposed replacements: apoptotic DNA fragmentation

Summary: DFFB/CAD is the conserved caspase-activated DNase for apoptotic DNA fragmentation.

Reason: The PAINT node is the CAD/DFFB family and supports inherited apoptotic DNA fragmentation; human DFFB itself has direct evidence that DFF40 is sufficient for DNA fragmentation after DFF45 cleavage.

Summary: DFFB/CAD released from the DFF complex cleaves DNA during apoptosis.

Reason: The DNA-bound DFF study directly supports CAD-dependent DNA degradation after DFF activation; it also shows that DFFB mediates DNA binding while DFFA inhibits cleavage until activation.

Summary: A cytosolic DFF40/CAD pool enables oligonucleosomal apoptotic DNA fragmentation.

Reason: The cited full-text study showed that increasing the cytosolic level of DFF40/CAD restores DNA laddering in otherwise deficient SK-N-AS neuroblastoma cells.

Summary: DFF40-family InterPro mappings correctly assert apoptotic DNA fragmentation.

Reason: IPR015311 and IPR039729 mark DFF40/CAD domains of the apoptotic DNA-fragmentation nuclease.

Summary: Top-level apoptotic process is true but imprecise for DFFB/CAD.

Reason: DFFB acts at the execution-stage CAD step by cutting DNA into apoptotic oligonucleosomal fragments. The generic CIDE-N InterPro2GO apoptosis mapping should be narrowed to apoptotic DNA fragmentation.

Proposed replacements: apoptotic DNA fragmentation

Summary: Hydrolase activity is a broad parent of DFFB nuclease activity.

Reason: CAD/DFF40 is a DNA endonuclease hydrolase, so this InterPro mapping is mechanistically correct but far less specific than the established DNA endonuclease activity.

Proposed replacements: DNA endonuclease activity

Summary: CAD association increases TOP2A decatenation activity in vitro.

Reason: PMID:10959840 reports that CAD binds TOP2A and that their association enhances TOP2A decatenation in vitro. Enzyme activator activity describes this measured effect more precisely than enzyme binding. This is a contextual activity; it does not make DFFB a topoisomerase or make every condensation event CAD-dependent.

Proposed replacements: enzyme activator activity

Summary: DFFB/CAD contributes to apoptotic chromosome condensation.

Reason: CAD can induce chromatin condensation in isolated nuclei and DFF40 is sufficient to trigger chromatin condensation in the DFF reconstitution system, even though TOP2A and other nuclear factors also contribute to the full morphology.

Summary: DFFB forms the functional DFF40-DFF45 regulatory heterodimer.

Reason: Full PMID:11371636 directly resolves the human heterodimer. Complex formation couples folding and nuclease inhibition and is central to DFFB biology. Retain the general complex term at the available ontology resolution.

Summary: Active DFF40/CAD oligomerizes as part of nuclease activation.

Reason: Homomeric association of DFF40 is demonstrated in the full N-terminal-domain structural study and is linked to activation after DFF45 dissociation. Retain this interaction without treating the observed higher-order N-terminal-domain oligomers as a uniquely resolved full-length dimer.

Summary: The negative-regulation assignment requires distinguishing mutual chaperoning from direct nuclease inhibition.

Reason: Full PMID:11371636 demonstrates that DFF40 induces folding of DFF45, which then chaperones the DFF40 catalytic domain; the interaction maintains an inactive 1:1 complex. DFF45 supplies the established direct nuclease inhibition, while DFF40 supplies more than passive membership by folding its inhibitor. These results do not cleanly isolate a DFF40 negative-regulatory process contribution from nuclease maturation. The prior confident REMOVE overstated the division of labor; retain uncertainty about this specific process assignment without questioning DFFB nuclease activity.