ERCC8 encodes CSA, a WD-repeat substrate adaptor of the CUL4AโDDB1โRBX1 ubiquitin ligase. In the nucleus, CSA connects this ligase to CSB, UVSSA and the stalled RNA polymerase II repair assembly. Its recruitment and positioning interfaces support ubiquitination of polymerase and associated repair proteins, TFIIH recruitment and transcription-coupled nucleotide-excision repair. CSA supplies substrate recognition and assembly; CSB supplies the DNA motor activity and the RING/E2 machinery mediates ubiquitin transfer. These mechanisms are established for full-length CSA, whereas equivalent activity of the 205-residue alternative product remains unestablished.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000012 single strand break repair | IDA PMID:29545921 CSA and CSB play a role in the response to DNA breaks. | KEEP AS NON CORE | Summary: CSA contributes to recovery from single-strand breaks in the tested human-cell context. Reason: PMID:29545921 Results and alkaline-comet Methods compare resting G1 primary CSA-deficient patient and control human fibroblasts after methyl methanesulfonate. Delayed removal of alkaline-comet-detected breaks supports the existing single-strand-break repair assertion as a contextual contribution. A separate transformed-cell wild-type complementation experiment is reported in the main text as Supplementary Figure S1, which was not independently recovered. This does not identify CSA as a strand-break ligase, glycosylase or end-processing enzyme. Its experimentally defined core work remains substrate recruitment and repair-complex assembly in transcription-coupled NER. The neutral-comet double-strand-break and irradiation signaling experiments are distinct readouts and do not replace the single-strand-break result. Supporting Evidence: |
| GO:0000109 nucleotide-excision repair complex | IBA GO_REF:0000033 | ACCEPT | Summary: CSA participates in the conserved transcription-coupled nucleotide-excision repair assembly. Reason: PTHR46202 places human leaf PTN002504689 below PTN000523156; the aligned target is an exact 396-residue match to Q13216. All six asserted IBD records occur on that ancestry, without a target-path NOT. The fungal Cul4A-complex loss is on a different descendant branch. Human self-WITH support is legitimate experimental grounding, not circular transfer. GO:0000109 includes protein complexes acting in NER. In human cells, PMID:32355176 Figures 1 and 5 shows CSA-dependent recruitment of DDB1 and TFIIH to damage-stalled RNAPII; PMID:34526721 Figure 1 resolves human CSA in a reconstituted TCR assembly. The fission-yeast donor Ckn1 has an independently read Ddb1 association and strand-specific CPD-repair phenotype in PMID:18794354 Figures 2, 6 and 7. This supports a repair assembly without asserting permanent membership in every downstream incision intermediate or equivalent function of the 205-residue product. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000523156 SUPPORTS TRANSFER Valid target ancestry and experimentally grounded human and fission-yeast repair-complex roles. |
| GO:0000109 nucleotide-excision repair complex | IDA PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | ACCEPT | Summary: CSA forms a ligase-associated assembly contributing to transcription-coupled nucleotide-excision repair. Reason: PMID:12732143 Figures 1 and 4 and purification/complementation Methods identify a human FLAG/HA-CSA complex containing DDB1, CUL4A, ROC1/RBX1 and COP9 signalosome components. The tagged CSA restores UV-induced RNA-synthesis recovery in CSA-deficient cells, whereas DDB2 does not substitute. Independent human recruitment experiments in PMID:32355176 connect CSA-dependent DDB1/CRL4 assembly to UVSSA/TFIIH recruitment at stalled RNAPII. The complex term is supported by its repair role; it does not imply that CSA is a nuclease or a permanent member of every downstream incision intermediate. |
| GO:0000109 nucleotide-excision repair complex | IPI PMID:22118460 The molecular basis of CRL4DDB2/CSA ubiquitin ligase archite... | ACCEPT | Summary: The DDB1โCSA assembly supplies a substrate-recognition module to the repair complex. Reason: PMID:22118460 Figure 6 and the operative structure/purification Methods resolve the DDB1โCSA assembly using a full-length human CSA construct; CSA residues 364โ396 lack resolved density. Figure 7 and the ubiquitination Methods test a CSA-containing CUL4A ligase and CSB substrate. These observations establish the physical module; independent human-cell PMID:32355176 demonstrates its recruitment to stalled RNAPII and downstream repair-factor assembly. The repair-complex interpretation combines these actual observations, without transferring the paperโs separate DDB2 lesion-recognition mechanism to CSA. |
| GO:0000209 protein polyubiquitination | IBA GO_REF:0000033 | ACCEPT | Summary: CSA supplies substrate recognition to a complex that polyubiquitinates CSB. Reason: PTHR46202 places human leaf PTN002504689 below PTN000523156; the aligned target is an exact 396-residue match to Q13216. All six asserted IBD records occur on that ancestry, without a target-path NOT. The fungal Cul4A-complex loss is on a different descendant branch. Human self-WITH support is legitimate experimental grounding, not circular transfer. PMID:34526721 Results โUbiquitylation by CRL4CSA,โ Figure 3a and the in vitro ubiquitylation Methods show CSB polyubiquitination by reconstituted CRL4CSA containing full-length human CSA. CSA contributes substrate recruitment and assembly; ubiquitin transfer is executed by the E2/RING system, so this process annotation does not assign intrinsic ligase chemistry to CSA. The reconstitution contains mouse RBX1 and pig Pol II, and E2โubiquitin positioning in Figure 3c is modeled. It does not establish the same activity for the shorter natural product. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000523156 SUPPORTS TRANSFER Verified polyubiquitination IBD with human target evidence; CSA is an active substrate-recognition component of the reaction. |
| GO:0000209 protein polyubiquitination | IDA PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | ACCEPT | Summary: CSA participates in substrate-directed protein polyubiquitination within CRL4CSA. Reason: PMID:12732143 Figure 4 and Results show polyubiquitin-chain formation and CUL4A self-modification by CSN-depleted CSA complexes, with inhibition by COP9 signalosome. This is activity of the multicomponent ligase rather than autonomous CSA ubiquitin-transfer chemistry. Independent PMID:16751180 Figure 3 and reconstitution Methods establish CSA-dependent CSB polyubiquitination, using E1/E2/ubiquitin omission controls and a DDB2 ligase comparator that does not substitute for CSA. Together these support CSA doing substrate-recruitment work in polyubiquitination, while leaving the separate claim of CSA autoubiquitination unresolved. |
| GO:0005515 protein binding | IPI PMID:10944529 XAB2, a novel tetratricopeptide repeat protein involved in t... | KEEP AS NON CORE | Summary: CSA associates with XAB2 in purified binding and human-cell experiments. Reason: PMID:10944529 Results and Figure 4 caption report reciprocal GST pull-downs between CSA and XAB2, plus anti-HA recovery of XAB2 from human cells expressing functional HA/His-tagged CSA. The actual Methods distinguish the CSA-deficient recipient and the UV-complementing tagged CSA construct. These are CSA-specific observations, not transfer of the paperโs CSB experiments. Retain the supported physical interaction, but protein binding alone does not describe CSAโs substrate-recognition activity. No untested mechanistic role for the XAB2 interaction is invented; figure pixels and separate supplementary material were not inspected. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | KEEP AS NON CORE | Summary: CSA binds the DDB1 scaffold of its ubiquitin-ligase assembly. Reason: PMID:12732143 Figure 1 and Results/Methods show DDB1 in tandem-purified human CSA complexes and formation of a CSAโDDB1 complex upon coexpression in insect cells. This supports the imported DDB1 interaction. Generic binding is retained outside the core summary because the more informative ligase-substrate adaptor activity is independently present among the reviewed annotations. DDB1 is the scaffold partner, not automatically the substrate, and this pairwise association alone is not treated as a complete substrate-transfer mechanism. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:16949367 A family of diverse Cul4-Ddb1-interacting proteins includes ... | KEEP AS NON CORE | Summary: CSA associates with DDB1 and CUL4A in a DCAF ligase assembly. Reason: The actual publisher Results and Figures 1โ2 captions of PMID:16949367 describe human 293T DDB1-associated complexes and coexpression/coimmunoprecipitation of DCAFs, including CSA, with DDB1 and CUL4A. CSA DDB-box/WDXR substitutions alter DDB1 association. These observations support the physical associations with the supplied DDB1/CUL4A identifiers. They do not establish that every detected pair interacts directly in isolation. Retain the binding assertion as non-core; CSAโs substrate-adaptor mechanism is reviewed separately. Full Experimental Procedures and the individual supplemental CUL4B panels were not recovered, so a CSA-specific CUL4B interaction is not inferred from a general DCAF statement. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:16949367 A family of diverse Cul4-Ddb1-interacting proteins includes ... | KEEP AS NON CORE | Summary: CSAโs DDB1 interaction depends on a defined binding interface. Reason: PMID:16949367 Results and Figure 2EโG captions identify CSA as a DDB1-associated DCAF in human 293T cells and show reduced DDB1 association with CSA K174A, R217A and disease-associated A205P, while R218A retains association. The DDB1 W953 surface is also tested. These target-specific observations support the DDB1-binding annotation, which is retained as non-core alongside the more informative substrate-adaptor activity. The operative text/captions were recovered from the publisher search rendering; full experimental procedures, supplemental blots and figure pixels were not independently inspected. Supporting Evidence: |
| GO:0005515 protein binding | IPI PMID:22466612 Mutations in UVSSA cause UV-sensitive syndrome and destabili... | KEEP AS NON CORE | Summary: CSA associates with UVSSA in human-cell repair complexes. Reason: The original publisher supplement to PMID:22466612, Figure S4 and its caption, directly shows ERCC8/CSA in FLAG/HA-UVSSA immunoprecipitates from human Kps3 soluble and chromatin fractions. The tagged UVSSA is described as expressed near endogenous abundance, with parental/control material distinguished. The actual Figure S4 pixels and captions for S4โS6 were read. This supports association with UVSSA but is not a purified binary-binding assay. Keep the supported interaction as non-core; the main article remained inaccessible and its uninspected details are not claimed as verified. Supporting Evidence: |
| GO:0005634 nucleus | EXP PMID:26620705 The C-terminal Region and SUMOylation of Cockayne Syndrome G... | MODIFY | Summary: CSA has a nucleoplasmic pool and is recruited to extraction-resistant nuclear repair material. Reason: PMID:26620705 Methods and Figure 2B establish CSA-FLAG/HA movement from a soluble fraction into a UV- and CSB-dependent DNase-resistant nuclear fraction. Independently, PMID:11782547 Results explicitly describe diffuse nucleoplasmic CSA staining and foci after UV and Triton extraction, in cells expressing functional full-length tagged CSA. That independent spatial observation supports refining nucleus to nucleoplasm; nuclear-matrix retention alone would not establish this finer compartment. Human Reactome entity 52835 also specifies Q13216 residues 1โ396 in nucleoplasm. The 205-residue product is not independently localized by these experiments. Proposed replacements: nucleoplasm |
| GO:0005634 nucleus | IDA PMID:11782547 Translocation of Cockayne syndrome group A protein to the nu... | MODIFY | Summary: Full-length human CSA is present in the nucleoplasm. Reason: PMID:11782547 uses sequence-verified full-length human CSA bearing C-terminal His6/HA tags and demonstrates UV-survival complementation. Its Results describe diffuse nucleoplasmic staining and foci after UV and Triton extraction. Uniform nuclear staining without extraction is reported separately as data not shown. This directly supports the more informative nucleoplasm location. After UV, a fraction becomes resistant to detergent, DNase and high-salt extraction; that separately supports the nuclear-matrix annotation and is not treated as proof of permanent scaffold membership. No equivalent localization is established for the short natural product. Proposed replacements: nucleoplasm Supporting Evidence: |
| GO:0005634 nucleus | IDA PMID:32355176 The cooperative action of CSB, CSA, and UVSSA target TFIIH t... | MODIFY | Summary: Human CSA is recruited to chromatin-associated repair assemblies at stalled RNA polymerase II. Reason: PMID:32355176 Figure 1 and chromatin-immunoprecipitation/CPD slot-blot Methods isolate endogenous human CSA with UV-induced RNAPII repair assemblies from the chromatin fraction of U2OS cells; the associated DNA is enriched for CPDs. CSB-dependent CSA recruitment and loss/rescue of downstream TFIIH assembly establish the repair context. This source directly supports GO:0000785 chromatin, consistent with the chromosome refinement from the same paper. Independent diffuse nucleoplasmic staining in PMID:11782547 establishes another CSA pool, but does not identify the compartment of this chromatin-associated assembly. The location correction follows the actual source experiment, not the imported annotation relationship. It does not assert direct CSA binding to damaged DNA or equate the artificial LacO array with an induced lesion. The purified ligase experiment in the same paper uses Xenopus CSA and is kept separate from these human-cell observations. Proposed replacements: chromatin |
| GO:0005634 nucleus | IEA GO_REF:0000044 | MODIFY | Summary: The nuclear location mapping can be refined to the nucleoplasmic repair compartment. Reason: SL-0191 correctly maps to nucleus, and the official Q13216 location comment cites human CSA localization. The 19 Reactome source contexts independently trace to the human 1โ396 CSA entity 52835 with an explicit nucleoplasm compartment. Human CSA-dependent recruitment in PMID:32355176 Figures 1โ5 corroborates its nuclear repair role. Retain this localization evidence with GO:0005654 rather than only its broad nucleus ancestor. HPA029328 nuclear-speckle staining is corroborative nuclear evidence, but its shared N-terminal antigen does not distinguish the two natural products. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: UniProtKB-SubCell:SL-0191 SUPPORTS TRANSFER The mapping is valid; independent human pathway and repair-assembly evidence permits finer localization. Proposed replacements: nucleoplasm |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6781833 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6781833, โERCC8 (CSA) binds stalled RNA Pol II,โ reaches entity 52835 through 6781833 input 6781842; 6781842 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6781867 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6781867, โERCC8:DDB1:CUL4:RBX1 ubiquitinates ERCC6 and RNA Pol II,โ reaches entity 52835 through 6781867 input 6781839; 6781839 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782004 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782004, โAssembly of the pre-incision complex in TC-NER,โ reaches entity 52835 through 6782004 input 6781866; 6781866 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782069 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782069, โUVSSA:USP7 deubiquitinates ERCC6,โ reaches entity 52835 through 6782069 input 6782063; 6782063 hasComponent 6781866; 6781866 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782131 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782131, โERCC2-facilitated RNA Pol II backtracking in TC-NER,โ reaches entity 52835 through 6782131 input 6782066; 6782066 hasComponent 6782068; 6782068 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782138 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782138, โERCC5 and RPA bind TC-NER site,โ reaches entity 52835 through 6782138 input 6782111; 6782111 hasComponent 6782122; 6782122 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782141 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782141, โBinding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in TC-NER,โ reaches entity 52835 through 6782141 input 6782134; 6782134 hasComponent 6782111; 6782111 hasComponent 6782122; 6782122 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782204 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782204, โ5' incision of damaged DNA strand by ERCC1:ERCC4 in TC-NER,โ reaches entity 52835 through 6782204 output 6782205; 6782205 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782208 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782208, โRepair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in TC-NER,โ reaches entity 52835 through 6782208 input 6782222; 6782222 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782211 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782211, โDNA polymerases delta, epsilon or kappa bind the TC-NER site,โ reaches entity 52835 through 6782211 input 6782205; 6782205 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782224 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782224, โ3' incision by ERCC5 (XPG) in TC-NER,โ reaches entity 52835 through 6782224 input 6782219; 6782219 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782227 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782227, โLigation of newly synthesized repair patch to incised DNA in TC-NER,โ reaches entity 52835 through 6782227 input 6782220; 6782220 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-6782234 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-6782234, โRecovery of RNA synthesis after TC-NER,โ reaches entity 52835 through 6782234 output 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8952638 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-8952638, โAcM-UBE2M transfers NEDD8 to CRL4 E3 ubiquitin ligase complex,โ reaches entity 52835 through 8952638 output 8952585; 8952585 hasComponent 8952584; 8952584 hasComponent 976118; 976118 hasMember 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route passes through DCAF DefinedSet 976118, whose explicit member is human CSA; it is a family-set representation rather than a pair-specific assay of CSA in this entire reaction. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8952639 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-8952639, โNEDD8:AcM-UBE2M binds CRL4 E3 ubiquitin ligase complex,โ reaches entity 52835 through 8952639 input 8955268; 8955268 hasComponent 976149; 976149 hasComponent 976118; 976118 hasMember 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route passes through DCAF DefinedSet 976118, whose explicit member is human CSA; it is a family-set representation rather than a pair-specific assay of CSA in this entire reaction. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8955245 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-8955245, โCAND1 binds CRL4 E3 ubiquitin ligase in the nucleus,โ reaches entity 52835 through 8955245 input 976149; 976149 hasComponent 976118; 976118 hasMember 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route passes through DCAF DefinedSet 976118, whose explicit member is human CSA; it is a family-set representation rather than a pair-specific assay of CSA in this entire reaction. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8955285 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-8955285, โCOMMDs displace CAND1 from CRL4 E3 ubiquitin ligase complex,โ reaches entity 52835 through 8955285 input 8955244; 8955244 hasComponent 976149; 976149 hasComponent 976118; 976118 hasMember 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route passes through DCAF DefinedSet 976118, whose explicit member is human CSA; it is a family-set representation rather than a pair-specific assay of CSA in this entire reaction. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-8956045 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-8956045, โCOP9 signalosome deneddylates nuclear CRL4 E3 ubiquitin ligase complex,โ reaches entity 52835 through 8956045 input 8952585; 8952585 hasComponent 8952584; 8952584 hasComponent 976118; 976118 hasMember 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route passes through DCAF DefinedSet 976118, whose explicit member is human CSA; it is a family-set representation rather than a pair-specific assay of CSA in this entire reaction. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-9684118 | ACCEPT | Summary: Human CSA is explicitly represented in the nucleoplasm in this pathway context. Reason: The current Reactome event R-HSA-9684118, โERCC3-facilitated RNA Pol II backtracking in TC-NER,โ reaches entity 52835 through 9684118 input 9684117; 9684117 hasComponent 9684121; 9684121 hasComponent 6781841; 6781841 hasComponent 52835. That entity has referenceEntity 52836/Q13216, human species and coordinates 1โ396, with GO:0005654 nucleoplasm. The route explicitly contains CSA in a human repair assembly. The location is additionally consistent with human CSA recruitment/assembly in PMID:32355176. This decision accepts the participant compartment; it does not transfer the eventโs nuclease, polymerase, helicase, deubiquitinase, neddylation or deneddylation activity to CSA, nor independently verify every modeled reaction sequence. The 205-residue product is not the entity specified here. |
| GO:0005694 chromosome | EXP PMID:32355176 The cooperative action of CSB, CSA, and UVSSA target TFIIH t... | MODIFY | Summary: CSA associates with chromatin in the human transcription-coupled repair system. Reason: PMID:32355176 Results Figures 1โ3 and Methods for chromatin immunoprecipitation and immunofluorescence establish endogenous CSA in UV-induced, chromatin-enriched RNAPII complexes and CSA-GFP recruitment to a chromosomal LacO array by tethered CSB. The latter provides an independent spatial recruitment assay beyond biochemical fractionation. Chromatin describes the DNAโprotein material in which CSA acts more precisely than the whole chromosome. This does not assert constitutive structural chromosome membership or direct CSAโDNA binding, and does not extrapolate the tagged/full repair-system results to the short natural product. Proposed replacements: chromatin Supporting Evidence: |
| GO:0005694 chromosome | IEA GO_REF:0000044 | MODIFY | Summary: CSA recruitment to damaged, transcribed chromatin is more precise than the broad chromosome location. Reason: The SL-0468 chromosome mapping is genuine and the official Q13216 record cites PMID:32355176. Its human RNAPII co-immunoprecipitation and chromatin-tethering experiments, Figures 1โ3 and chromatin-tethering Methods, place CSA in chromatin-associated repair assemblies and recruit CSA-GFP to an integrated LacO array through CSB. Refine the location to GO:0000785 chromatin without inventing direct DNA-binding activity, a constitutive structural chromosome role or localization of both natural products. The tagged tethering assay is an engineered recruitment experiment; it complements the endogenous stalled-RNAPII association. Propagation Review Root cause: TERM SCOPING PROBLEM Sources checked: UniProtKB-SubCell:SL-0468 SUPPORTS TRANSFER The source chromosome mapping is correct; human chromatin recruitment supports a more precise location. Proposed replacements: chromatin |
| GO:0005737 cytoplasm | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: A contextual cytoplasmic pool is supported by rat neurons and human cell-line immunofluorescence. Reason: The exact rat donor G3V7B8/ENSRNOP00000013598 carries direct PMID:22900489 annotations. The original Methods pp. 758โ760 and Results/Figures 3โ8 pp. 761โ764 use male Long-Evans rats, anti-CSA sc-25369 at 1:100, omission controls and blinded neuronal-pattern scoring. The study distinguishes diffuse, cytoplasmic, nuclear and perinuclear staining; it does not assay human CSA or resolve isoforms. CSA-positive spiral-ganglion neurons show cytoplasmic staining under control and noise-exposed conditions (Figures 3โ5). Independently, current HPA029328 approved ICC/IF records include cytosol in human A-549 cells, alongside nuclear-speckle staining. These observations support a cytoplasmic pool outside the principal nuclear repair setting, without claiming cytoplasmic repair catalysis or neuronal localization in all human tissues. HPA antigen residues 28โ166 are shared by the reported products, so the antibody cannot assign this distribution to one product. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:G3V7B8 SUPPORTS TRANSFER Actual rat CSA neuronal localization supports the conserved contextual location; HPA adds human cell-line corroboration without isoform resolution. |
| GO:0006283 transcription-coupled nucleotide-excision repair | IBA GO_REF:0000033 | ACCEPT | Summary: CSA has a conserved substrate-recognition and assembly role in transcription-coupled NER. Reason: PTHR46202 places human leaf PTN002504689 below PTN000523156; the aligned target is an exact 396-residue match to Q13216. All six asserted IBD records occur on that ancestry, without a target-path NOT. The fungal Cul4A-complex loss is on a different descendant branch. Human self-WITH support is legitimate experimental grounding, not circular transfer. The fission-yeast Ckn1 donor original PMID:18794354 measures CPD removal separately on transcribed and nontranscribed strands; Figures 6โ7 connect Ddb1-binding mutations to loss of the Ckn1-dependent TCR component. Human PMID:32355176 Figures 1โ5 establishes CSA-dependent CRL4/UVSSA/TFIIH assembly at stalled RNAPII, with the CSA-knockout XR-seq comparison reported in the main Results and performed once. PMID:34526721 resolves human CSA bridging CSB and UVSSA and supporting CRL4 substrate positioning. CSA therefore performs part of the repair-coupling work; it is not simply a lesion substrate or a nonspecific survival determinant. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000523156 SUPPORTS TRANSFER Valid ancestral TCR placement, strand-specific yeast repair data and direct human CSA assembly role. |
| GO:0006283 transcription-coupled nucleotide-excision repair | IDA PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | ACCEPT | Summary: CSA supplies a ligase-associated recruitment function in transcription-coupled nucleotide-excision repair. Reason: PMID:12732143 shows restoration of UV-induced RNA-synthesis recovery by functional tagged human CSA and identifies its DDB1โCUL4AโROC1 complex. The recovery phenotype alone is not a strand-specific lesion-removal assay, but independent human-cell recruitment and XR-seq experiments in PMID:32355176 establish CSA-dependent assembly and preferential repair of the transcribed strand. CSA therefore performs repair-coupling work through assembly/substrate recognition. DDB2โs global-genome lesion-recognition experiments are kept separate and do not assign CSA a lesion-binding or incision activity. |
| GO:0006283 transcription-coupled nucleotide-excision repair | IDA PMID:32142649 Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcr... | ACCEPT | Summary: CSA promotes assembly of the repair machinery at UV-stalled RNA polymerase II. Reason: PMID:32142649 Results on TFIIH recruitment and Figures 2D, 3 and S3A report human CSA-dependent RNAPII ubiquitination and loss of UV-induced TFIIH association with RNAPII in ฮCSA HeLa cells. These recruitment steps contribute to transcription-coupled nucleotide-excision repair. The recovered author manuscript includes operative Results and main/supplementary figure captions, but the detailed STAR Methods were not recovered. Independent human CSA complex-assembly and repair measurements in PMID:32355176 resolve the same process without pretending that the missing STAR Methods were inspected. Mouse RPB1-K1268R disease phenotypes are separate from the human CSA experiments. |
| GO:0006283 transcription-coupled nucleotide-excision repair | IDA PMID:32355176 The cooperative action of CSB, CSA, and UVSSA target TFIIH t... | ACCEPT | Summary: CSA recruits downstream factors in transcription-coupled nucleotide-excision repair. Reason: PMID:32355176 Results Figures 1 and 4โ7, the CSA-knockout experiments and Methods for XR-seq show that human CSA connects CSB to UVSSA/TFIIH recruitment at damage-stalled RNAPII. The CSA-knockout XR-seq comparison further loses preferential repair of the transcribed strand; that CSA-knockout sequencing condition was a single experiment, unlike some other replicated conditions. The mechanistic assembly data establish participation beyond a generic damage-sensitivity phenotype. The purified ligase used in the separate CSB ubiquitylation experiment was Xenopus, which is not presented as purified human CSA evidence. Supporting Evidence: |
| GO:0006283 transcription-coupled nucleotide-excision repair | IDA PMID:34526721 Structural basis of human transcription-DNA repair coupling. | ACCEPT | Summary: CSA supplies a ligase-associated recruitment interface in the transcription-coupled repair complex. Reason: PMID:34526721 Results and Figures 1โ3, with Methods for protein expression, complex formation and in vitro ubiquitylation, place full-length human CSA between CSB, UVSSA and DDB1โCUL4AโRBX1. Reconstituted assemblies connect stalled polymerase to ligase-dependent modification. CSA stimulates CSB ATPase activity in this system but does not itself become the ATPase or DNA translocase. The reconstitution combines human repair factors with pig thymus Pol II and mouse RBX1 expressed with the ligase in insect cells. The existing process assertion concerns CSAโs own recruitment contribution, with no equivalence claim for its 205-residue natural product. Supporting Evidence: |
| GO:0006283 transcription-coupled nucleotide-excision repair | IDA PMID:38316879 Structural basis for RNA polymerase II ubiquitylation and in... | ACCEPT | Summary: CSAโs repair-complex interface is required for productive transcription-coupled repair. Reason: PMID:38316879 Results Figures 1โ4 show ELOF1 docking the CSA-containing ligase near Pol II and define the CSAโUVSSA interface. Crucially, the CSA Y334A interface mutant in human CSA-knockout RPE1 cells compromises recovery of RNA synthesis after UV and the trabectedin-associated incision readout compared with wild-type CSA. These CSA-specific experiments support participation in repair, while the latter readout remains an indirect incision proxy rather than a CSA nuclease assay. Methods describe GFP-CSA complementation, RNA-synthesis recovery and mixed-species reconstitution inherited from PMID:34526721; the short natural product was not separately tested. Supporting Evidence: |
| GO:0006283 transcription-coupled nucleotide-excision repair | IDA PMID:38600235 Transcription-coupled repair of DNA-protein cross-links depe... | ACCEPT | Summary: CSA participates in UV-triggered transcription-coupled nucleotide-excision repair, alongside a distinct cross-link response. Reason: PMID:38600235 Results Figure 5b and Methods for recovery of RNA synthesis directly compare human CSA-deficient RPE1 cells after UVC or formaldehyde: the UV condition fails to recover transcription, whereas the cross-link condition shows delayed recovery. The paper explicitly distinguishes the formaldehyde/DNAโprotein cross-link pathway from classical nucleotide-excision repair; its cross-link phenotype is not relabeled as TC-NER. The UV control and independent CSA-dependent UVSSA/TFIIH recruitment and strand-biased repair in PMID:32355176 establish the imported TC-NER assertion. No new cross-link process is proposed. |
| GO:0006283 transcription-coupled nucleotide-excision repair | IEA GO_REF:0000002 | ACCEPT | Summary: The ERCC8 family mapping to transcription-coupled NER is supported by target-specific biology. Reason: The current IPR042238 family explicitly maps to GO:0006283, contains the Q13216 match, and is integrated with PTHR46202. Independent human experiments in PMID:32355176 Figures 1โ5 and the human CSA-containing structure/reconstitution in PMID:34526721 demonstrate CRL4 substrate recruitment and repair-factor assembly at stalled RNAPII. Thus this is not a functional inference from a generic WD40 repeat alone. The familyโs budding-yeast Rad28 member is not used to assert universal identical TCR behavior; the target has its own experimental grounding. No equivalent activity is assigned to the 205-residue product. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR042238 SUPPORTS TRANSFER The exact family-to-process mapping and target membership are recovered, with independent human role evidence. |
| GO:0006289 nucleotide-excision repair | NAS PMID:22118460 The molecular basis of CRL4DDB2/CSA ubiquitin ligase archite... | MODIFY | Summary: CSAโs established nucleotide-excision repair role is the transcription-coupled branch. Reason: PMID:22118460 Figures 6โ7 establish the human DDB1โCSA module and CSA-containing ligase activity, while its separate DDB2 complexes explain global-genome lesion recognition. CSAโs specific process is supported by human-cell repair-factor recruitment and strand-biased XR-seq in PMID:32355176. Refine the broad nucleotide-excision repair assertion to transcription-coupled nucleotide-excision repair. This uses direct CSA assembly and repair evidence, rather than transferring DDB2โs damaged-DNA recognition or the paperโs DDB2โCUL4B structures to CSA. Proposed replacements: transcription-coupled nucleotide-excision repair |
| GO:0006974 DNA damage response | IDA PMID:11782547 Translocation of Cockayne syndrome group A protein to the nu... | KEEP AS NON CORE | Summary: CSA undergoes a measured nuclear redistribution in response to several DNA-damaging treatments. Reason: PMID:11782547 Results and Figures 1, 3 and 5 show functional tagged human CSA entering a detergent-, DNase- and salt-resistant nuclear fraction after UV, hydrogen peroxide or cisplatin, but not dimethyl sulfate in the tested conditions. The response requires CSB and occurs in the tested XPA/XPC-deficient cells. This directly supports a damage-triggered change in cellular protein localization, which fits GO:0006974. Retain the experimentally observed multi-insult redistribution response as non-core alongside the separately established TC-NER repair mechanism. The original paper links the response to TCR, but does not restrict every measured redistribution event to the same lesion-removal pathway. The non-core judgment concerns this conditional response phenotype; it is not a claim that a correctly supported term should be discarded merely for being an ancestor of repair. Supporting Evidence: |
| GO:0006979 response to oxidative stress | IDA PMID:11782547 Translocation of Cockayne syndrome group A protein to the nu... | KEEP AS NON CORE | Summary: CSA undergoes a CSB-dependent nuclear redistribution after oxidative stress. Reason: PMID:11782547 Results and the hydrogen-peroxide exposure/fractionation Methods show CSA retention in an operational nuclear-matrix fraction after oxidative treatment. This directly supports a change in CSA localization in response to oxidative stress. It does not identify CSA as a peroxide-detoxifying enzyme or an oxidative-base glycosylase. Retain this contextual response outside the core substrate-adaptor and transcription-coupled repair functions; the CSB dependency and extraction-defined nature of the observation remain explicit. Supporting Evidence: |
| GO:0006979 response to oxidative stress | IMP PMID:17297471 The role of CSA in the response to oxidative DNA damage in h... | KEEP AS NON CORE | Summary: CSA affects the response to oxidative DNA damage in a cell-context-dependent manner. Reason: PMID:17297471 actual author-original Results and Methods compare primary human CSA-deficient keratinocytes/fibroblasts, transformed cells and full-length EGFP-CSA complementation. Primary cells show altered potassium-bromate sensitivity and genome-wide removal of oxidized lesions; complementation improves repair kinetics in the tested transformed cells without a matching cytotoxicity rescue. The bulk HPLC/LC-MS measurements and oligonucleotide-incision assay do not establish strand-specific TC-NER regulation or CSA glycosylase catalysis. Keep the broad oxidative-stress response as non-core, preserving the primary-versus-transformed difference rather than asserting a universal phenotype. Supporting Evidence: |
| GO:0009411 response to UV | IDA PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | KEEP AS NON CORE | Summary: CSA-containing complexes respond to UV exposure. Reason: PMID:12732143 Results show UV-dependent changes in the COP9-signalosome association and ligase activity of CSA complexes, together with functional rescue of RNA-synthesis recovery by tagged CSA. CSA ligase activity is inhibited early and restored later under the tested conditions; the DDB2 complex follows a distinct response. The broad UV-response annotation is supported but retained as non-core because transcription-coupled repair and substrate-adaptor annotations describe CSAโs principal molecular work more precisely. Supporting Evidence: |
| GO:0009411 response to UV | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: CSAโs UV response is supported, but is broader than its specific repair-coupling role. Reason: The current ARBA00028103 condition set 21 matches the official target FunFam 2.130.10.10:FF:000130 and Mammalia lineage and emits GO:0009411. Human CSA is recruited to UV-stalled RNAPII and supplies DDB1/CRL4 and downstream factor recruitment in PMID:32355176 Figures 1โ5; human CSA-FLAG/HA also enters the operational DNase-resistant nuclear-matrix fraction after UV in PMID:26620705 Figure 2B. These are positive UV-dependent changes. Retain the broad response term as contextual while the more informative TC-NER and ligase-substrate adaptor annotations describe the principal work. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: ARBA:ARBA00028103 SUPPORTS TRANSFER Exact matching rule condition set and UV-dependent human target evidence; broad response is retained outside the core summary. |
| GO:0010996 response to auditory stimulus | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Noise-dependent redistribution of CSA supports a contextual auditory-stress response. Reason: The exact rat donor G3V7B8/ENSRNOP00000013598 carries direct PMID:22900489 annotations. The original Methods pp. 758โ760 and Results/Figures 3โ8 pp. 761โ764 use male Long-Evans rats, anti-CSA sc-25369 at 1:100, omission controls and blinded neuronal-pattern scoring. The study distinguishes diffuse, cytoplasmic, nuclear and perinuclear staining; it does not assay human CSA or resolve isoforms. The current GO:0010996 definition includes a change in cellular state or activity after an auditory stimulus. In PMID:22900489, 105-dB, four-hour noise exposure changes the CSA perinuclear distribution relative to controls (Figure 8 and the CSA-specific pairwise comparisons on p. 764); the finding is not simply constitutive expression in an auditory organ. The independently traced second donor PMID:23022597 reports regional CSA redistribution in its abstract, but its full Methods/Results were not recovered and are not claimed as independently verified. Retain the broad response as a non-core orthology-based context without asserting auditory signal transduction, a demonstrated otoprotective CSA mechanism, or a human neuron perturbation result. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:G3V7B8 SUPPORTS TRANSFER Direct donor noise-exposure localization experiment supports the broad response context; the second source remains preview/abstract-only. |
| GO:0016363 nuclear matrix | IDA PMID:11782547 Translocation of Cockayne syndrome group A protein to the nu... | KEEP AS NON CORE | Summary: CSA has a conditional association with an operational nuclear-matrix fraction. Reason: PMID:11782547 Methods sequentially extract human cells with detergent, DNase I and salt. Results and Figures 1โ3 detect functional full-length tagged CSA in retained material after UV, with DNase removal of DNA, nuclear-pore controls and CSB dependence. This is positive localization evidence for the experimentally defined nuclear-matrix fraction. Retain it as non-core because it describes a conditional extraction-resistant CSA pool rather than the chromatin repair-assembly location chosen for the defining adaptor activity. The experiment does not require CSA to be a permanent scaffold component and is not interpreted as a homogeneous purified matrix; those limits do not negate the observed association. Supporting Evidence: |
| GO:0016363 nuclear matrix | IDA PMID:26620705 The C-terminal Region and SUMOylation of Cockayne Syndrome G... | KEEP AS NON CORE | Summary: CSA associates with a UV- and CSB-dependent DNase-resistant nuclear fraction. Reason: PMID:26620705 Methods for CSA translocation combine soluble CSA-FLAG/HA material from human CS3BESV cells with UV-treated insoluble fractions from CSB-complemented cells. After incubation, washing and DNase I treatment, Figure 2B detects retained CSA with wild-type CSB but not the tested C-terminal CSB deletions. This positively supports a conditional nuclear-matrix-associated pool, retained as non-core alongside the defined chromatin repair assembly. It does not establish permanent structural membership, direct CSAโDNA binding, or equivalent localization of the shorter natural product. Supporting Evidence: |
| GO:0016363 nuclear matrix | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: The nuclear-matrix mapping is supported for a conditional extraction-defined CSA pool. Reason: The official SL-0181 mapping to GO:0016363 cites PMID:26620705. Its CSA-translocation Methods and Results/Figure 2B use human CSA-FLAG/HA soluble material, UV-treated CSB-complemented insoluble fractions, DNase I digestion and anti-HA detection. Retention occurs with wild-type CSB and is lost with the tested CSB C-terminal deletions. Preserve that positive source-specific localization as non-core: it represents an experimentally conditioned nuclear pool, not the sole location of the molecular adaptor activity. A permanent scaffold role or homogeneous matrix preparation is not inferred. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB-SubCell:SL-0181 SUPPORTS TRANSFER The source mapping and cited human DNase-resistant fractionation assay agree; extraction and UV dependence are explicit. |
| GO:0016567 protein ubiquitination | IDA PMID:34526721 Structural basis of human transcription-DNA repair coupling. | ACCEPT | Summary: CSA contributes substrate positioning to CRL4-dependent protein ubiquitination. Reason: PMID:34526721 Results Figure 3 and Methods for in vitro ubiquitylation and mass spectrometry show a reconstituted CSAโDDB1โCUL4AโRBX1 assembly modifying Pol II and associated repair proteins; RPB1 K1268 is the most prominent measured RPB1 site in that reaction. CSA provides recruitment/positioning within the ligase rather than ubiquitin-transfer chemistry independently of the RING/E2 machinery. The preparation uses full-length human CSA and other human repair factors, mouse RBX1 and pig Pol II. The E2โdonor ubiquitin placement in the structural figure was modeled and is not represented here as observed catalytic transfer. Supporting Evidence: |
| GO:0016567 protein ubiquitination | IEA GO_REF:0000041 | ACCEPT | Summary: CSA participates in protein ubiquitination through substrate recognition within CRL4CSA. Reason: The official Q13216 pathway comment explicitly cites PMID:12732143, PMID:16751180 and PMID:34526721 and links UPA00143 to protein ubiquitination. The separately retrieved legacy UniPathway webpage is not treated as an operative assay. PMID:34526721 Results/Figure 3a and ubiquitylation Methods directly reconstitute ubiquitination using full-length human CSA in CRL4CSA, with mouse RBX1 and pig Pol II. The broad process is retained because the system supports both substrate-site ubiquitination of RPB1/UVSSA and polyubiquitination of CSB; narrowing every such assertion to chain formation would omit the former scope. CSA provides substrate-recognition/assembly activity rather than independent ubiquitin-transfer chemistry. The natural 205-residue product is not established as equivalent. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniPathway:UPA00143 SUPPORTS TRANSFER The official target pathway source and direct human-CSA-containing reconstitution support participation; distinct ubiquitination forms justify the broader process. |
| GO:0031464 Cul4A-RING E3 ubiquitin ligase complex | IBA GO_REF:0000033 | ACCEPT | Summary: CSA is the substrate-recognition component of a Cul4A-RING ligase assembly. Reason: PTHR46202 places human leaf PTN002504689 below PTN000523156; the aligned target is an exact 396-residue match to Q13216. All six asserted IBD records occur on that ancestry, without a target-path NOT. The fungal Cul4A-complex loss is on a different descendant branch. Human self-WITH support is legitimate experimental grounding, not circular transfer. PMID:34526721 Methods explicitly coexpresses full-length human CSA, DDB1 and CUL4A with mouse RBX1; Figure 3 and its structural analysis resolve the CRL4CSA assembly and substrate-dependent positioning. CSA is not itself the RING catalytic core. The current GO:0031464 definition explicitly permits an adaptor conferring substrate specificity. The targetโs own human experimental grounding supports this placement even though a separate fungal descendant has a curated loss of this Cul4A-specific complex assertion. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000523156 SUPPORTS TRANSFER The human target inherits the positive IBD and is experimentally present in the Cul4A complex; the fungal NOT is not on its ancestry. |
| GO:0031464 Cul4A-RING E3 ubiquitin ligase complex | IDA PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | ACCEPT | Summary: CSA is the substrate-recognition component of a CUL4AโDDB1โROC1 ligase complex. Reason: PMID:12732143 Figure 1 and tandem-affinity purification/identification Methods recover human CSA with DDB1, CUL4A and ROC1/RBX1, together with COP9 signalosome components. Figure 4 shows ubiquitin-ligase activity after CSN depletion and inhibition upon CSN addition. The membership assertion is supported by the actual composition, while ubiquitin transfer belongs to the assembled ligase rather than CSA alone. Tagged CSA function was checked by complementation; the short natural product was not separately tested. Supporting Evidence: |
| GO:0031464 Cul4A-RING E3 ubiquitin ligase complex | IPI PMID:22118460 The molecular basis of CRL4DDB2/CSA ubiquitin ligase archite... | ACCEPT | Summary: CSA forms a DDB1-bound substrate receptor in a CUL4A ligase. Reason: PMID:22118460 Figure 6 resolves human DDB1 with CSA produced from the full-length human construct (CSA residues 364โ396 lack resolved density), and Figure 7A is explicitly a CRL4AโCSA ubiquitination assay. The associated protein-production and ubiquitination procedures define human CSA/DDB1 and the CUL4A-containing preparation. The CSA signal and Results identify the assay despite a DDB2 wording inconsistency in one caption. These actual observations support CUL4A-complex membership; the paperโs separate DDB2/CAND1 CUL4B preparations are not evidence for CSAโCUL4B. Supporting Evidence: |
| GO:0031465 Cul4B-RING E3 ubiquitin ligase complex | NAS PMID:22118460 The molecular basis of CRL4DDB2/CSA ubiquitin ligase archite... | UNDECIDED | Summary: The inspected original establishes DDB1โCSA and CRL4AโCSA; CSA membership in a Cul4B complex remains unresolved. Reason: GO:0031465 specifically requires a Cul4B-containing catalytic core. In PMID:22118460, Figure 6 and the structure Methods describe human DDB1โCSA, and the Figure 7A ubiquitination assay is explicitly labeled CRL4AโCSA. The inspected Cul4B constructs and structures concern DDB2 or CAND1. The shared DCAF architecture makes a CSAโCul4B assembly plausible, but these particular observations do not establish it. Keep the specific assertion unresolved; this is not evidence that CSA cannot associate with Cul4B. Operative locators: DOI 10.1016/j.cell.2011.10.035, Results and Figures 6โ7; the author thesis reproduction, chapter 2, Figures 6โ7 and Supplementary Experimental Procedures. Supporting Evidence: |
| GO:0032991 protein-containing complex | IDA PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | MODIFY | Summary: The identified CSA complex can be named more specifically as a CUL4A-RING ligase. Reason: PMID:12732143 identifies DDB1, CUL4A and ROC1/RBX1 in the purified human CSA complex and tests its ubiquitin-ligase activity in Figures 1 and 4. Protein-containing complex is correct but unnecessarily broad for this resolved assembly. Refine to Cul4A-RING E3 ubiquitin ligase complex, retaining CSA as a substrate-recognition subunit rather than assigning it the RING catalytic function. COP9 coassociation does not make CSA a structural subunit of the COP9 signalosome. Proposed replacements: Cul4A-RING E3 ubiquitin ligase complex Supporting Evidence: |
| GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: CSA directs CSB ubiquitination and subsequent proteasomal degradation after UV exposure. Reason: PTHR46202 places human leaf PTN002504689 below PTN000523156; the aligned target is an exact 396-residue match to Q13216. All six asserted IBD records occur on that ancestry, without a target-path NOT. The fungal Cul4A-complex loss is on a different descendant branch. Human self-WITH support is legitimate experimental grounding, not circular transfer. PMID:16751180 Results and Figure 2 show loss of CSB four hours after UV in human fibroblasts, its prevention by MG132, failure in CSA-deficient cells and restoration by myc-CSA. Figure 3 and reconstitution Methods connect this outcome to CSA-dependent substrate recognition: the CSA complex polyubiquitinates CSB with E1/E2/ubiquitin, whereas an active DDB2 complex does not substitute. This establishes CSA participation in substrate targeting, not protease activity. The original notes cell-line-dependent disagreement with earlier work; no universal requirement is asserted. Original operative text and captions were recovered through the official PMC search rendering; no figure pixels or supplements were inspected. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000523156 SUPPORTS TRANSFER Valid target ancestry and positive human substrate-targeting/degradation experiments support the process; CSA supplies recognition rather than proteolysis. |
| GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process | IDA PMID:16751180 CSA-dependent degradation of CSB by the ubiquitin-proteasome... | ACCEPT | Summary: CSA directs CSB toward ubiquitination and proteasomal degradation after UV. Reason: PMID:16751180 Results and Figure 2 compare human CSA-deficient fibroblasts and myc-CSA complementation, showing CSA-dependent loss of CSB after UV that is prevented by MG132. Figure 3 and the recovered reconstitution Methods show CSB polyubiquitination by CSAโDDB1โCUL4AโROC1 with E1, E2 and ubiquitin; omission controls and an active DDB2 complex distinguish CSA-dependent substrate recognition. CSA therefore performs targeting work in this degradation process and is not merely a substrate or a protease. The article notes differences from earlier cell-line observations; no universal degradation requirement is claimed. Original text and captions were recovered, but figure pixels and separate supplements were not read. Supporting Evidence: |
| GO:0043204 perikaryon | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Rat neuronal soma staining supports a contextual perikaryon location. Reason: The exact rat donor G3V7B8/ENSRNOP00000013598 carries direct PMID:22900489 annotations. The original Methods pp. 758โ760 and Results/Figures 3โ8 pp. 761โ764 use male Long-Evans rats, anti-CSA sc-25369 at 1:100, omission controls and blinded neuronal-pattern scoring. The study distinguishes diffuse, cytoplasmic, nuclear and perinuclear staining; it does not assay human CSA or resolve isoforms. Figures 3โ5 show CSA signal in spiral-ganglion neuronal cytoplasm and perinuclear regions; current GO:0043204 means the neuronal soma excluding its nucleus. This is positive donor support for the location, not an inference from expression in whole cochlea. Retain the orthology-based localization as non-core, with the distinction that human HPA cytosol staining supports a cytoplasmic pool but does not independently establish a human neuronal perikaryon assay. The observations do not resolve natural products or establish a cytoplasmic repair mechanism. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:G3V7B8 SUPPORTS TRANSFER Rat CSA soma localization is directly observed; transfer is contextual and does not claim an equivalent human neuronal experiment. |
| GO:0051865 protein autoubiquitination | IDA PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | UNDECIDED | Summary: CSA modification in CRL4AโCSA is established, but its mechanistic contribution to its own ubiquitination remains unresolved. Reason: GO:0051865 includes a protein acting in ubiquitination of itself or an identical protein. PMID:12732143 Figure 4A and ubiquitin-ligase Results describe Cul4A autoubiquitination by the CSN-depleted CSA complex. Independent PMID:22118460 Figure 7A, Results and experimental procedures directly show ubiquitinated CSA in recombinant CRL4AโCSA, with E2, CSN and CSB controls. CSA is a functional ligase adaptor as well as the modified protein in that preparation, so these observations are compatible with an active contribution to its own modification. They do not discriminate such self-targeting or positioning from modification of an accessible ligase-associated CSA molecule without a CSA-specific adaptor step. Retain UNDECIDED because this mechanistic alternative remains unresolved, not because substrate status rules participation out or because CSA must itself catalyze ubiquitin transfer. Original locators: DOI 10.1016/S0092-8674(03)00316-7, Figure 4A; DOI 10.1016/j.cell.2011.10.035, Figure 7A and supplementary experimental procedures. |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | IDA PMID:32355176 The cooperative action of CSB, CSA, and UVSSA target TFIIH t... | MODIFY | Summary: CSA is a component of the CUL4โDDB1โRBX1 ubiquitin ligase assembled at stalled polymerase. Reason: PMID:32355176 Results Figure 1 recovers endogenous CSA together with DDB1, CUL4 and RBX1 in UV-induced human RNAPII complexes, and CSA loss prevents DDB1 recruitment. These observations support complex membership. The separate purified ligase experiment in Figure 3 and Methods uses Xenopus laevis CSA/DDB1/CUL4A/RBX1, so it is supporting conservation rather than a mislabeled human reconstitution. No autonomous CSA RING-catalytic activity or activity of the short natural product is inferred. Refine the broad Cul4 complex term to its experimentally defined CUL4A assembly: PMID:34526721 protein-expression and complex-formation Methods explicitly use full-length human CSA, DDB1 and CUL4A with mouse RBX1. This independent human-CSA evidence preserves the separate Xenopus preparation in the 2020 study and does not establish or exclude CSAโCUL4B assembly. Proposed replacements: Cul4A-RING E3 ubiquitin ligase complex |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | IDA PMID:34526721 Structural basis of human transcription-DNA repair coupling. | MODIFY | Summary: Full-length human CSA forms the substrate-recruiting subunit of the reconstituted CRL4 complex. Reason: PMID:34526721 Results Figure 3 and protein-expression/complex-formation Methods directly assemble CSAโDDB1โCUL4AโRBX1 with the stalled-Pol-II repair system. CSA is human and full length, RBX1 is mouse, and the polymerase preparation is from pig thymus. The defined assembly and biochemical activity support membership in the Cul4-RING E3 ligase complex. Modeling of the flexible RING/E2 region does not undermine membership but is not treated as direct observation of every catalytic contact; no equivalence is assigned to the 205-residue product. Refine the broad Cul4 complex term to its experimentally defined CUL4A assembly: PMID:34526721 protein-expression and complex-formation Methods explicitly use full-length human CSA, DDB1 and CUL4A with mouse RBX1. This independent human-CSA evidence preserves the separate Xenopus preparation in the 2020 study and does not establish or exclude CSAโCUL4B assembly. Proposed replacements: Cul4A-RING E3 ubiquitin ligase complex Supporting Evidence: |
| GO:0080008 Cul4-RING E3 ubiquitin ligase complex | IMP PMID:16949367 A family of diverse Cul4-Ddb1-interacting proteins includes ... | MODIFY | Summary: CSA is a DDB1-associated subunit of a CUL4-RING ligase. Reason: PMID:16949367 actual Results and Figures 1โ2 captions identify CSA among human DDB1-associated DCAFs, recover its association with CUL4A, and test CSA DDB1-binding interface mutations. The current Cul4-RING complex term includes the CUL4A assembly, whose composition is independently established in PMID:12732143. Refine the broad complex term to the experimentally supported CUL4A assembly, without assigning Cdt2-dependent replication phenotypes to CSA. Supplemental panels and full Experimental Procedures from the 2006 paper remain uninspected, so the broader source term is not taken to demonstrate that a CSAโCUL4B assembly was independently demonstrated. Proposed replacements: Cul4A-RING E3 ubiquitin ligase complex |
| GO:0090262 regulation of transcription-coupled nucleotide-excision repair | IMP PMID:17297471 The role of CSA in the response to oxidative DNA damage in h... | MODIFY | Summary: CSA is directly supported as a participant in transcription-coupled nucleotide-excision repair. Reason: The original PMID:17297471 human patient/complementation experiments quantify genome-wide oxidative-lesion removal using LC-MS/HPLC and an oligonucleotide-incision readout (Figures 2โ6 and Methods). Its Discussion distinguishes the genome-wide findings from the established TCR defect and proposes, rather than directly assays, a chromatin-accessibility mechanism. These results do not by themselves identify modulation specifically of TC-NER. Independent PMID:32355176 demonstrates the positive alternative role: human CSA recruits the CRL4/UVSSA assembly at stalled RNAPII, supports TFIIH recruitment with knockout/complementation controls, and its knockout loses transcribed-strand CPD repair bias in XR-seq. The CSA-knockout XR-seq was one experiment; the recruitment/rescue evidence is separate corroboration. MODIFY to GO:0006283 records that directly established repair participation. This is a lateral role correction, not an ontology-child refinement or a claim that a repair participant can never also regulate repair. The original IMP reference and its oxidative-damage scope remain preserved. Proposed replacements: transcription-coupled nucleotide-excision repair |
| GO:0090734 site of DNA damage | IDA PMID:32355176 The cooperative action of CSB, CSA, and UVSSA target TFIIH t... | ACCEPT | Summary: CSA accumulates in repair assemblies at DNA-lesion-stalled RNA polymerase II. Reason: PMID:32355176 Results Figure 1 and the CPD slot-blot/ chromatin-immunoprecipitation Methods establish UV-induced CSA association with stalled RNAPII complexes whose associated DNA is enriched for cyclobutane pyrimidine dimers. CSB-dependent CSA recruitment and downstream UVSSA/TFIIH assembly provide mechanistic corroboration. This supports activity at DNA-damage sites, without claiming that CSA-GFP was directly imaged at a laser track, that CSA directly recognizes the lesion, or that the artificial LacO array itself contained DNA damage. Supporting Evidence: |
| GO:0097680 double-strand break repair via classical nonhomologous end joining | IDA PMID:29545921 CSA and CSB play a role in the response to DNA breaks. | UNDECIDED | Summary: DNA-break response evidence does not yet establish CSA participation specifically in classical end joining. Reason: GO:0097680 specifies classical nonhomologous end joining, characterized by its KU/XRCC4/ligase IV/DNA-PK machinery. PMID:29545921 reports persistent ฮณH2AX/53BP1-associated damage signaling after 3 Gy irradiation, including G1 cells, and interprets this as consistent with an NHEJ defect. However, its 10 Gy neutral-comet assay finds no significant repair-kinetic difference between CSA-deficient and complemented cells. These doses and readouts differ, so the latter does not establish absence of a CSA role. The inspected main text does not resolve classical versus alternative end joining; the detailed supplement remains inaccessible after failed retrievals. Retain the IDA assertion as unresolved, without dismissing the positive damage-response observations. Locators: DOI 10.18632/oncotarget.24342, Results and Figures 4โ5, Discussion, neutral-comet and immunostaining Methods. Supporting Evidence: |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: CSA supplies ubiquitin-ligase substrate recognition and recruitment. Reason: PTHR46202 places human leaf PTN002504689 below PTN000523156; the aligned target is an exact 396-residue match to Q13216. All six asserted IBD records occur on that ancestry, without a target-path NOT. The fungal Cul4A-complex loss is on a different descendant branch. Human self-WITH support is legitimate experimental grounding, not circular transfer. GO:1990756 describes bringing a ubiquitin-like ligase together with its substrate. Human cell experiments in PMID:32355176 Figure 1h demonstrate CSA-dependent DDB1/CRL4 recruitment to stalled RNAPII; Figures 2โ3 map the CSBโCSA recruitment interface. PMID:34526721 Figures 1 and 3 place full-length human CSA between CSB/UVSSA and DDB1โCUL4A and directly assay substrate ubiquitination. This is a specific recognition/assembly role, not an inference that every physical interaction is an adaptor. The E2โubiquitin geometry is modeled, mouse RBX1 and pig Pol II are used in reconstitution, and no function is assigned by analogy to the 205-residue product. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000523156 SUPPORTS TRANSFER Verified substrate-adaptor IBD and independent human recruitment/interface evidence support this molecular function. |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:12732143 The ubiquitin ligase activity in the DDB2 and CSA complexes ... | ACCEPT | Summary: CSA brings the ubiquitin ligase together with repair-associated substrates. Reason: PMID:12732143 establishes the CSAโDDB1โCUL4AโROC1 assembly and ligase activity. Independent PMID:16751180 directly links the CSA rather than DDB2 complex to CSB substrate polyubiquitination, and PMID:34526721 places full-length human CSA between substrate-associated repair factors and DDB1โCUL4A in a reconstituted repair complex. This supports the binding/recruitment work named by ubiquitin-like ligase-substrate adaptor activity. CSA does not need to be the RING/E2 catalyst to perform this step; conversely, not every generic interaction is treated as evidence for adaptor activity. The mixed-species reconstitution and untested short natural product remain separate. |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:32142649 Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcr... | ACCEPT | Summary: CSA brings the CUL4 ligase into the stalled-polymerase repair assembly. Reason: PMID:32142649 Results and Figures 2D/S2/S3A show that loss of human CSA reduces UV-induced RNAPII ubiquitination and blocks TFIIH recruitment. Its Discussion appropriately calls CRL4CSA a strong candidate for the observed RPB1 modification; those loss-of-function data alone do not define every direct catalytic contact. Independently, PMID:34526721 assembles full-length human CSA with DDB1โCUL4AโRBX1 and the polymerase repair substrate, and PMID:38316879 resolves CSA-dependent docking and the CSAโUVSSA interface with cellular mutant tests. Together these establish the ligaseโsubstrate recruitment role named by GO:1990756, without assigning RING/E2 chemistry to CSA or relying on inaccessible STAR Methods from the 2020 manuscript. |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:34526721 Structural basis of human transcription-DNA repair coupling. | ACCEPT | Summary: CSA recruits and positions the ubiquitin ligase relative to its repair substrates. Reason: PMID:34526721 Results Figures 1โ3 and reconstitution Methods show full-length human CSA binding DDB1 and engaging CSB/UVSSA in the Pol II repair assembly, bringing CUL4AโRBX1 near substrate proteins and enabling complex-dependent ubiquitination. This is the binding/recruitment work of a ubiquitin-like ligaseโsubstrate adaptor. CSA need not directly contact every acceptor lysine to organize this assembly, and the annotation does not assign it the RING/E2 catalytic mechanism. The mouse RBX1/pig Pol II components and modeled E2โubiquitin position are retained as assay boundaries. Supporting Evidence: |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:38316879 Structural basis for RNA polymerase II ubiquitylation and in... | ACCEPT | Summary: CSA is the ligase adaptor docked by ELOF1 and stabilized by UVSSA at Pol II. Reason: PMID:38316879 Results Figures 1โ5 and Methods for reconstitution, GFP-CSA complementation and RNA-synthesis recovery define CSAโs contacts with ELOF1/UVSSA and the positioning of CRL4 relative to Pol II. The human CSA Y334A mutant disrupts productive CSAโUVSSA coupling and impairs cellular repair readouts. These are structural and functional tests of CSAโs own adaptor role, not a transfer of ELOF1, CSB ATPase or RBX1 activity to CSA. The stable E2โubiquitin proxy experiment yielded a dissociated ligase subcomplex; superposition onto the Pol II assembly is a model, not an observed complete transfer intermediate. The short natural CSA product is untested. Supporting Evidence: |
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Download this section (compressed HTML)Q: Does the 205-residue CSA product accumulate endogenously and assemble a functional DDB1โCUL4A substrate-adaptor complex, or does it have a different molecular role?
Q: Does CSA actively recruit or position a CSA molecule for its own ubiquitination, and how does that event relate to repair-complex assembly and turnover?
Q: Does CSA contribute directly to classical nonhomologous end joining under defined conditions, and how can this be separated from its effects on DNA-damage signaling?
Experiment: First establish endogenous abundance of each product using product-specific transcript analysis and proteotypic peptides. Compare the 396- and 205-residue products at matched near-endogenous expression in CSA-null human cells, measuring DDB1/CUL4A assembly, recruitment to stalled polymerase, RPB1 ubiquitination and strand-specific excision repair. Include full-length rescue, empty-vector and expression/stability controls.
Hypothesis: The two natural CSA products differ in stable ligase assembly and repair activity.
Type: Product-resolved expression, complex assembly and repair complementation
Experiment: Reconstitute CRL4CSA with separately distinguishable ligase-bound and candidate substrate CSA molecules. Combine CSA interface mutants with verified folding and complex-assembly controls, map modified lysines and quantify ubiquitin transfer to each CSA species alongside RPB1 and CSB substrates. Compare substrate recruitment with modification to determine whether CSA supplies a specific adaptor step in its own ubiquitination.
Hypothesis: CSA ubiquitination can be distinguished mechanistically from passive modification of CSA as a nearby substrate.
Type: Defined-complex reconstitution and ubiquitination-site mapping
Experiment: Use acute CSA depletion and wild-type rescue in cell-cycle-matched human cells. Measure a defined end-joining reporter and repair-junction sequences with KU/LIG4 perturbations as pathway controls, alongside physical break-resolution and gamma-H2AX/53BP1 signaling time courses. A repair-specific change should be separated from altered signaling, viability or cell-cycle distribution before assigning a direct end-joining mechanism.
Hypothesis: A CSA-dependent double-strand-break phenotype may reflect signaling rather than direct classical end-joining work.
Type: Pathway-controlled end-joining and damage-signaling assays
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