ERCC8/CSA is represented by the source-described 396-residue Q13216-1 and 205-residue Q13216-2 products. Full-length repair-complex experiments are not evidence of equivalent short-product function. The following sections document actual primary reads, original access limits and curated database chains. Normal source caches remain unchanged.
These sources support database-origin annotations. Protein products, assay species, modeled participant roles and actual reading limits are distinguished below.
Original publication · Recovered original PDF
Methods pp. 758–761: animals, noise exposure, immunolabeling and analysis; complete operative Results pp. 761–764; Figures 3–8 captions and actual page 761–763 pixels.
Male Long-Evans rats, control 5/noise 5/CAE 3/combined 3; noise 105 dB for 4 h; sc-25369 anti-CSA 1:100, primary-antibody omission controls, blinded count of neuronal staining patterns. CSA cytoplasmic/perinuclear soma staining; significant control-vs-noise perinuclear change on p. 764/Figure 8.
Limits: No human localization, CSA-selective perturbation, hearing-protection rescue or isoform-specific antibody validation. Other figures were read as captions/text only, and no supplements were read.
Abstract and visible publisher Animals/Impaired cochlear function/Discussion snippets; no full original Methods/Results or figure pixels.
Abstract explicitly describes rats, noise exposure and regional CSA redistribution.
Limits: Do not treat preview as full original verification. Main full_text_unavailable true; independent PMID:22900489 supports the conserved broad response scope.
Indexed Methods 16–33; Results 36–46,52–76; Discussion 79–81; operative Figure 2/4–7 captions. No figure pixels or separate supplements read.
S.pombe Ckn1/Ddb1 co-IP and recombinant heterodimer; strand-specific CPD-removal defects with ckn1 deletion and DDB-box mutations, Figures 6–7. Figure 5B also uses human CSA in heterologous insect-cell DDB1 competition/co-IP, distinct from yeast repair experiments.
Limits: Yeast Rhp26 ubiquitination persisted without ckn1 (main text reporting supplementary experiment); do not transfer every human substrate relationship to all family branches. Supplementary constructs/raw blots not independently inspected.
Saved indexed lines 112–136 (selected nonduplicated Results/Figures 1–3),166–174 (TFIIH recruitment/XR-seq Results),298–318 (tethering/XR-seq/recombinant Methods).
Human U2OS CSA-dependent DDB1/CRL4 and TFIIH recruitment to UV-stalled RNAPII; CSA-GFP chromosomal tether recruitment through CSB. CSA-KO loses transcribed-strand bias in XR-seq main report; CSA-KO XR-seq performed once.
Limits: Recombinant ligase in Figure 3 is Xenopus CRL4CSA, including when substrate CSB is human; not a human ligase assay. No images/supplement independently read by this lane.
Indexed Results 81/83/89/91/115/119/125/129; Methods 145/147/149/153/163/175/177/187.
Full-length human CSA/DDB1/CUL4A with mouse RBX1, pig Pol II; CSA bridge between CSB and UVSSA, CSA-containing ligase substrate positioning, CSB polyubiquitination and RPB1 site ubiquitylation Figure 3.
Limits: The E2–ubiquitin complex/RBX1 geometry includes modeling, not a fully directly observed transfer intermediate. No figure pixels/supplement read here. No 205-aa equivalence.
Normal main lines 101/113/119/133 and relevant Discussion 165.
Human CSA-FLAG/HA source soluble fraction added to UV-treated CSB-cell insoluble fraction, DNaseI treatment and antiHA blot; Figure 2B detects retained CSA with WT CSB but not tested deletions.
Limits: Operational extraction-resistant nuclear-matrix fraction; no pure-matrix composition, permanent scaffold role or 205-aa assignment.
Results on UV-dependent CSB loss and CSA rescue, Figure 2 caption, recombinant-CSB ubiquitination Results and Materials and methods: Cells; Reconstitution of DDB2/CSA E3 complexes; In vitro ubiquitin ligase assay.
Human CSA-deficient/myc-CSA-rescued fibroblasts and MG132 distinguish CSA-dependent proteasomal CSB loss. Recombinant CSA complex, E1/E2/ubiquitin omission controls and active DDB2 comparator support substrate recognition.
Limits: The study notes historical cell-line discordance. CSA is not a protease. No figure pixels or supplements read; no short-product or universal degradation assertion.
PAINT: PTHR46202 tree, MSA and current IBD source. Human PTN002504689 descends PTN000523156; 396-aa sequence exact. Six positive assertions, no target-path NOT. A fungal Cul4A loss is on another descendant branch, not a human negative.
Reactome: CSA entity 52835 is human Q13216, residues 1–396, nucleoplasm. DCAF set 976118 explicitly includes it. The nineteen source roots all have forward participant paths to this entity. Location does not transfer a neighboring reaction’s chemistry to CSA.
Electronic sources: InterPro IPR042238 maps the actual target family to TC-NER. ARBA00028103 matches condition set 21: FunFam 2.130.10.10:FF:000130 plus Mammalia. UniProt Q13216 carries the source location and UPA00143 pathway statements with their publication provenance.
HPA: ERCC8 subcellular record and official XML, antibody HPA029328. Approved ICC/IF reports nuclear speckles in A-549/MCF-7 and cytosol in A-549. Antigen 28–166 is shared with the short product; no isoform-specific location is inferred. Images were not independently inspected.
Products: Q13216-1 is 396aa; Q13216-2 is 205aa after the source VSP013914/013915 edits. The PAINT match, Reactome 1–396 entity and full-length human recombinant experiments do not establish functional equivalence of the short product.
These five originals support CSA recruitment, Cul4 ligase membership and the adaptor step in transcription-coupled nucleotide-excision repair. The molecular observations do not establish equivalent activity of the 205-residue natural product. The full-length human CSA reconstitution is distinguished from Xenopus ligase, pig polymerase and mouse RBX1 components. No new annotations or publication quotations are proposed.
Original DOI; accessible original.
Operative locations. Results Figures 1–7; Methods: Cell culture, plasmids, chromatin immunoprecipitation, slot blot, immunofluorescence, XR-seq, protein purification and in vitro ubiquitylation.
Human U2OS endogenous/CSA-GFP nuclear chromatin recruitment and TFIIH assembly; CSA-knockout XR-seq is one experiment. Purified ligase CSA/DDB1/CUL4A/RBX1 is Xenopus laevis; human and Xenopus CSB are distinguished. Detailed CSA coding bounds are not independently supplied in the inspected main Methods.
Access and reading limit. Main text and captions read; no figure pixels or separate supplementary datasets inspected.
Original DOI; accessible original.
Operative locations. Author manuscript Results (RNAPII ubiquitination, cullin dependence, TFIIH recruitment, strand-specific ChIP-seq); Discussion; Figures 1–3/S2/S3 captions.
Human HeLa/HEK293 CSA-deletion controls reduce RPB1 ubiquitination and abolish UV-induced TFIIH recruitment. Main RPB1 lysine and UVSSA mutants and mouse RPB1/Xpa disease models are separate experiments. CRL4CSA called a strong candidate in Discussion; no purified CSA reconstitution claimed here.
Access and reading limit. Main Results/Discussion and selected operative main/supplementary captions recovered/read. STAR Methods are referenced but absent from this searchable repository PDF; repository lists only this PDF and publisher request returned 403. No figure pixels inspected. Detailed extraction/clone specifications beyond Results/captions remain unverified.
Original DOI; accessible original.
Operative locations. Results Figures 1–3 and extended captions; Methods: protein expression, purification, RNA extension, ubiquitylation, ATPase assay, crosslinking/MS, complex formation and model building.
Full-length human CSA, CSB, DDB1, CUL4A and UVSSA; mouse RBX1; pig-thymus Pol II; recombinant repair factors expressed in insect cells. CSA recruits/stimulates CSB but is not the ATPase. Pol II and repair-factor ubiquitination directly assayed; flexible RING and E2–donor ubiquitin position modeled.
Access and reading limit. Main text and captions read; no figure pixels, deposited maps or separate supplementary tables independently inspected.
Original DOI; accessible original.
Operative locations. Results Figures 1–5 (especially CSA Y334A Figure 4); Methods protein preparation, complex formation, ubiquitylation, cells, CSA constructs/complementation, RRS and chromatin IP.
Human CSA Y334A versus wild-type complementation in CSA-knockout RPE1; UV RRS and trabectedin-associated gamma-H2AX incision proxy. Reconstitution inherits full human CSA/mouse RBX1 and pig Pol II. ATPase-deficient CSB used in some complex/ubiquitylation reactions. Stable E2 C85K–Ub proxy generated a dissociated ligase subcomplex; complete transfer geometry is inferred by superposition.
Access and reading limit. Listed main blocks/captions read; no independent figure-pixel, cryo-EM map or supplementary-dataset inspection; unlisted blocks not claimed read.
Original DOI; accessible original.
Operative locations. Results Figures 1–5 (especially CSA-deficient UVC recovery Figure 5b); Discussion; Methods cells, screens, viability, RNAPII IP, Dsk2, RPB1 degradation, RRS/EU detection and NER excision assay.
Human CSA-knockout RPE1 UVC positive control supports the existing TC-NER process. Formaldehyde/DNMT1 cross-link repair is explicitly a distinct pathway, not canonical NER; CSA/CSB upstream contributions do not identify the downstream protease. CSB ATPase complementation is not a CSA ATPase assay.
Access and reading limit. Listed main text/captions read; no separate Supplementary Table 5 cell inventory or other supplementary datasets/figure pixels inspected; exact short-product behavior not tested.
Current official QuickGO definitions were retrieved for every source term and the chromatin/nucleoplasm alternatives. Chromatin is the organized DNA–protein material forming a chromosome; the actual human chromatin recruitment experiments support refinement of chromosome to chromatin. Nucleoplasm excludes chromosomes and the nucleolus, so chromatin association alone is not used to assert that finer location. A separate whole-gene source can support that refinement.
CSA brings ligase components and substrate-associated repair factors together. This satisfies adaptor activity without attributing CSB motor chemistry or RBX/E2 ubiquitin transfer to CSA. The 2024 DNA–protein cross-link study contains a CSA-specific UV control and explicitly distinguishes its cross-link pathway from TC-NER. No new cross-link-process assertion is introduced.
The following read scopes distinguish recovered originals, supplementary material and remaining access limitations. No source-cache text was rewritten and no publication quotation was added. CSA substrate recognition is distinguished from ubiquitin-transfer catalysis, and the 396-residue experiments do not demonstrate equivalent function of the 205-residue product.
Recovered original or supplement.
MMS alkaline-comet delay supports contextual SSBR contribution. 3-Gy signaling and 10-Gy neutral-comet DSB results differ; classical end-joining specificity unresolved. Main text’s supplementary claims are not counted as independent supplementary reads.
Main Results and Figures 1–5 captions; Discussion; alkaline/neutral-comet and immunostaining Methods.
Reading limit. Main original text and captions only. Detailed supplement retrievals failed and were retained as failed receipts; no supplemental rescue or pathway experiment independently verified.
Recovered original or supplement.
Human functional FLAG/HA-CSA, DDB1/CUL4A/ROC1/COP9 assembly; CSN-dependent polyubiquitination/CUL4A self-modification. Actual Figures 1 and 4 pixels read. No CSA-specific autoubiquitination mechanism established.
Figures 1 and 4; Results on complex purification, cellular complementation and ubiquitin-ligase regulation; protein-purification and ubiquitination Methods.
Reading limit. Only listed sections/captions and Figures1/4 pixels; no separate supplementary material.
Recovered original or supplement.
Human CSA 1–396 and DDB1 1–1140, DDB1–CSA structure, CRL4A–CSA ubiquitination with CSN/CSB controls; CSA-Ub and CSB-Ub distinguished. Actual Figures 6 and 7 pixels read. DDB2/CAND1 CUL4B preparations do not establish CSA–CUL4B.
Chapter 2 of the author thesis: narrative Results printed pp. 47–49, Figures 6–7 printed pp. 68–69 (physical PDF pp. 69–70), and supplementary procedures printed pp. 88–94.
Reading limit. Published2011 paper chapter2 identified by title/authors/journal metadata. Only listed primary chapter and its supplementary procedures; not entire thesis. Fig7caption contains DDB2 label inconsistency; actualCSA blot, Results and CRL4A-CSA header identify CSA assay.
Recovered original or supplement.
Reciprocal GST-CSA/XAB2 binding and human HA-CSA co-IP; functional tagged CSA rescue. No figure pixels read.
Methods for human tagged-CSA cells and recombinant binding; CSA/XAB2 interaction Results and Figure 4 caption.
Reading limit. Actual CSA reciprocalGST pull-down and humanHA-CSA co-IP Methods/Results/Fig4caption, no pixels or separate supplement.
Recovered original or supplement.
Actual publisher Results/Figures 1–2 captions: human 293T DDB1/CUL4A association, CSA K174A/R217A/A205P versus R218A interface effects. Cdt2 replication phenotypes are separate. Full Methods and supplemental CSA-specific CUL4B panels unread.
Publisher Results: identification/validation of DCAFs, distinct DDB1 surfaces and WDXR mutations; Figures 1–2 captions.
Reading limit. Actualpublishersearch-renderedtext; directpage/PDF failed. No fullExperimentalProcedures orsupplementS1B/S1C/S2pixels. Human293TCSA/DDB1/Cul4recruitment andCSA K174/R217/A205P mutants are explicit; Cdt2 replicationphenotypes separate.
Recovered original or supplement.
Publisher supplementary Figure S4 pixels show ERCC8 association with near-endogenous tagged UVSSA in soluble/chromatin human-cell fractions; S4–S6 captions read. Main article inaccessible; not a purified binary-binding result.
Publisher supplementary Figures S4–S6 captions; Figure S4 image on physical PDF page 5.
Reading limit. Supplement Figures4-6captions and actualFig4pixels; mainarticle inaccessible. ActualERCC8 co-IP withnearendogenousFLAGHA-UVSSA in humanKps3 soluble/chromatin fractions.
Recovered original or supplement.
Human CSA-FLAG/HA translocation into UV-treated, CSB-dependent DNase-resistant material in the cell-free assay, actual Methods/Figure 2B Results.
Methods, Analysis of Translocation of CSA; Results and Figure 2B.
Reading limit. Actual Methods113/Results133Fig2B including CS3BESV CSAFLAGHA and CSB-complemented cell-free matrix assay. No figure pixels/separate supplement. PMCID verified against genuine normal record frontmatter.
Recovered original or supplement.
Functional full-length C-terminal His6/HA-tagged human CSA, diffuse nucleoplasmic staining and damage/CSB-dependent retention after detergent/DNase/salt extraction. Hydrogen peroxide/cisplatin and UV responses distinguished from dimethyl sulfate.
Methods for CSA expression/complementation, immunostaining and sequential extraction; nuclear redistribution Results and Figures 1–5 captions.
Reading limit. Actual taggedfullCSA, detergent/DNasefractionation and imaging Methods/Results, Figures1-5caption references; no pixels or supplement.
Recovered original or supplement.
Author original bulk oxidative-lesion assays and full-length EGFP-CSA rescue. Primary versus transformed cells differ. No strand-specific regulation assay or CSA glycosylase assignment.
Author original Results, Figures 2–6 captions, Discussion and Materials and methods for human cells, EGFP-CSA complementation, bulk lesion measurements and incision assays.
Reading limit. ActualauthoruploadResults/Methods andlistedcaptions; nofigurepixels/separatesupp. Primarypatients vsSV40 differences retained. Full-lengthEGFP-CSArescue demonstrated; noCSA glycosylase assigned.
Recovered original or supplement.
CSA-deficient/myc-CSA rescue and MG132 support UV-dependent CSB degradation; reconstructed CSA ligase polyubiquitinates CSB, with active DDB2 comparison and E1/E2/ubiquitin omission controls. Historical cell-line disagreement retained.
Results and Figures 2–3 captions; Methods, Cells, Reconstitution of DDB2/CSA E3 complexes, and In vitro ubiquitin ligase assay.
Reading limit. Official PMC search-rendered operative original text/captions, not merely abstract. Direct opening encountered a challenge. No figure pixels or separate supplementary material read.
Nucleus source contexts supported by diffuse nucleoplasmic staining in PMID:11782547 and the exact human Reactome participant retain their nucleoplasm refinement. The PMID:32355176 chromatin-assembly context is separately refined to chromatin, as explained in the feedback clarification below. Broad Cul4-complex annotations are refined to CUL4A using the defined human CSA/DDB1/CUL4A preparation in PMID:34526721. The 2020 purified Xenopus ligase remains distinguished, and the separate CSA–CUL4B assertion remains unresolved.
The core represents CSA's own substrate-adaptor step in the CUL4A–DDB1–RBX1 ligase, supporting protein ubiquitination and transcription-coupled nucleotide-excision repair. The two process terms describe distinct supported outputs; they do not assign CSA the CSB motor or RING/E2 ubiquitin-transfer chemistry. The 396-residue full-length human CSA evidence does not establish equivalent activity of the 205-residue product.
PMID:32355176(https://doi.org/10.1038/s41467-020-15903-8), Results Figures 1h and 3–6 and chromatin-IP/XR-seq Methods, establishes CSA-dependent DDB1/CRL4, UVSSA and TFIIH recruitment in human U2OS cells, with loss of transcribed-strand excision bias. The CSA-KO XR-seq comparison was performed once. Its purified CRL4CSA experiment uses Xenopus proteins, separate from the human cellular evidence.
PMID:34526721(https://doi.org/10.1038/s41586-021-03906-4), Figures 1/3 and cloning, purification and ubiquitylation Methods, directly reconstitutes substrate modification with full-length human CSA and other human repair factors, mouse RBX1 and pig-thymus Pol II. The E2–ubiquitin geometry is modeled. PMID:38316879(https://doi.org/10.1038/s41594-023-01207-0), Figure 4 and corresponding cellular/reconstitution Methods, tests the human CSA Y334A interface and ELOF1/UVSSA stabilization. Trabectedin gamma-H2AX is an incision proxy. Its E2 C85K–Ub preparation yields a dissociated ligase subcomplex, and positioning on complete Pol II is inferred by superposition. Neither observation alone proves CSA performs an adaptor step in its own ubiquitination.
A separate nucleoplasmic CSA pool, rather than the revised core location, is supported by PMID:11782547(https://doi.org/10.1073/pnas.012473199), tagged-human construct/immunofluorescence Methods and printed pages 203–204: diffuse nucleoplasmic signal and foci occur after UV plus Triton extraction, while unextracted uniform nuclear signal is separately reported as data not shown. The main text reports complementation referring to unread supplementary Figure 6. No figure-pixel or separate supplementary-data inspection is claimed for this core synthesis.
The proposed end-joining experiment follows the distinction in PMID:29545921(https://doi.org/10.18632/oncotarget.24342), Figures 3–5, Discussion and neutral-comet Methods, between persistent signaling and physical break resolution. The 3-Gy signaling and 10-Gy physical assays differ; unread supplementary material and those assay limits preclude a universal negative conclusion. CUL4B membership, self-ubiquitination and classical end joining remain unresolved contexts, and no additional core or annotation is introduced for them.
The CSA adaptor core and the source-specific nucleus assertion from PMID:32355176(https://doi.org/10.1038/s41467-020-15903-8) now use chromatin. Actual human U2OS chromatin-IP and CPD slot-blot experiments (Figure 1; corresponding Methods) identify the assembly's chromatin context, complemented by CSB-dependent recruitment and TFIIH loss/rescue. Diffuse nucleoplasmic CSA and the operational nuclear-matrix pool remain distinct supported observations. This correction follows the experiment; the imported annotation relationship is not used as a biological decision rule. No direct CSA lesion-binding or damage at the artificial LacO array is inferred. The same paper's purified ligase experiments use Xenopus CSA and remain separate.
The three nuclear-matrix assertions are retained as non-core conditional localization. PMID:11782547(https://doi.org/10.1073/pnas.012473199), Methods and Figures 1–5, and PMID:26620705(https://doi.org/10.1074/jbc.M115.683235), CSA-translocation Methods and Figure 2B, establish retention under detergent/nuclease extraction with UV and CSB dependence. This is positive association evidence without a claim of permanent scaffold membership. The broad damage-response assertion remains non-core for the actually observed redistribution after multiple insults; generality alone is not the reason for that action.
The regulation-of-TC-NER assertion is corrected laterally to directly supported TC-NER participation. PMID:17297471(https://doi.org/10.1038/sj.onc.1210232) measures genome-wide oxidative-lesion removal and discusses a chromatin-access hypothesis; those experiments are not relabeled as strand-specific repair. Independent PMID:32355176(https://doi.org/10.1038/s41467-020-15903-8), Figures 1, 4–5, Results on XR-seq and associated Methods, establishes CSA's assembly contribution and loss of transcribed-strand repair bias. The CSA-knockout XR-seq was one experiment. Repair participation does not categorically exclude a separate regulatory function.
Autoubiquitination remains uncertain. PMID:12732143(https://doi.org/10.1016/S0092-8674(03)00316-7), Figure 4A, assays Cul4A modification; PMID:22118460(https://doi.org/10.1016/j.cell.2011.10.035), Figure 7A and Results/experimental procedures in the author thesis, directly shows CSA modification in recombinant CRL4A–CSA. CSA is both a functional adaptor and modified protein there. The unresolved question is its mechanistic contribution to targeting or positioning itself, rather than a presumption that being a substrate excludes participation. No new figure pixels or additional supplementary experiments were inspected for this feedback assessment.