All 139 primary contexts have been reviewed. The eleven external CSB–PGBD3 assertions are shown in the separate public table below and in linked supporting data; they are not appended as NEW annotations. This guide consolidates accepted source consultations; it does not claim new original acquisition during integration. Normal-cache bytes remain unchanged and reviewer access is distinguished from cache flags. No publication quotations were added.
The five broad canonical nucleus contexts are consistently refined to nucleoplasm using independently read human imaging. Conditional nucleolar localization remains separate; neither the nucleus refinement nor the HPA puncta establish a named nuclear-body class. The tagged fusion retains separate nucleus support and unresolved finer compartments.
Read scope. Verified publisher abstract; original main inaccessible. Independent PMID:22032989 actual Results/Figures 4–5 supplies human complex evidence.
Evidence. The original abstract explicitly reports p53–CSB binding. Independently read human reciprocal and sequential immunoprecipitation establishes CSB in a p53-containing complex, supporting the specific p53-binding annotation with the direct-binary limitation stated.
Limits. Do not claim the inaccessible original was read or infer its constructs from the independent paper.
Read scope. Verified Cell abstract/metadata only; original main unavailable after bounded routes.
Evidence. Independent human CSB CIM-dependent CSA recruitment in PMID:32355176 and biochemical/structural PMID:34526721 establish CSA association; independent PMID:9326587 directly establishes a Pol II elongation contribution.
Limits. No source-specific operative assay or wrong-gene claim from the abstract.
Actual original access route: publisher/archive/author text.
Read scope. Recovered author-upload original via ResearchGate: Methods web 168–229,344–375,406–553; Results 656–889; Figs 2–3/Table 1; Fig 4 operative text720–736. The original Methods, Results and figure-caption bounds are listed here. No pixels.
Evidence. Full-length human CSB purified from Sf21 has DNA-stimulated ATPase; anti-CSB inhibition distinguishes contaminant hypothesis. Gel shift binds90bp duplex. Labeled24mer annealed circular ssDNA is not released by CSB, with UvrD positive control; supports explicit NOT helicase in tested substrate conditions. CSB fragment528–1222 associates TFIIH and binds TFIIE p34/XPA (Fig 5); not all full-length binary affinity assays.
Limits. No universal absence across every substrate; no transfer of bacterial Mfd polymerase-displacement mechanism. Follow up Fig 5 caption for exact binding constructs.
Actual original access route: publisher/archive/author text.
Read scope. Actual PMC original recovered through indexed archive access: complete displayed Materials/Methods; Results CSB stimulates transcription elongation and RNAPII interaction; Figs 1–2 captions. No pixels.
Evidence. Actual PMC original Materials and Methods, Results CSB Stimulates Transcriptional Elongation and RNAPII interaction, and Figures 1–2 captions were read (database decoded original lines 64–104; mechanistic saved original capture). Figure 1 displays positive human-CSB stimulation of human RNAPII elongation after a 112-nucleotide U-less cassette and loss of stimulation following CSB immunodepletion. The separate promoter-independent-template result is reported as data not shown; it is not a displayed experiment inspected here. Human polymerase/factors and yeast TBP are distinguished. The polymerase-binding assay separately uses a CSB528–1222 MBP fusion fragment. No pixels, obligatory stable-complex stoichiometry or natural-fusion equivalence is claimed.
Limits. Purified elongation assay supports regulation; complex membership inferred from functional interaction and binding, not an isolated obligatory constitutive CSB-containing multisubunit elongation factor.
Original publication · PubMed · Institutional author-thesis reproduction, Elisabetta Citterio
Read scope. Original Methods and Results from the institutional author-thesis reproduction, pp. 87–90; Figures 2–5 and Table II on pp. 89–90 inspected as images. This access route is an author reproduction rather than a publisher-hosted copy.
Evidence. Full-length human N-HA/C-His6 CSB and K538R from Sf21: DNA-stimulated ATP hydrolysis, structured-DNA stimulation with M13 secondary-structure caveat, negative helicase assay with positive TFIIH control. Injected wild-type CSB restores post-UV RNA synthesis in CS1AN cells; K538R gives partial rescue.
Limits. Independent peer read, not a claim that the mechanistic review independently inspected those pixels. Nucleosomal-DNA-stimulated ATPase alone does not demonstrate chromatin remodeling.
Actual original access route: publisher/archive/author text.
Read scope. Actual OUP main Methods 119–138, Results 145–171, Discussion 173–178 and Figures 1–4 captions.
Evidence. Human CSB patient fibroblasts and complemented cells differ in whole-extract incision of 8-oxoguanine oligonucleotides and in OGG1 mRNA. CSB restoration rescues both; thymine-glycol/uracil controls distinguish substrates. The data support an effect on repair capacity and OGG1 expression but do not identify CSB as the glycosylase or establish its own step in base-excision repair.
Limits. No pixels/supplement. Regulation and participation remain distinct. The source is not the separate retracted PMID:10786832.
Read scope. Original cache Methods 101–115,135–143; Results 165/Table 1 and177. No pixels.
Evidence. Entire human CSB cDNA (WT and E646Q versus acidic-region mutants) expressed in hamster UV61 cells. CPD removal from active DHFR gene measured by T4endoV/Southern: WT and acidic mutants restore repair, E646Q does not. This is a human-protein complementation experiment in hamster host, not native-human repair kinetics.
Limits. ATPase domain requirement supports mechanistic TCR; repair readout distinct from mere survival/RNA recovery.
Actual original access route: publisher/archive/author text.
Read scope. Author-upload original Methods web 543–563; Results 802–859; Figure 5 caption 1078–1090 (original pp. 34932–34933).
Evidence. Functional HA/His-tagged human CSB in CS1AN-SV cells coimmunoprecipitates XAB2 and RNAPII; fractionation also places XAB2 and CSB in a large assembly. This is a cellular complex assay, not a purified binary XAB2–CSB experiment.
Limits. No figure pixels. Separate purified XAB2–XPA and XAB2–CSA assays are not transferred to CSB.
Read scope. Normal original cache Methods 89–129, Results 147–179, Table 2/Figs 2–6 text; no pixels.
Evidence. Purified recombinant HA/His CSB expressed in HiFive cells: DNA-stimulated ATP hydrolysis by gamma-32P TLC; direct ATPgammaS and 166bp dsDNA filter binding. E646Q lacks hydrolysis while still binding; V/VI mutants retain reduced hydrolysis/binding. CSB-ECFP in human CS1AN.S3.G2 cells shows homogeneous nuclear distribution and additional bright foci in ~20%. Damaged plasmids do not significantly increase ATPase relative to undamaged, so no direct lesion-specific sensor conclusion from this assay alone.
Limits. ATPase activity and ATP binding are separate measured properties; heterologous insect production is human protein, not insect ortholog; no isoform equivalence.
Read scope. Bounded original-access attempts: author PDF404, Cell403, Elsevier metadata-only200, FULL401, PDF406; verified abstract/metadata only.
Evidence. No operative CSB assay was recovered; its BRG1/SNF2h abstract does not establish misattribution. Independent human CSB-dependent histone eviction in PMID:29203878 resolves the biological chromatin-remodeling assertion.
Limits. Source-specific original support unverified.
Actual original access route: publisher/archive/author text.
Read scope. Actual main Results/Figures 1–3,6–8 and author-upload Methods web 378–548,667–747; Results 790–893,1499–1551,1758–1831; Figure 5 caption 1559–1660; Table 1 2006–2051.
Evidence. Purified human CSB and PARP1 interact in ELISA and immunoprecipitation assays with DNA-removal controls; CSB N-terminal fragment maps the interaction. HeLa CSB is diffusely nucleoplasmic before oxidative stress and forms PARP-dependent foci after peroxide. PARP1-mediated modification inhibits CSB ATPase; CSB does not stimulate PARP1 activity in the tested assay. Table 1 summarizes prior DNA/ATP-binding work rather than independently measuring each listed property.
Limits. No pixels. Nucleolar assignment is resolved independently by PMID:17626041 rather than asserted from this source; neither focus formation nor drug sensitivity identifies a CSB base-excision chemical step.
Actual original access route: publisher/archive/author text.
Read scope. Author-upload original Results web 1063–1169; Figure 4 caption 1174–1225 and full caption C–E; Methods 2057–2178.
Evidence. Insect-expressed full-length human CSB, reported here with N-terminal His and C-terminal HA tags, is assayed with XPG, native human Pol II/TFIIH and DNA bubbles. Purified XPG C-terminal fragment binds CSB by far-western; cooperative DNA-bubble binding and gamma-32P ATPase measurements show XPG stimulates CSB hydrolysis preferentially on bubble substrate. TFIIH-dependent polymerase remodeling in the minimal Figure 5 assay is CSB-independent.
Limits. No pixels or supplement; source-reported tag orientation retained without harmonizing it to other studies. No attribution of TFIIH helicase activity to CSB.
Actual original access route: publisher/archive/author text.
Read scope. Recovered author-upload original via ResearchGate: Methods 403–468, Results 731–763/821–859 and1075–1160, Fig 2/3 captions39–48; no pixels/supplement.
Evidence. HeLa nuclear extract B-WICH isolation co-purifies 168kDa CSB identified by mass spectrometry and antibody (Fig 2). WSTF/SNF2h/NM1 occupancy at5S and7SL genes and WSTF knockdown reduce their RNA (Fig 4), while source-specific CSB enzymatic/process contribution in PolIII activation is not itself manipulated. Supports complex membership; do not equate WSTF silencing with selective CSB perturbation.
Limits. Core WSTF-SNF2h-NM1 versus larger CSB-containing assembly boundary; positive regulatory participation may be contextual but needs bounded judgment, not wrong-gene assertion.
Read scope. Original cache Methods 81–121; Results 148–156,188–208/Figs 1–2,5–6; no pixels.
Evidence. Direct purified CSB/c-Abl pull-down and fragment mapping support kinase binding. ECFP-CSB in human CS1AN cells redistributes into nucleolar sites after H2O2. Immunoprecipitated c-Abl from WT-complemented versus CSB-deficient human cells shows CSB-dependent activation toward GST-Crk after H2O2; E646Q fails rescue.
Limits. Cellular activator evidence, not CSB catalysis of phosphorylation; some kinase assays separately use mouse c-Abl and MEFs, distinguished from human assays.
Actual original access route: publisher/archive/author text.
Read scope. Actual main Results/Figures 4–5 and cell/construct/extract Methods, plus author-upload web 458–478,567–695,1061–1146; normal original Methods 191–211.
Evidence. Human primary fibroblast/CS1AN/HeLa experiments use reciprocal and sequential immunoprecipitation to place full-length CSB in a p53–Mdm2–CSA assembly. Figure 5 distinguishes full-length 1493-aa CSB from the shorter CSB–PGBD3 fusion; both can associate with p53 but the fusion does not support the same CSA linkage. Immunopurified CSB complexes contribute to Mdm2-dependent p53 ubiquitination; Mdm2 is the E3 catalyst.
Limits. No purified binary CSB–p53 affinity assay claimed; no E3 activity assigned to CSB and no extra fusion annotation manufactured. Genuine normal cache added separately.
Read scope. Verified Nature identifier/abstract and Figure 3 title; original Methods/Results and full caption unavailable through the recorded publisher routes.
Evidence. The publisher preview is consistent with UVSSA/ERCC6 association but is not counted as an operative binding assay. Independent human UVSSA pull-down and co-IP in PMID:32355176 Figure 5 support CSB-containing UV-induced complexes.
Limits. Source-specific original support remains unverified. No false substitution with the neighboring Nature Genetics paper.
Read scope. Original cache Methods 110–146; Results 154–166,182–208,234–240; Figs 2–4 referenced in Results; no separate supplements or pixels.
Evidence. Distinct full CSB and fusion ORFs expressed in CSB-null human UVSS1KO cell pools. Fusion partly restores UV RNA-synthesis recovery and synergizes with CSB in damaged-reporter reactivation; oxidative reporter differs. Fusion expression increases STAT1/antiviral gene program and STAT1 serine727 phosphorylation, suppressed by coexpressed full CSB. Partially purified tagged fusion or separate PGBD3 produced in Sf9 binds selected MER85 DNA sequences in EMSA with nonspecific competitor.
Limits. Overexpression, host-cell reactivation and expression program are bounded readouts. No viral-challenge protection assay or fusion ATPase/repair-incision reconstitution. Do not import fusion DNA specificity into canonical CSB. External raw assertion list remains separate.
Read scope. Normal original Methods 197–243; Results 101–115,161–163,181–189 and relevant captions; introductory context80–84.
Evidence. Human HeLa/HEK293 experiments assay NM1/WSTF/SNF2h rDNA occupancy, NM1 perturbation, pre-rRNA synthesis and histone changes. No selective CSB perturbation was verified in these operative sections. Independent human CSB/Nucleolin experiments in PMID:31970402 establish the positive PolI role; PMID:17626041 establishes nucleolar localization.
Limits. No claim that CSB is absent from every supplementary experiment. The source-specific NAS support is not represented as a CSB-selective assay.
Read scope. Original cache Results 92–140/Figs 1–8; Methods 162–168. No pixels or supplementary files.
Evidence. Human ReNcell VM progenitor differentiation: CSB shRNA impairs MAP2/Tuj1 induction, polarity and neurite extension. CSB occupies MAP2 and NEUROD1 promoters; CSB depletion lowers Pol II/BAF recruitment. Full-length human CSB-TAP from CS1AN co-purifies BAF subunits, some tagged interactions confirmed Fig 6d.
Limits. Positive transcriptional contribution to developmental process, kept contextual/non-core; no claim CSB builds neurite microtubules. TAP interaction is not purified binary affinity.
Read scope. Original cache Results 101–139,149–179/Figs 2–8; Methods 243–257. No separate supplement or pixels.
Evidence. Human hTERT-RPE KO and HeLa DR-GFP assay support higher NHEJ and lower HR after CSB loss, with altered checkpoint ATM/Chk2 and premature G2/M exit. Full CSB WT rescue, ATPase-dead W851R does not restore pathway regulation. Etop/CPT chromatin-associated CSB salt-fractionation is positive even for W851R, distinct from UV association.
Limits. KO removes both CSB and fusion, but main Results 149 explicitly reports differential complementation: full CSB rescues HR-associated defects, fusion does not. Do not transfer CSB ATPase/remodeling to fusion.
Read scope. Normal original Results including Figures 5–6 and Methods 167–187; introductory context79–85.
Evidence. Mouse fibroblast NM1 knockdown and human HEK293 NM1-mutant studies address SNF2h/WSTF/Pol II/PCAF occupancy and transcription. The reviewed operative experiments do not isolate CSB. Independent human PMID:9326587 directly shows CSB stimulation of Pol II elongation; human PMID:24874740 supplies contextual transcriptional recruitment evidence.
Limits. No title-based wrong-gene claim; no selective CSB experiment asserted from this source.
Read scope. Normal original cache lines 197–213, 259–277, 283, 309 (Results/Figures 2–3, western/IHC/laser Methods, plasmid construction caption); no figure pixels or separate supplementary file read.
Evidence. Tagged full-length human CSB-PGBD3-RFP enters U2OS nuclear laser-damage sites (Fig 3A–D); fusion-eGFP associates with HeLa chromatin after H2O2 (3E). Rhesus-oocyte anti-PGBD3 localization and RNA in situ (Fig 2A/B) are separate from human ovary protein western (2C). Construct caption S1 explicitly amplifies fusion CDS from Weiner plasmid; not canonical CSB. Supports external8 nucleus; no unique nuclear-body inference.
Limits. Human tagged-expression experiment, not endogenous human oocyte localization; HPA antibody ambiguity unresolved by that antibody assay.
Actual original access route: publisher/archive/author text.
Read scope. Actual main Methods p.1388, cell lines/constructs/fractionation, Results SUMO–CSB chromatin association Figure 4C and UV RNA recovery Figures 4B/7D.
Evidence. Human WI38/CS1AN and other repair-deficient cell lines with tagged human CSB variants show SUMO-associated CSB in the Triton-insoluble chromatin fraction. Wild-type CSB rescues UV RNA recovery; K205R/deletion variants and UBC9 perturbation distinguish the regulated response.
Limits. Operative main text/captions read through indexed original access; no figure pixels. RNA recovery is not a direct lesion-excision assay.
Read scope. Normal original cache Results 106–135 Figs 1–3, Methods 147–159; no pixels.
Evidence. Human CSB and rat Elongin A (AAA82095/Q63187) in human cells show damage/stall-induced AP-FRET proximity with Elongin A and CUL5. CSB deficiency and inducible rescue alter recruitment of the ligase partners to damage stripes.
Limits. Cellular interaction/recruitment, not purified binary binding; the rat Elongin A construct is preserved explicitly.
Read scope. Normal original cache Results/Fig 1 lines 99–105; Fig 5/Results 148–154; Fig 6–9 text154–203; Methods 223–235,269–277; no supplementary files or pixels.
Evidence. HCT116 endogenous reciprocal IP supports CSB–RIF1 association. U2OS tethering maps CSB C-terminal interaction to RIF1 CTD. hTERT-RPE CSB knockout and WT versus W851R rescue: WT restores loss of histone H2A/H2B surrounding I-PpoI DSB on chromosome1, ATPase-dead mutant does not (Fig 5). Supports human ATP-dependent chromatin remodeling through targeted cellular histone-occupancy readout, not purified nucleosome sliding in this paper.
Limits. S/G2 DSB and tested constructs; phosphorylation-dependent autoinhibition model is inference. Specific kinase is upstream modifying CSB, not CSB kinase activity.
Read scope. Normal original cache Results 93–143/Figs 1–5 and Methods 163–175; no pixels.
Evidence. Human CSB-deficient and complemented fibroblasts show altered alkaline/neutral comet repair kinetics after MMS/IR, with gamma-H2AX/53BP1 and cell-cycle analyses.
Limits. SSB/DSB repair contribution is supported; no specific KU/LIG4/DNA-PKcs dependence was established in the read operative sections, so classical NHEJ remains more specific than the evidence.
Actual original access route: publisher/archive/author text.
Read scope. Actual main human cell/construct Methods; Results CSB–Nucleolin and Figures 5–6 captions, including rDNA occupancy and pre-rRNA readouts.
Evidence. Human CS1AN stable GFP–CSB wild-type versus UBD LL1427/1428GG rescue, at near-endogenous abundance, and U2OS CSB knockdown establish positive rRNA synthesis. Wild-type CSB restores Nucleolin and PolI occupancy at rDNA coding regions and unprocessed pre-rRNA; Nucleolin depletion distinguishes the recruitment-dependent effect.
Limits. No figure pixels/supplement; CSB regulates PolI access/elongation rather than synthesizing RNA itself. Genuine normal cache added separately.
Read scope. Normal original Results/Figures 1–5 lines 112–172, human cell/construct Methods 296–310 and recombinant Methods 322–328. No pixels/supplement.
Evidence. Human U2OS KO/rescue and chromatin tethering: CSB associates with UV-stalled RNAPII; CSA recruitment requires CSB, and specific CSB CIM1385–1399 is needed. CSB deletion variants tethered at LacO distinguish CSA recruitment. Human and Xenopus recombinant CSB are distinguished; CRL4CSA ubiquitylation and egg nucleoplasmic extract assays use Xenopus partners. Supports recruitment/adaptor activity in human cells without transferring frog-only assay species. Human GFP–UVSSA pull-down/Co-IP Figure 5b/c includes CSB; UV-induced TFIIH recruitment to RNAPII is lost in CSB knockout and restored by wild-type CSB. The CIM/LacO assays demonstrate recruitment rather than association alone.
Limits. Human recruitment and assembly are distinguished from Xenopus CRL4/NPE biochemistry. Pol II-coupled damage recognition is assessed jointly with ATP-dependent arrest passage in PMID:34526721; no autonomous lesion-specific binding claim.
Read scope. Normal original cache lines 79–137 Results/Figs 1–4,145–163 and187 Methods; no pixels/supplement.
Evidence. Recombinant full human CSB and repair factors with pig thymus Pol II and mouse RBX1 form the elongation/TCR complex. CSB promotes arrest-sequence passage; CSA enhances its ATPase; K538R and F796A impair the tested activity. Cryo-EM grips upstream DNA, supporting a translocase mechanism.
Limits. Motor movement is inferred from conformational states plus functional assays, not directly tracked stepping. Mixed-species reconstitution is explicit.
Read scope. Normal original cache compound Results 103/115, captions107–119, model239, Methods 247–255/285.
Evidence. Human CSB and other human TCR factors with pig Pol II form the ELOF1-containing complex; CSB binds upstream DNA while ELOF1 stabilizes CSA/UVSSA interactions.
Limits. Structural and biochemical assembly supports TCR; ELOF1-specific recruitment results are not reassigned to CSB. No full incision-cycle assay or figure pixels read.
Read scope. Normal original cache Results 139–151 Fig 1,195–205 Fig 5,225–235 Fig 7; Methods 257–267 and381–387.
Evidence. Human HAP1/RPE1 CSB deficiency and WT versus K538R rescue establish CSB-dependent repair responses. UV RNA-synthesis recovery and illudin controls support TC-NER separately from the new DNA-protein-crosslink repair pathway.
Limits. DPC repair is explicitly distinct from NER. The TCR annotation is grounded in UV/illudin controls, not reclassification of formaldehyde DPC repair.
Current official QuickGO definitions and typed is_a/part_of ancestry support the proposed duplex-DNA, p53, protein-tyrosine-kinase, chromatin, nucleoplasm, DNA-translocase and positive-Pol II-elongation refinements. ATP hydrolysis is retained as separately measured chemistry. The broader DSB-repair replacement preserves positive human repair evidence while leaving classical end-joining attribution unresolved. Pol II-coupled DNA-damage sensing does not imply naked-lesion specificity. Base-excision participation and CSB-specific PolIII activation remain unresolved.
Current DNA translocase definition, positive Pol II elongation, ATP-dependent DNA damage sensor, base-excision repair, and classical end joining.
The frozen normal record describes Q03468-1 (1,493 residues) and the external product with the literal imported ID P0DP91-1, Q03468-2 (1,061 residues). P0DP91 is the CSB–PGBD3 fusion record; Q8N328 is standalone PGBD3, a different gene product. The 11 external QuickGO assertions are preserved separately from all 139 primary source contexts. No domain/activity equivalence is inferred.
Original. Normal original Methods lines 89–129 and Results 153–179, Figures 2–6 captions; no figure pixels or separate supplements.
Human CSB with N-terminal HA and C-terminal His tags expressed in HiFive insect cells. Direct ATP hydrolysis and ATPγS binding are distinct measurements. Wild-type CSB-ECFP is predominantly homogeneous in human CS1AN.S3.G2 nuclei; brighter foci have no identified nuclear-body identity. The full canonical motor experiment does not establish activity of CSB–PGBD3.
Original. Normal original Results 197–213, Methods 270–312 and construct caption 309; no figure pixels or separate supplements.
Tagged human CSB–PGBD3-RFP in U2OS and fusion-eGFP in HeLa establish nuclear/damage-associated chromatin localization. Rhesus-oocyte antibody localization is separate from human tagged constructs; human ovary western is expression evidence. Nucleus is supported. The precise nucleoplasm/nuclear-body assignment is not independently resolved; the fusion is not canonical CSB.
Original. Actual original JATS Methods nuclear purification and MS (indexed10,13), Results 22/26; actual original S1 Table.xlsx S1A row642 and S1B row576, including headers. No figure pixels.
Procyclic T. brucei donor Tb927.7.4080/Q57UN8 is detected with five peptides and imputed nuclear enrichment NES2.306, p0.01793; whole-cell values are absent. It is not one of the six fluorescent-fusion validations. Proteomic nuclear enrichment supplies donor grounding. It is not human direct localization and is not imaging of this donor.
Original. Normal original Results 142–158/Figure 5 caption and ChIP/I-PpoI Methods 267–279; no figure pixels or actual supplementary panels.
Human hTERT-RPE CSB knockout with chromosome1 I-PpoI breaks: wild-type Myc-CSB restores H2A/H2B eviction while ATPase-dead W851R does not. Direct cellular ATP-dependent chromatin remodeling; no claim of purified sliding or ATP dependence of every CSB–chromatin association.
Original. Actual author-upload original main Results 331–779 and Figure 2 caption 1233–1260; STAR Methods 2294–2728, especially clonogenic2508–2533, qRT-PCR2535–2543, EU2545–2563, UDS2565–2581 and CPD2595–2612. Supplementary S2C/D panels and primer table not independently inspected; no pixels.
Rat R571X primary fibroblasts model human R652X. Post-UV RNA-synthesis recovery/CPD removal is impaired while UDS is preserved. Potassium-bromate clonogenic sensitivity does not by itself distinguish DNA-damage prevention from repair or survival. The normal cache is abstract-only, but actual original main text and operative Methods were separately recovered. Do not manufacture an unavailable-main flag from cache metadata. Detailed supplementary elongation/protection assays remain unread.
Original. Actual PMC original, saved decoded lines 64–104: Methods, Results CSB stimulates transcriptional elongation and RNAPII interaction, Figures 1–2 captions; no pixels.
Purified human CSB accelerates elongation from a 112-nt U-less cassette; immunodepletion removes stimulation. Reconstitution uses human polymerase/factors plus yeast TBP. Separate polymerase-binding reagent is CSB528–1222 fused to MBP. Promoterless-template result is reported as data not shown. No claim of fusion equivalence or isolated obligatory CSB-containing elongation-factor complex.
PANTHER PTHR45629 places human leaf PTN002473896 below PTN001326493. The actual ungapped MSA matches all 1,493 residues of Q03468. The three assigned IBD terms are nucleus, TC-NER and ATP-dependent chromatin remodeling; no target-path NOT record is present. Human self-WITH and the single target donor for remodeling are legitimate experimental grounding. The trypanosome donor Q57UN8 is Tb927.7.4080; its actual nuclear-proteome table provides donor support with missing-value/imputation limits described above.
InterPro IPR000330 is an actual target SNF2 domain match; direct human nucleotide assays support ATP binding. ARBA00029008 matches the actual target FunFam 3.40.50.300:FF:000863 in condition set 36; membership alone is not experimental proof. RHEA:13065 supplies ATP-hydrolysis chemistry, corroborated by direct human TLC assays. None of these mappings assigns motor function to the fusion.
HPA ERCC6 subcellular page uses HPA071297. Its complete 141-residue antigen is absent from Q03468, matches P0DP91 residues 472–612, and also matches standalone PGBD3 residues 4–144. The official western annotation has a predicted 119.5 kDa target and additional bands. The selected U2OS image shows nuclear signal/puncta, but image appearance cannot uniquely identify the fusion or canonical protein. This is not a measured cross-reactivity experiment.
Canonical nucleus/nucleoplasm have independent tagged-human and exact Reactome support. Canonical nuclear body remains unresolved. Tagged-fusion experiments independently support external nucleus; the narrower external nucleoplasm and nuclear-body assertions remain unresolved. No absence claim is made.
Each row below is an explicit forward route in the current official record. The terminal entity is human Q03468 residues 1–1493 in nucleoplasm; entity 6781853 is its ubiquitinated state, not another natural product. These are localization assertions. Other components perform acetylation, ubiquitination, deubiquitination, incision, DNA synthesis or ligation. The two R-NUL models are explicitly mixed-species: human CSB is retained alongside mouse components, not described as a wholly human reconstitution.
| Source row | Official event | Exact forward route |
|---|---|---|
| 64 | R-HSA-5250930 | 5250930 → 5250923 → 5250626 → 5365864 → 54429 |
| 65 | R-HSA-5250938 | 5250938 → 5250927 → 5250942 → 5250923 → 5250626 → 5365864 → 54429 |
| 66 | R-HSA-5250947 | 5250947 → 5365864 → 54429 |
| 67 | R-HSA-6781833 | 6781833 → 6781837 → 54429 |
| 68 | R-HSA-6781840 | 6781840 → 54429 |
| 69 | R-HSA-6781867 | 6781867 → 6781839 → 6781837 → 54429 |
| 70 | R-HSA-6782004 | 6782004 → 6781866 → 6781848 → 6781849 → 6781853 |
| 71 | R-HSA-6782069 | 6782069 → 6782066 → 6782068 → 6782065 → 54429 |
| 72 | R-HSA-6782131 | 6782131 → 6782066 → 6782068 → 6782065 → 54429 |
| 73 | R-HSA-6782138 | 6782138 → 6782111 → 6782122 → 6782112 → 54429 |
| 74 | R-HSA-6782141 | 6782141 → 6782134 → 6782111 → 6782122 → 6782112 → 54429 |
| 75 | R-HSA-6782204 | 6782204 → 6782205 → 54429 |
| 76 | R-HSA-6782208 | 6782208 → 6782222 → 54429 |
| 77 | R-HSA-6782211 | 6782211 → 6782205 → 54429 |
| 78 | R-HSA-6782224 | 6782224 → 6782219 → 54429 |
| 79 | R-HSA-6782227 | 6782227 → 6782220 → 54429 |
| 80 | R-HSA-6782234 | 6782234 → 6782230 → 54429 |
| 81 | R-HSA-9684118 | 9684118 → 9684117 → 9684121 → 9684120 → 54429 |
| 82 | R-NUL-573373 | 573373 → 573387 → 573330 → 54429 |
| 83 | R-NUL-573385 | 573385 → 54429 |
The chromosome mapping is refined to GO:0000785 chromatin using direct human chromosomal-break remodeling context. The definition describes the organized DNA–protein material; this is a location refinement, not a new activity. The rat DNA-protection transfer remains unresolved because clonogenic oxidative-stress sensitivity does not distinguish preventing damage from repairing damage or surviving it. The main paper reports supplementary endpoints, whose detailed panels were not independently inspected. Positive human elongation reconstitution supports refinement to GO:0032968 positive regulation of transcription elongation by RNA polymerase II, independently of those unavailable details.
No new process annotations or core functions are introduced at this annotation checkpoint. Database assertions have been integrated with the direct-source reviews; source fields remain exact.
Nicolai and colleagues' original article reports human CSB-TAP purification and follow-up co-immunoprecipitation in CS1AN fibroblasts. The operative Methods and Results, Figures 1, 2, 4, 5 and 6, and the populated cells of original S1 Table were read. The table was parsed without modifying its original values or formula errors. Official UniProt records map all 33 imported partner accessions to the tested protein names.
The TAP construct contained the full human CSB coding region. A selected stable clone expressed CSB near the wild-type comparison level and restored UV resistance; TAP-only cells were the purification control. Follow-up transient CSB-Flag/partner-Myc experiments confirmed 19 associations in both immunoprecipitation directions (Figure 4A–S), nine only with anti-Myc capture (Figure 5A–I), and five only with anti-Flag capture (Figure 6A–E). The three negative follow-ups in Figure 6F–H are EFTUD2, HLTF and PSMD2; none is among these 33 imported rows. Weak SMARCA2 reciprocal bands were checked with unfused-tag controls in Figure 4T–U.
S1 Table reports nonzero TAP-only unique peptide counts for SF3B2, DDX5, PSMD12, DDX41 and PRPF4. Therefore the broad main-text statement that identified proteins were absent from control purification is not repeated as a universal observation. The subsequent co-IP evidence supports retention of these associations, with its one-direction or reciprocal limits made explicit per row.
All 33 assertions are retained as non-core protein binding. Cellular co-recovery does not establish purified direct contact or assign the partner's catalytic activity to CSB. The experiments were conducted without exogenous DNA damage; the operative methods do not describe nuclease treatment. No DNA-damage-dependent association, RNA-splicing activity, proteasome activity or new process annotation is inferred from the interaction network. Figure 1 detects an endogenous CSB–PGBD3 band in control fibroblasts, but the tested full-length CSB constructs do not establish these interactions for the fusion. Figure 4E's p72/p82 bands belong to DDX17 alternative translation products.
These 11 source contexts belong to UniProt P0DP91 (product aliases P0DP91-1 and Q03468-2). They remain separate from the 139 canonical-CSB contexts. The schema-backed fusion review preserves all eleven review decisions; its complete source records retain annotation IDs, literal qualifiers, evidence, source extensions and WITH/FROM partners. These are reviewed external assertions, not NEW primary annotations.
| Context | GO term | Evidence | Reference | Action | WITH/FROM partner | Extension |
|---|---|---|---|---|---|---|
| 0 | GO:0043565 sequence-specific DNA binding | IDA | PMID:22483866(https://pubmed.ncbi.nlm.nih.gov/22483866/) | ACCEPT | — | — |
| 1 | GO:0002230 positive regulation of defense response to virus by host | IMP | PMID:22483866(https://pubmed.ncbi.nlm.nih.gov/22483866/) | UNDECIDED | — | — |
| 2 | GO:0010628 positive regulation of gene expression | IMP | PMID:22483866(https://pubmed.ncbi.nlm.nih.gov/22483866/) | KEEP_AS_NON_CORE | — | has_input UniProtKB:P42224 |
| 3 | GO:0010628 positive regulation of gene expression | HMP | PMID:22483866(https://pubmed.ncbi.nlm.nih.gov/22483866/) | KEEP_AS_NON_CORE | — | has_input UniProtKB:Q9BYX4, has_input UniProtKB:O95786, has_input UniProtKB:Q10589, has_input UniProtKB:P42224, has_input UniProtKB:P52630, has_input UniProtKB:Q00978 |
| 4 | GO:0033141 positive regulation of peptidyl-serine phosphorylation of STAT protein | IMP | PMID:22483866(https://pubmed.ncbi.nlm.nih.gov/22483866/) | KEEP_AS_NON_CORE | — | has_input UniProtKB:P42224 |
| 5 | GO:0045739 positive regulation of DNA repair | IMP | PMID:22483866(https://pubmed.ncbi.nlm.nih.gov/22483866/) | KEEP_AS_NON_CORE | — | — |
| 6 | GO:0045739 positive regulation of DNA repair | IGI | PMID:22483866(https://pubmed.ncbi.nlm.nih.gov/22483866/) | KEEP_AS_NON_CORE | UniProtKB:Q03468 | — |
| 7 | GO:0005634 nucleus | IEA | GO_REF:0000044 | ACCEPT | UniProtKB-SubCell:SL-0191 | — |
| 8 | GO:0005634 nucleus | EXP | PMID:26218421(https://pubmed.ncbi.nlm.nih.gov/26218421/) | ACCEPT | — | — |
| 9 | GO:0005654 nucleoplasm | IDA | GO_REF:0000052 | UNDECIDED | — | — |
| 10 | GO:0016604 nuclear body | IDA | GO_REF:0000052 | UNDECIDED | — | — |
Three contexts are ACCEPT, five KEEP_AS_NON_CORE and three UNDECIDED. IMP and IGI repair-regulation contexts remain distinct: the IGI record specifically names canonical CSB Q03468 as its partner. The HMP expression context retains all six imported targets; STAT1-specific contexts retain their own extensions. HPA antibody HPA071297 recognizes a sequence shared by the fusion and standalone PGBD3, and absent from canonical CSB; its signal does not uniquely identify either product. Human tagged-fusion imaging supports the broad nucleus assertion, while the finer nucleoplasm/nuclear-body assertions remain unresolved.
These four activity descriptions concern canonical human CSB. They describe different measured properties of the same protein. The separately assessed CSB–PGBD3 fusion is not assigned these motor activities.
The fusion sentence in the biological description is grounded in PMID:22483866, DOI 10.1016/j.dnarep.2012.02.004, Methods on distinct full-length-CSB and fusion expression, Results on gene-expression changes, and MER85 electrophoretic-mobility-shift assays. The source tests separately expressed products and selected DNA sequences. Its antiviral-like expression program is not converted into a demonstrated antiviral-defense activity.
Current official ontology records: ATP hydrolysis, DNA translocase, ATP-dependent chromatin remodeler, and chromatin-protein adaptor. The captured current is-a and is-a/part-of closures show no ancestor/descendant redundancy among these four molecular functions. ATP hydrolysis remains its own measured chemistry. The accepted damage-sensor annotation is preserved; a separate core unit would repeat the Pol-II-coupled sensing and recruitment mechanism. No new publication quotations were added.
The two canonical-CSB HPA annotations now carry structured source defects. The HPA071297 immunogen sequence mismatch is established, but the observed staining cannot be uniquely assigned between CSB–PGBD3 and standalone PGBD3; the requested upstream action is to check the product assignment, not silently repoint it. The separate retracted PMID:10786832 is explicitly marked invalid and is not positive functional evidence. Suggested questions and experiments distinguish CSB’s own BER work, PolIII regulation, product-specific nuclear-body localization and prevention of damage from repair or survival.