GATAD2B

Summary: Ancestral negative regulation of PolII transcription is supported by target-specific corepressor evidence.

Reason: The actual PTHR13455 tree places the exact 593-residue human GATAD2B sequence at AN16/PTN002491641 below the Eumetazoa IBD AN0/PTN001003231 for GO:0000122. Its literal FlyBase donor is inside that clade, and no target-lineage negative record was found. Human p66beta repression and knockdown experiments in PMID:16415179 independently support this inherited regulatory role. The ancestral inference is assessed by node placement and target biology, not by donor count.

Summary: The p66-related electronic assignment agrees with experimentally demonstrated transcriptional repression.

Reason: The InterPro IPR040386 inference is consistent with the human p66beta results in PMID:16415179: p66beta enhances MBD2-tethered repression, its selective knockdown relieves part of that repression, and Gal4-tethered p66beta represses the reporter in mouse fibroblasts. This supports a core role in negative regulation of PolII transcription. Gal4 supplies DNA recruitment in the tethered assay, and neither ATPase nor histone-deacetylase catalysis is assigned to p66beta.

Summary: Telomeric localization is supported in the alternative-lengthening context.

Reason: The selected original PMID:25150861 Results and Figure 1/2 textual captions identify p66β recruitment and telomeric ChIP in the ZNF827-associated NuRD pathway of alternative lengthening of telomeres. This supports the stated location in the assayed ALT cells. It is a specialized chromatin setting rather than the general defining location of GATAD2B. The evidence is not generalized to all telomeres, all cell types or an intrinsic telomere-sequence recognition activity; source images and supplemental target tables were not independently inspected.

Summary: Chromatin association is consistent with the original nuclear complex and independent histone-binding evidence.

Reason: PMID:16217013 purifies a nuclear chromatin-remodeling assembly using a DNA affinity substrate and tests its behavior on nucleosomal templates; the target-specific peptide panel has not been independently recovered from the inspected main text. Human p66beta histone-tail binding and repression experiments in PMID:16415179, together with GATAD2B membership in the NuRD chromatin machinery in PMID:33283408, independently support chromatin association. This does not claim that the LARC study isolated GATAD2B as its sequence-specific DNA-contact subunit: the reported direct DNA-contact result concerns hnRNPC1/C2.

Summary: The PAINT curator infers an ancestral DNA-recognition function in transcriptional regulation.

Reason: The actual PAINT assertion at AN0/PTN001003231 is inherited by the exact GATAD2B AN16 target; worm DCP-66/G5ED89 is a descendant at AN97. PMID:16159881 supplies yeast one-hybrid recognition of the non-GATA Ex-1 promoter element, competitive EMSA with a 122-residue fragment in reticulocyte lysate, and reporter loss/genomic rescue. This experimentally grounded ancestral judgment supports the inferred transcriptional function. The human-versus-canonical-GATA comparison is assessed separately in the source guide; it does not demonstrate loss relative to the p66 donor recognizing the non-GATA Ex-1 element. ACCEPT records a conserved inferred facet of transcriptional regulation, while the single core synthesis emphasizes directly tested human NuRD corepression rather than creating a second unit from this inference. No human recognition sequence, endogenous occupancy or purified-human affinity is claimed. Binding a transcription factor and recognizing DNA are not mutually exclusive activities.

Summary: The PRKAB2 screen interaction is positive but does not identify a specific GATAD2B activity.

Reason: The exact PMID:24722188 IntAct record pairs Q8WXI9 with O43741 in a positive two-hybrid array experiment, with Table S3/S4 provenance. That evidence is retained; removal addresses the lack of functional information in GO:0005515, not the truth of the interaction. The screen does not establish that GATAD2B performs AMPK chemistry or acts as its regulatory subunit, and the inspected record does not justify a natural-product-specific mechanism.

Summary: MBD3 association supports transcription coregulator binding.

Reason: The authentic PMID:25123934 structured abstract explicitly reports an MBD3–GATAD2B pulldown interaction; the original occurs_in nucleus atom is retained. Independently, the reviewed MBD3 record and inspected PMID:16428440 establish MBD3 as a NuRD transcription coregulator that couples regulatory proteins to chromatin-modifying components. Thus the positive pair supports GO:0001221 transcription coregulator binding, a verified descendant of protein binding, without requiring a unique heterodimer stoichiometry or a transcriptional outcome from this particular pulldown. MBD3’s weak DNA association is distinct from a demonstrated sequence-specific transcription-factor role. The original PMID:25123934 full Methods and purified binary affinity remain outside the inspected scope.

Proposed replacements: transcription coregulator binding

Summary: ZNF827-associated NuRD recruitment is supported, but the bare binding term adds little function.

Reason: Selected original PMID:25150861 Results, Fig. 2g labels/caption and co-immunoprecipitation Methods identify p66β among NuRD proteins associated with ZNF827 in human ALT cells. ZNF827 overexpression, nuclear-extract IP and IgG controls are explicit; these are not a purified GATAD2B–ZNF827 affinity measurement. The positive complex association and specialized telomere recruitment are retained. Remove only the uninformative GO:0005515 assertion, without transferring ZNF827 telomere recognition or homologous-recombination chemistry to GATAD2B.

Summary: The HI-II-14 PRKAB2 interaction is retained as a positive screen result.

Reason: Original PMID:25416956 Supplementary Table S2G row 4520 pairs GATAD2B GeneID 57459 with PRKAB2 GeneID 5565; the matching current IntAct accession pair O43741–Q8WXI9 is positive in the two-hybrid records. This is genuine interaction evidence, not a source-identity failure. GO:0005515 is removed because it supplies no informative GATAD2B molecular function. Neither the AMPK partner role nor a canonical clone sequence is inferred from the gene-level table.

Summary: The positive MBD3 screen pair supports binding to a transcription coregulator.

Reason: Original PMID:25416956 S2G row 10931 records GATAD2B (GeneID 57459)–MBD3 (GeneID 53615) and matches the positive O95983–Q8WXI9 IntAct two-hybrid records. Preserve the original occurs_in nucleus atom. Independent MBD3 function and NuRD-composition evidence in its reviewed UniProt record and PMID:16428440 establish the partner’s transcription-coregulator class, supporting GO:0001221 rather than bare protein binding. This is a partner-class refinement; it does not require the screen to demonstrate an endogenous regulatory outcome, purified affinity or heterodimer stoichiometry. No exact natural clone sequence or sequence-specific DNA-recognition function is inferred for MBD3.

Proposed replacements: transcription coregulator binding

Summary: The TRIM27 pair is a verified positive screening observation.

Reason: PMID:25416956 S2G row 5138 pairs TRIM27 GeneID 5987 with GATAD2B 57459; the current P14373 accession has a matching positive IntAct two-hybrid pair. The interaction remains valid evidence. Its generic GO:0005515 annotation is uninformative, and these source records do not establish ubiquitin-transfer catalysis or a TRIM27-dependent regulatory mechanism performed by GATAD2B. No natural-product clone identity or independent orthogonal validation of this individual pair is claimed.

Summary: The GOLGA2 screen pair does not establish a GATAD2B Golgi function.

Reason: The authentic PMID:25416956 S2G row 2126 records GOLGA2 GeneID 2801–GATAD2B 57459, with exact Q08379–Q8WXI9 positive IntAct two-hybrid evidence. Remove only the generic protein-binding annotation as uninformative. The positive experimental pair is preserved; partner identity is not evidence that GATAD2B occupies the Golgi or performs Golgi organization. Gene-level identity does not by itself resolve the sequence of every screened clone.

Summary: The TRAF1 two-hybrid result is positive, with its functional consequences unresolved.

Reason: Original PMID:25416956 S2G row 6306 joins TRAF1 7185 to GATAD2B 57459, and current IntAct records explicitly pair Q13077 with Q8WXI9 without a negative flag. GO:0005515 is removed for lack of functional information, not because this interaction is false. No receptor-signaling adaptor function or downstream TRAF1 pathway is assigned to GATAD2B from this pair alone; the actual assay and gene-level identity remain recorded.

Summary: CALCOCO2 association in the interaction screen is retained without pathway extrapolation.

Reason: PMID:25416956 S2G row 8550 records CALCOCO2 10241 with GATAD2B 57459 and agrees with the positive Q13137–Q8WXI9 IntAct pair. The generic binding annotation is uninformative and is removed under the standing binding policy. This does not deny the measured interaction or establish autophagic cargo recognition, receptor activity or another CALCOCO2-associated process for GATAD2B. Individual clone sequence and all-pair orthogonal validation are not claimed.

Summary: The TEX11 pair is a positive two-hybrid interaction rather than a defined GATAD2B activity.

Reason: The original PMID:25416956 S2G row 11651 pairs TEX11 GeneID 56159 with GATAD2B 57459; Q8IYF3–Q8WXI9 is also a positive exact IntAct pair. Preserve the interaction evidence and remove only the uninformative GO:0005515 assertion. These assays do not show that GATAD2B performs a TEX11 meiotic role, and no sequence-specific equivalence between a tested clone and the complete natural product is inferred.

Summary: The USHBP1 interaction is supported but does not resolve a specific molecular role.

Reason: PMID:25416956 S2G row 11882 contains USHBP1 83878–GATAD2B 57459, with a positive matching Q8N6Y0–Q8WXI9 IntAct two-hybrid pair. This is positive source evidence, not an absent-target or wrong-protein finding. Remove GO:0005515 because it is uninformative. The screened association does not establish a sensory or localization function for GATAD2B, and the original gene-level table is not treated as a complete clone-sequence crosswalk.

Summary: CEP70 is a verified screening partner, without a demonstrated GATAD2B microtubule role.

Reason: The genuine PMID:25416956 S2G row 11881 pairs CEP70 80321 with GATAD2B 57459, and the exact Q8NHQ1–Q8WXI9 IntAct records are positive. Remove the generic protein-binding annotation for lack of functional information while preserving that observed interaction. The partner name and its known cellular roles do not establish GATAD2B microtubule organization, centrosome localization or a specific adaptor activity.

Summary: The RPGRIP1 screen interaction remains positive evidence.

Reason: Original PMID:25416956 S2G row 11768 records RPGRIP1 57096–GATAD2B 57459 and matches the positive Q96KN7–Q8WXI9 IntAct pair. The generic GO:0005515 annotation provides no informative molecular function and is removed. This judgment does not deny the pair or transfer RPGRIP1-associated ciliary functions to GATAD2B. The gene-level match is distinguished from an unverified full-length natural-product clone assignment.

Summary: CSB-associated GATAD2B was detected, but its bare binding annotation is uninformative.

Reason: Selected original PMID:26030138 Results and Methods describe TAP-CSB interactome experiments in human CS1AN fibroblasts and confirm GATAD2B association in the anti-Myc co-immunoprecipitation direction; the anti-FLAG reciprocal direction did not confirm this target. Preserve this directional positive evidence without calling the pair reciprocally validated. Remove GO:0005515 for lack of functional specificity. The assay does not establish CSB ATPase or repair chemistry for GATAD2B, and the paper’s GATA-factor discussion is not used to infer a hematopoietic mechanism for p66β.

Summary: GATAD2B binds the DNA-binding transcription factor LRF/ZBTB7A in a repression complex.

Reason: PMID:26816381 identifies GATAD2B using the human LRF/ZBTB7A BTB domain in yeast two-hybrid analysis and confirms endogenous LRF–GATAD2B association by reciprocal co-immunoprecipitation in human CD34-derived erythroblasts. The inspected original also establishes LRF sequence-specific promoter occupancy and a globin-repression context, so the partner’s transcription-factor role is experimentally grounded rather than guessed from its name. GO:0140297 DNA-binding transcription factor binding is a verified is_a descendant through GO:0008134 of the original protein-binding term. This refinement preserves complex-associated binding without claiming purified affinity or that GATAD2B itself performs LRF’s sequence recognition.

Proposed replacements: DNA-binding transcription factor binding

Summary: Endogenous DISC1-associated GATAD2B is supported in human neural progenitor cells.

Reason: The actual PMID:29961565 original describes CRISPR C-terminal 3×FLAG tagging of endogenous DISC1 in human iPSCs and affinity-proteomics after neural differentiation. Its inspected Results explicitly identify GATAD2B in the human neural-progenitor interactome. The cell line’s common DISC1 R264Q background and the distinct expression-enhancement experiment are retained as experimental limits; no target-specific peptide confidence tier or astrocyte-positive result is inferred from the unread supplementary row. Remove uninformative GO:0005515 while preserving the positive association, without assigning a neuronal pathway or direct binary mechanism to GATAD2B.

Summary: A DISC1 two-hybrid fragment interaction is positive but does not define GATAD2B function.

Reason: The exact PMID:31413325 IntAct record IM-26801-455 pairs DISC1 Q9NRI5 with GATAD2B Q8WXI9 in a positive two-hybrid fragment-pooling assay. The GATAD2B interaction region is recorded as residues 334–525; it is an assayed fragment, not an independently demonstrated natural isoform. Remove the generic protein-binding term as uninformative while retaining the actual positive source and construct scope. No endogenous neuronal association or specific DISC1 pathway role is manufactured from this assay.

Summary: The TRAF1 variant-screen interaction is retained with its measured variant scope.

Reason: The positive PMID:31515488 IntAct record IM-27438-3426 pairs TRAF1 Q13077 with GATAD2B Q8WXI9 in a two-hybrid array. Its GATAD2B feature at position 490, rs145131801, is annotated as a mutation with no effect on the tested interaction. Retain that distinction rather than inventing a pathogenic gain or loss of binding. GO:0005515 is removed for lack of functional information; the pair is not rejected and no TRAF1 signaling mechanism is assigned from this screen.

Summary: The HuRI SBK3 pair is supported, without a specific GATAD2B kinase-related function.

Reason: The original PMID:32296183 HuRI records contain literal P0C264–Q8WXI9 and the current IntAct pair is positive. The GATAD2B ORF is linked to ENST00000368655.4/ENSP00000357644.4 in the source. Preserve this screen and construct identity without claiming an independently verified natural-product sequence or endogenous association. Remove the uninformative protein-binding annotation; SBK3 partner identity alone does not assign kinase catalysis or kinase regulation to GATAD2B.

Summary: The CDKN2D HuRI interaction does not define a GATAD2B cell-cycle activity.

Reason: Literal P55273–Q8WXI9 is present in the original PMID:32296183 HuRI data and matching positive IntAct two-hybrid records. The positive interaction is retained, but the bare GO:0005515 assertion is uninformative. No cyclin-dependent-kinase inhibition or cell-cycle mechanism is inferred for GATAD2B from its partner. Screen ORF/transcript identifiers remain distinct from an unverified physiological product assignment.

Summary: The FHL2 interaction supports transcription coregulator binding.

Reason: The positive PMID:32296183 HuRI source specifies Q14192-1 with Q8WXI9, while the incoming assertion uses unsuffixed Q14192; both literal forms are preserved. Official UniProt identifies Q14192-1 as the displayed 279-residue FHL2 product. Selected original PMID:15692560 Results and Methods independently demonstrate full-length human FHL2 interaction-mediated modulation of FOXO1 transcription, including increased FOXO1–SIRT1 association, establishing a coregulator role. Positive binding to this independently characterized partner supports GO:0001221 without requiring the HuRI experiment to reproduce that regulatory outcome. No GATAD2B–FHL2 physiological mechanism or exact sequence identity between historical experimental clones is asserted.

Proposed replacements: transcription coregulator binding

Summary: The NOXA1 isoform-2 interaction is a genuine screen observation.

Reason: Original PMID:32296183 HuRI data and current positive IntAct evidence match the literal Q86UR1-2–Q8WXI9 pair. The partner suffix is preserved; it is not broadened to all NOXA1 products or converted into a GATAD2B isoform assertion. Remove GO:0005515 because it is uninformative, retaining the experimental interaction. The assay does not establish oxidase activity or a reactive-oxygen signaling function performed by GATAD2B.

Summary: The ZGPAT isoform-2 interaction supports DNA-binding transcription factor binding.

Reason: The original PMID:32296183 HuRI and positive IntAct records match literal Q8N5A5-2–Q8WXI9. Independently, PMID:19644445 assays a 511-residue human ZIP/ZGPAT cDNA BC032612 with sequence-selective CASTing, promoter occupancy and transcriptional repression. Its linked AAH32612.1 protein matches the current isoform-2 splice architecture and differs only at the officially documented S61R natural variant; the sequences are not claimed identical. Isoform 2 retains the DNA-binding region and is distinct from non-DNA-binding short isoform 4. These data support GO:0140297 DNA-binding transcription factor binding for the positive pair, without requiring the HuRI assay to demonstrate an EGFR outcome or assigning the partner’s DNA recognition to GATAD2B.

Proposed replacements: DNA-binding transcription factor binding

Summary: The neuroglobin HuRI interaction is positive but functionally nonspecific.

Reason: The original PMID:32296183 source records explicitly pair NGB Q9NPG2 with Q8WXI9, and the current IntAct two-hybrid records are positive. Preserve this observation while removing the uninformative GO:0005515 annotation. It does not demonstrate oxygen binding, heme chemistry or a neuroglobin-mediated physiological function for GATAD2B. The tested ORF identity is not generalized to every endogenous product or tissue context.

Summary: The GPSM3 screen pair does not establish a GATAD2B G-protein signaling function.

Reason: Literal Q9Y4H4–Q8WXI9 occurs in the original PMID:32296183 HuRI data and exact positive IntAct two-hybrid evidence. The measured interaction remains supported. Remove only the generic protein-binding annotation because it is uninformative; partner identity does not show GATAD2B performing GPSM3’s signaling role. No natural full-length clone identity or endogenous association is inferred beyond the retained source record.

Summary: The NME7 HuRI interaction is retained with its original construct identity.

Reason: The original PMID:32296183 HuRI records use Q9Y5B8-1 with Q8WXI9, whereas GOA lists unsuffixed Q9Y5B8; matching IntAct evidence is positive. Preserve these original representations rather than silently rewriting the incoming partner. GO:0005515 is removed for lack of functional information, not because the association is false. The pair does not assign NME7 enzymatic or microtubule-related activities to GATAD2B.

Summary: BioPlex MBD3 association supports a transcription-coregulator binding refinement.

Reason: Three positive PMID:33961781 IntAct affinity/co-immunoprecipitation records match O95983 MBD3 with Q8WXI9, retaining the original occurs_in nucleus atom. The independently established MBD3 NuRD-coregulator role in the reviewed UniProt record and inspected PMID:16428440 makes GO:0001221 more informative than generic protein binding. The partner-class inference does not require an exact heterodimer or a regulatory outcome from each screen. The abstract and experimental records, rather than uninspected target Methods, define this BioPlex evidence; an exact source cell line, purified affinity and natural clone sequence are not asserted for this pair.

Proposed replacements: transcription coregulator binding

Summary: The BRAF-mutant interaction is experimentally supported but does not define a GATAD2B signaling activity.

Reason: The exact PMID:35512704 IntAct records include split-luciferase, pulldown and BRET evidence for P15056–Q8WXI9, with BRAF residue 600 mutation features and increased or mutation-dependent interaction recorded in the latter assays. Preserve this mutant context; do not generalize it to wild-type BRAF or all natural GATAD2B products. The local cache contains the abstract, introduction and discussion but not the target Methods/Results; the target-specific assay scope comes from the retained experimental records. Remove uninformative GO:0005515 without denying the measured interaction or inventing a BRAF signaling mechanism for GATAD2B.

Summary: The nucleus is an established location of human p66β.

Reason: Selected original PMID:27732854 describes GFP-p66β-containing nuclear NuRD assemblies and chromatin-associated behavior in the tested human cell systems. This agrees with independent human p66 localization and the exact nuclear/nucleoplasmic Reactome models. Retain the nucleus assertion under the root-organelle policy; more specific supported chromatin locations elsewhere do not invalidate it. GFP-tagged assay constructs are distinguished from an independently demonstrated sequence-identical natural product, and no splicing-speckle marker is inferred.

Summary: Human nuclear CHD/NuRD preparations contain p66beta.

Reason: PMID:28977666 identifies p66beta together with p66alpha in CHD3/CHD4 affinity-purified complexes from human HEK293-derived preparations, including nuclear extracts. This supports the nuclear localization of the associated GATAD2B pool and agrees with independent human p66beta nuclear localization studies. The paper's live-cell imaging and motor comparisons principally concern CHD3 and CHD4; they are not presented as beta-specific fluorescent imaging or GATAD2B ATPase assays. Retain the valid nucleus claim under the root-organelle policy.

Summary: Human NuRD purification supports the nuclear pool of GATAD2B.

Reason: PMID:33283408 purifies NuRD assemblies from HeLa Kyoto nuclear extracts and reports GATAD2A/B in their cross-link topology. This establishes a nuclear complex-associated pool and agrees with the human p66beta localization experiments in PMID:16415179. The tagged affinity baits and GATAD2A deletion constructs are distinguished from the endogenous GATAD2B present in the purified mixtures; the study is not described as direct GFP-GATAD2B imaging.

Summary: GATAD2B is a nuclear NuRD-associated regulatory protein.

Reason: The UniProt location-vocabulary mapping to nucleus is supported independently by human p66beta GFP constructs and the endogenous p66 repression context in PMID:16415179, as well as recovery of GATAD2B-containing NuRD from human nuclear extracts in PMID:33283408. The nucleus is retained as a valid root-organelle assertion rather than replaced by a subcompartment. Specific nuclear foci are evaluated separately and are not assumed to be splicing speckles.

Summary: Nucleoplasmic localization agrees with the independently established nuclear NuRD pool.

Reason: This HPA IDA context is retained with its original GO_REF:0000052 provenance; the original HPA image panel has not been independently inspected. Independent human nuclear NuRD experiments and verified Reactome participant chains place Q8WXI9 residues 1–593 in nucleoplasm. Those sources support the biological location without claiming to reproduce the HPA experiment or treating an uninspected image as negative evidence.

Summary: The ARBA nucleoplasm inference is consistent with direct and curated target evidence.

Reason: The incoming electronic rule is ARBA00026290. Independently, human p66β-containing NuRD is recovered from nuclear preparations, and the verified Reactome Q8WXI9 participant chains explicitly specify nucleoplasm. This supports the location as part of the protein’s ordinary nuclear function. The rule is not treated as a separate imaging experiment, and no cytoplasmic exclusion or nuclear-speckle specificity is inferred.

Summary: The SUMOylation model explicitly places human GATAD2B in nucleoplasm.

Reason: Reactome R-HSA-9940458 contains unmodified GATAD2B input 3702079 and monoSUMO1-K33 product 9940398. Both resolve to human Q8WXI9 residues 1–593 with compartment GO:0005654. This directly supports the modeled nucleoplasmic pool, consistent with the protein’s established nuclear NuRD role. GATAD2B is the substrate in this reaction; neither SUMO-transferase activity nor an additional SUMOylation-process assertion is inferred from the location annotation.

Summary: Core-NuRD recruitment includes an explicit nucleoplasmic GATAD2B alternative.

Reason: The actual R-HSA-9940462 input set 9940428 and output core complex 9940439 lead through hasMember to monoSUMO1-K33 GATAD2B 9940398, human Q8WXI9 residues 1–593 in nucleoplasm. The typed component/member path supports GO:0005654 as a core location. GATAD2A and GATAD2B are modeled alternatives; this does not require both paralogs in one complex or establish every binary contact mentioned in the event summation.

Summary: The CHD/CDK2AP recruitment model retains nucleoplasmic GATAD2B.

Reason: R-HSA-9940468 recruits additional components to partial NuRD 9940439 and produces assembly 9940443. The explicit path through GATAD2A/B set 9940428 reaches human GATAD2B 9940398 with GO:0005654. Accept the nucleoplasm claim as part of its nuclear scaffold role. The model does not make GATAD2B the ATPase: CHD performs the catalytic remodeling chemistry, and the alternative set does not imply obligatory A/B co-occupancy.

Summary: MBD3L2-associated NuRD contains a modeled GATAD2B pool in nucleoplasm.

Reason: The actual R-HSA-9940474 input MBD3-specific core 9941680 and output 9941689 contain the defined GATAD2A/B set, whose GATAD2B member resolves to human Q8WXI9 residues 1–593 in GO:0005654. This is positive curated location support, not a claim that GATAD2B independently binds MBD3L2. The model’s alternative composition is preserved and the underlying event-cited papers are not represented as newly inspected target-specific experiments.

Summary: The MBD2-core event supports nucleoplasmic GATAD2B despite a summation wording defect.

Reason: R-HSA-9941683 uses the actual MBD2-specific core 9941677 and output 9941686; their typed component path reaches the GATAD2B alternative 9940398, human Q8WXI9 in nucleoplasm. Accept GO:0005654. The first summation sentence mentions MBD3 inconsistently with the event title and explicit MBD2 core, so that sentence is not used to infer a different partner or a direct GATAD2B–MBD3L1 assay. The target’s compartment is unambiguous in the retained objects.

Summary: Telomeric NuRD recruitment is consistent with a nucleoplasmic GATAD2B component.

Reason: R-HSA-9941697 links NuRD assembly 9940443 to telomeric complex 9941696. The component/member chain explicitly includes GATAD2B 9940398, Q8WXI9 residues 1–593 in GO:0005654. This supports the broad nucleoplasm claim as a core location even though the event describes a specialized ALT-cell recruitment context. ZNF827 and nuclear receptors mediate recruitment; their DNA recognition or homologous-recombination functions are not assigned to GATAD2B by this model.

Summary: The telomeric deacetylation model retains GATAD2B as a nucleoplasmic component.

Reason: R-HSA-9941704 has input, output and catalytic-complex paths through telomeric NuRD to the GATAD2B member 9940398, explicitly human Q8WXI9 in GO:0005654. Accept this location assertion. Membership of the active NuRD complex does not establish isolated p66β histone-deacetylase activity; the model is used here for its target-specific component and compartment facts, with A/B alternatives kept distinct from simultaneous occupancy.

Summary: PHF6-associated NuRD provides explicit modeled nucleoplasm support.

Reason: R-HSA-9941744 joins PHF6 to NuRD, and both the input 9940443 and output 9941738 trace through the GATAD2A/B set to human GATAD2B 9940398 in nucleoplasm. The positive component path supports GO:0005654. It is not treated as an independent purified PHF6–GATAD2B interaction experiment, nor are PHF6 DNA/histone-recognition functions transferred to GATAD2B.

Summary: GATAD2B is a nucleoplasmic component of the modeled ATP-dependent remodeling complex.

Reason: In R-HSA-9944091, catalystActivity 9944082 points to NuRD physical entity 9940443, whose explicit component/member chain contains human GATAD2B 9940398 in GO:0005654. Accept the location. The event summation assigns ATP hydrolysis to the CHD component; GATAD2B’s participation as a scaffold is kept separate from that chemistry. No autonomous ATPase activity or obligatory simultaneous A/B composition is inferred.

Summary: The deacetylation model explicitly retains a nucleoplasmic GATAD2B alternative.

Reason: R-HSA-9944092 connects catalystActivity 9944079 to NuRD assembly 9940443 and through its component/member relationships to Q8WXI9-containing entity 9940398 in GO:0005654. This supports the nucleoplasm annotation. HDAC1/2 provide the deacetylase activity according to the actual summation; GATAD2B membership is not converted into an isolated deacetylase claim or a universal complex stoichiometry.

Summary: The TCF19–FBP1 model contains GATAD2B in a nucleoplasmic NuRD assembly.

Reason: R-HSA-9944706 includes NuRD input 9940443 and promoter-associated output 9944698. Their explicit chains reach GATAD2B 9940398, human Q8WXI9 residues 1–593, in GO:0005654. Accept the location assertion. TCF19/CHD4 recruitment and perturbation experiments summarized by the model are not relabeled as direct GATAD2B promoter-occupancy assays, and no gluconeogenic enzyme activity is inferred.

Summary: The TCF19–G6PC event supports a modeled GATAD2B pool in nucleoplasm.

Reason: The actual R-HSA-9944712 input 9940443 and output 9944700 contain a typed route through the alternative GATAD2 set to human Q8WXI9 entity 9940398 in GO:0005654. Accept nucleoplasm as a core location. The described G6PC promoter IRE mutation and TCF19-dependent repression are model context, not a target-specific GATAD2B mutation or isolated GATAD2B binding assay.

Summary: The PCK1 recruitment model contains the same explicit nucleoplasmic GATAD2B alternative.

Reason: R-HSA-9944714 traces from NuRD input 9940443 and output 9944704 to GATAD2B 9940398 through actual hasComponent/hasMember edges. The endpoint is human Q8WXI9 residues 1–593 in nucleoplasm, supporting GO:0005654. This is a curated location/component assertion; it does not establish a separately inspected GATAD2B-specific PCK1 promoter experiment or transfer TCF19 recognition activity to p66β.

Summary: Ikaros-family recruitment retains a nucleoplasmic GATAD2B component.

Reason: R-HSA-9944893 connects NuRD input 9940443 to Ikaros-associated output 9944890, with an explicit route to human Q8WXI9-containing entity 9940398 in GO:0005654. The target and compartment support ACCEPT. The alternative Ikaros and GATAD2 sets do not imply that all paralogs coexist in one complex, and their modeled membership is not an independent binary-interaction assay for each possible pair.

Summary: The experimental chromosome context is best represented by chromatin.

Reason: Selected original PMID:27732854 describes chromatin-associated p66β-containing NuRD and GFP-p66β chromatin occupancy; the paper’s distinct p66 assemblies are not interpreted as alternative natural GATAD2B products. This supports GO:0000785 chromatin, directly part_of the original GO:0005694 chromosome. The source’s target figure images and supplemental occupancy panel were not independently inspected, so the refinement also draws on independent human p66β histone/NuRD evidence rather than claiming a new quantitative localization measurement.

Proposed replacements: chromatin

Summary: The chromosome mapping can be made more precise as chromatin localization.

Reason: The original UniProt location-vocabulary mapping cites SL-0468. Human p66β is a chromatin-associated NuRD component, supported by selected original PMID:27732854 and independent histone/NuRD experiments. GO:0000785 chromatin specifies the relevant chromosomal material; its verified direct part_of relation to GO:0005694 supports this spatial refinement. This is not an is_a claim and does not extend the annotation to centromeres, kinetochores or chromosome segregation.

Proposed replacements: chromatin

Summary: The LARC-associated annotation agrees with GATAD2B participation in chromatin remodeling.

Reason: PMID:16217013 isolates a human K562 nuclear LARC preparation containing SWI/SNF and NuRD/MeCP1 components and reports ATP-dependent remodeling of nucleosomal templates. The reviewed main text establishes complex-level activity; its individual p66beta peptide or figure row has not been independently inspected. The biological claim is independently supported by human p66beta chromatin/histone interactions and the NuRD structural network in PMID:16415179 and PMID:33283408. GATAD2B contributes noncatalytic recruitment or structural work within the remodeling machinery; this does not assign it the ATPase activity of CHD or SWI/SNF subunits.

Summary: GATAD2B contributes a structural and regulatory component to NuRD chromatin remodeling.

Reason: The actual Eumetazoa IBD AN0/PTN001003231 for GO:0006338 descends to the sequence-verified human AN16 target, with the two literal human GATAD2 donors and no lineage loss. The target appearing among the experimental descendants is legitimate grounding. Human p66beta binds histone tails and participates in MBD2-mediated repression in PMID:16415179; nuclear NuRD complex and cross-link analyses in PMID:33283408 support the conserved GATAD2 bridge between the core assembly and CHD remodeling module. The direct CR1/CR2 deletion tests in that latter paper use GATAD2A, so beta-specific details are not manufactured. Participation in remodeling is a structural/cofactor role; ATP hydrolysis and deacetylation remain activities of other subunits.

Summary: Chromatin remodeling is supported as a function of GATAD2B-containing NuRD.

Reason: The available PMID:9790534 abstract establishes a complex with histone deacetylation and ATP-dependent nucleosome-remodeling activities but does not by itself identify the exact GATAD2B experiment underlying this IDA. That original source-specific detail remains unverified, rather than being rejected from the abstract. Independent human p66beta experiments in PMID:16415179 and the native NuRD interaction topology in PMID:33283408 support the whole biological claim that GATAD2B participates in chromatin remodeling. Its role is structural and regulatory, not autonomous ATP hydrolysis or histone deacetylation.

Summary: The broad transcription-regulation inference can be refined to negative regulation of Pol II transcription.

Reason: The incoming inference cites InterPro IPR000679 and IPR013088. Independently, human p66β represses tethered reporters and enhances MBD2-mediated repression, with beta-directed depletion affecting that activity in PMID:16415179; PMID:11756549 also tests human p66 repression. This supports GO:0000122 negative regulation of transcription by RNA polymerase II. Official typed paths connect that term through GO:0045892 or GO:0006357 to the original GO:0006355. The refinement reflects the established corepressive work of GATAD2B in these assays, without asserting that every NuRD assembly invariably represses transcription.

Proposed replacements: negative regulation of transcription by RNA polymerase II

Summary: The conserved GATA-type zinc-finger domain supports the electronic zinc-binding assignment.

Reason: This IEA is specifically grounded in InterPro:IPR013088, the NHR/GATA-type zinc-finger domain. The official Q8WXI9 record annotates a GATA-type zinc-finger region at residues 414–467, within the conserved C-terminal region retained in the actual 593-residue target sequence and family alignment. Zinc coordination is consistent with that domain assignment. Retaining this structural molecular property does not establish a human GATA-family promoter motif or imply that a zinc-binding assay was performed on every experimental construct.

Summary: NuRD membership is inherited and independently demonstrated for human GATAD2B.

Reason: All four literal experimental donor lineages, including human GATAD2B itself, descend from AN0/PTN001003231 in the actual PTHR13455 tree. The exact 593-residue human target lies at AN16 and no blocking lineage loss was found. Human p66beta functional and biochemical evidence in PMID:16415179 and the human nuclear NuRD topology in PMID:33283408 independently support complex membership. Self-donor status is appropriate experimental grounding, not circularity. Mixed-paralog purifications do not imply that GATAD2A and GATAD2B necessarily coexist in one individual complex.

Summary: GATAD2B is a component of the NuRD complexes examined in human nuclear extracts.

Reason: PMID:33283408 reports GATAD2A/B in affinity-purified human NuRD cross-link networks, consistent with p66beta association and corepressor function in PMID:16415179. The source explicitly cautions that these are heterogeneous mixtures of paralog-defined complexes and that some cross-links are ambiguous. Thus NuRD membership is retained without claiming fixed stoichiometry, obligatory A/B co-occupancy, or a beta-specific deletion assay that the study performed on GATAD2A.

Summary: p66beta is directly identified in human MBD2- and MBD3-containing NuRD preparations.

Reason: The selected Methods and Results of PMID:16428440 describe tagged human MBD2/MBD3 purification from HEK293-derived cells and mass-spectrometric identification of p66alpha and p66beta in the resulting NuRD preparations. The explicit p66beta identification supports NuRD membership and agrees with later human nuclear NuRD topology in PMID:33283408. Detection of both paralogs across purified pools does not establish simultaneous p66alpha/p66beta occupancy of one complex, and deacetylase activity in those preparations is not attributed to GATAD2B.

Summary: The original p66 puncta do not resolve whether the compartment is a splicing-factor nuclear speck.

Reason: The selected original Methods, Results and Figure 2–5 captions of PMID:11756549 describe human p66 FLAG/GFP nuclear puncta in NIH3T3 cells, CR2 dependence and redistribution of coexpressed mouse MBD3; related HeLa observations are reported as data not shown. No splicing-factor marker was identified in that inspected material. GO:0016607 is more specific than any punctate nuclear pattern, so these positive localization observations do not yet resolve the exact annotated domain. This uncertainty does not deny nuclear localization or assert that the protein cannot occur in nuclear specks. This is uncertainty about compartment identity despite accessible evidence, rather than an inaccessible-paper default or a demonstrated exclusion.

Summary: The accessible abstract supports speckled colocalization but not the precise nuclear-speck compartment.

Reason: The authentic PMID:12183469 abstract reports that both p66 paralogs bind MBD2/MBD3 and show speckled colocalization. Its original full text remains inaccessible after the retained publisher attempts, leaving the defining compartment markers and exact beta experiment unresolved. The approximately 100-fold repression and specified co-immunoprecipitation described for p66alpha must not be reassigned to p66beta. Keep this specific GO:0016607 localization undecided without claiming wrong-paralog attribution or absence of the compartment.

Summary: CR2-dependent p66beta nuclear puncta are positive localization evidence with unresolved speck identity.

Reason: PMID:16415179 describes GFP-p66beta punctate nuclear localization and its dependence on the conserved C-terminal region and MBD2 in the tested fibroblast system. The inspected original prose does not identify those puncta with a diagnostic splicing-factor marker. Because GO:0016607 names the defined nuclear-speck compartment rather than nuclear puncta generally, the exact compartment remains uncertain. Retain the positive nuclear observations and their experimental context; this is not evidence that GATAD2B is excluded from nuclear specks. This is uncertainty about compartment identity despite accessible evidence, rather than an inaccessible-paper default or a demonstrated exclusion.

Summary: The electronic nuclear-speck mapping inherits an unresolved compartment-specific interpretation.

Reason: UniProt location mapping from SL-0186 is consistent with reports of punctate or speckled nuclear p66beta, but GO:0016607 denotes the specific nuclear domain characterized by localization of splicing factors. The inspected p66 literature demonstrates nuclear puncta and MBD redistribution without a diagnostic splicing-speckle marker. PMID:12183469 remains abstract-only in the available original-reading scope. These data neither verify this precise compartment nor demonstrate its absence. Preserve the general nuclear localization separately and leave this specific mapping undecided.

Summary: GATAD2B contributes to nucleosomal DNA binding in a chromatin-associated complex.

Reason: The literal contributes_to qualifier is essential. PMID:16217013 describes the human K562 LARC assembly, including NuRD/MeCP1 components, and complex-level binding and remodeling on nucleosomal templates. Its direct sequence-specific DNA-contact experiments concern hnRNPC1/C2, not isolated p66β, and the target-specific peptide panel has not been inspected. Independent human p66β NuRD membership and histone-tail association support its structural contribution to chromatin engagement. Retain the qualified complex-level function without converting it into autonomous nucleosomal DNA binding, ATPase activity or histone deacetylation by GATAD2B.

Summary: The generic protein-complex claim can be refined to NuRD complex membership.

Reason: PMID:16217013 identifies a human K562 LARC assembly containing SWI/SNF and NuRD/MeCP1 components; its target-specific p66β peptide panel remains uninspected. Independent human p66β biochemical and proteomic evidence establishes NuRD membership, supporting GO:0016581 NuRD complex. The official is_a chain through GO:0005667 reaches the original GO:0032991. This does not identify the whole LARC preparation as exclusively NuRD, erase the original source context, or transfer ATPase/deacetylase catalysis from other subunits to GATAD2B.

Proposed replacements: NuRD complex

Summary: NuRD-dependent fate control is demonstrated, but the GATAD2B-specific assignment remains unresolved.

Reason: This is a ComplexPortal NAS claim. The inspected original PMID:22560079 shows that mouse Mbd3 loss disrupts NuRD-dependent regulation of pluripotency genes and differentiation; Mbd3/Mbd3b restoration and Klf4/Klf5 manipulations connect transcriptional control with lineage commitment. These are positive complex-level results, not merely a disease association. However, the inspected experiments and occupancy assays identify Mbd3 and Mi2β/CHD4, without resolving a GATAD2B-containing assembly or its particular contribution to cell-fate specification. Human GATAD2B NuRD membership makes participation plausible but does not settle that source-specific assignment. Detailed supplementary procedures were not recovered. Preserve uncertainty without alleging a wrong paralog or denying the measured NuRD effects.

Summary: The electronic DNA-binding claim is assessed using independent p66-family evidence.

Reason: The incoming assertion derives from InterPro IPR000679, a GATA-type zinc-finger classification; that classification alone does not establish canonical GATA-site specificity. The broad sequence-specific DNA-binding claim has independent support from the actual PTHR13455 placement and its experimentally grounded ancestral DNA-binding-TF assertion. Original PMID:16159881 tests non-GATA Ex-1 recognition by a 122-residue worm DCP-66 fragment in yeast and competitive EMSA in reticulocyte lysate. ACCEPT therefore concerns the inherited biological claim, not an assumption that every GATA-type domain recognizes a GATA motif. The human comparison and unresolved mechanism are detailed in the source guide. This remains an inference, with no direct human sequence preference or affinity claimed. It is a potential recognition facet of the conserved transcriptional role, not evidence for an additional autonomous core unit. The queried ontology has no GO:0000981-to-GO:0043565 path; no hierarchical replacement is invented.

Summary: Negative transcription regulation can be refined using independent human p66β repression evidence.

Reason: Original PMID:22560079 directly supports NuRD-mediated restriction of pluripotency-gene transcription in mouse Mbd3 perturbation and rescue experiments, but does not identify a beta-specific p66 assay in the inspected main text. Independently, the human p66β reporter, interaction and depletion experiments in PMID:16415179 establish a corepressive contribution. These sources together support GO:0000122 negative regulation of transcription by RNA polymerase II, whose direct is_a parent is the original GO:0045892. Retain the original ComplexPortal NAS provenance and its mouse/Mbd3 scope; the specific human support is an independent source, not a reassignment of what the original paper tested.

Proposed replacements: negative regulation of transcription by RNA polymerase II

Summary: NuRD-dependent transcriptional activation is real, while p66β-specific participation remains unresolved.

Reason: Selected original PMID:19927129 Methods and Results show positive transcriptional effects of the FOG1–NuRD interaction: FOG1 motif/Δ45 mutants, MTA1/2/3 depletion, reporters and primary mutant-mouse cells demonstrate gene- and tissue-dependent activation as well as repression. Occupancy is measured using MTA2, RbAp46 and Mi2β/CHD4; the inspected main text names p66 without distinguishing alpha and beta. Thus the positive effect cannot be rejected because NuRD is commonly described as a corepressor. Nevertheless, this source does not resolve which p66 paralog executes the activating role, and the detailed supplement remains unavailable. Retain UNDECIDED for this human GATAD2B NAS context without claiming absence of a positive regulatory function.

Summary: The NuRD stem-cell differentiation result does not yet resolve the p66β-specific role.

Reason: PMID:22560079 demonstrates that mouse Mbd3-deficient embryonic stem cells incompletely silence pluripotency genes after LIF withdrawal, with partial differentiation and embryo-integration rescue after Klf4/Klf5 perturbation. Inducible Mbd3b restoration also restores NuRD recruitment and gene repression. These experiments establish a transcriptional mechanism for NuRD-dependent differentiation. They do not specifically perturb GATAD2B or identify its paralog composition in the relevant assembly within the inspected sections. Because the detailed supplement was not recovered, the particular GATAD2B assignment remains unresolved rather than contradicted. NuRD membership alone is not being used to copy every developmental outcome onto this subunit.

Summary: Human p66β performs transcription corepressor activity through NuRD recruitment.

Reason: Direct human recruitment/repression experiments establish this molecular function. The assay and construct limits are summarized in the source guide; no intrinsic HDAC activity or Gal4-independent DNA targeting is claimed.

Summary: Human p66β binds histone N-terminal tails in vitro.

Reason: PMID:16415179 tests in vitro translated human p66β with bacterially expressed GST tails of H2A, H2B, H3 and H4. All four tails retain p66β; acetylation of H2A, H3 or H4 reduces binding under the tested conditions. Detailed CR2 binding-domain mapping was performed on p66α, and H2B acetylation was not detected. This directly measured MF is distinct from the existing contributes_to nucleosomal DNA-binding claim. It describes a binding mechanism within the single NuRD corepression unit, without adding a separate core function or assigning histone modification catalysis.