BCL11A

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000122 negative regulation of transcription by RNA polymerase II	IDA PMID:19153051 BCL11A represses HBG transcription in K562 cells.	ACCEPT	Summary: BCL11A represses RNA polymerase II transcription. Reason: The source reports repression of HBG in human K562 cells. Later human erythroid promoter occupancy and genome-editing experiments independently establish direct gamma-globin repression. Retain the original experimental source without treating its reported proximal GGCCGG motif as the newer distal TGACCA mechanism.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA GO_REF:0000033	ACCEPT	Summary: BCL11A recognizes specific cis-regulatory DNA sequences. Reason: The phylogenetic assertion is supported by direct binding of human BCL11A to regulatory DNA. PMID29606353 combines protein-binding microarrays, purified-domain affinity measurements and human erythroid occupancy. The target in WITH/FROM reflects experimental grounding; the ancestral PAINT node was not independently reconstructed.
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA PMID:19153051 BCL11A represses HBG transcription in K562 cells.	ACCEPT	Summary: Sequence-specific promoter binding is an established BCL11A activity. Reason: The original HBG study reports promoter binding in K562 cells. Preserve this experimentally curated assertion while distinguishing its reported recognition site from the distal TGACCA motif established by later biochemical and human-cell experiments.
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA PMID:19153051 BCL11A represses HBG transcription in K562 cells.	ACCEPT	Summary: DNA-binding transcriptional repression is a principal BCL11A function. Reason: The original HBG repression assay is consistent with later direct promoter binding and perturbation. The strongest globin-rescue mechanism involves the XL isoform and its C-terminal ZnF456 array; the source row has no isoform field and is preserved as supplied.
GO:0003700 DNA-binding transcription factor activity	IBA GO_REF:0000033	MODIFY	Summary: The general DNA-binding transcription factor term can be refined to RNA polymerase II specificity. Reason: BCL11A directly regulates protein-coding promoters, including repression of gamma-globin and context-dependent activation in the corrected RAG study. RNA polymerase II-specific DNA-binding transcription factor activity retains both regulatory directions. This is refinement of an existing assertion, not a new annotation or a rejection of the PAINT node. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0005634 nucleus	IBA GO_REF:0000033	ACCEPT	Summary: BCL11A acts in the nucleus. Reason: Human XL/L localization, nuclear fractionation and promoter occupancy support the nuclear annotation. This is not a claim that every isoform is exclusively nuclear: the short S form can accumulate in the cytoplasm and relocalize upon interaction with longer forms.
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: BCL11A acts in the nucleus. Reason: Human XL/L localization, nuclear fractionation and promoter occupancy support the nuclear annotation. This is not a claim that every isoform is exclusively nuclear: the short S form can accumulate in the cytoplasm and relocalize upon interaction with longer forms.
GO:0005654 nucleoplasm	IDA GO_REF:0000052	ACCEPT	Summary: BCL11A is present in the nucleoplasm. Reason: The experimental imaging record and separate electronic prediction are consistent with nuclear BCL11A. Human-cell fractionation detects nucleoplasmic protein as well as chromatin and nuclear-matrix association; the individual imaging construct and cell record were not rederived.
GO:0005654 nucleoplasm	IEA GO_REF:0000117	ACCEPT	Summary: BCL11A is present in the nucleoplasm. Reason: The experimental imaging record and separate electronic prediction are consistent with nuclear BCL11A. Human-cell fractionation detects nucleoplasmic protein as well as chromatin and nuclear-matrix association; the individual imaging construct and cell record were not rederived.
GO:0005654 nucleoplasm	TAS Reactome:R-HSA-9934021	ACCEPT	Summary: BCL11A-containing neuronal progenitor BAF complexes are nuclear. Reason: This Reactome event assembles neuronal-progenitor BAF in the nucleoplasm. Retain the compartment statement and complex context; it does not make BCL11A the ATP-hydrolyzing subunit.
GO:0005654 nucleoplasm	TAS Reactome:R-HSA-9934024	ACCEPT	Summary: The BCL11A-containing BAF assembly is located in the nucleoplasm. Reason: The Reactome event places BCL11A/B with SMARCA4 in an ATPase module during BAF assembly. SMARCA4 supplies ATPase chemistry; this source assertion is a location, not BCL11A ATPase activity.
GO:0005694 chromosome	EXP PMID:29606353 Direct Promoter Repression by BCL11A Controls the Fetal to A...	ACCEPT	Summary: BCL11A occupies regulatory sites on chromosomes. Reason: The source maps BCL11A occupancy in human HUDEP-2 and primary differentiating CD34-positive erythroid cells using CUT&RUN. Direct promoter binding is supported by motif-centered footprints and loss of protection after targeted promoter editing. Peaks without the motif can also reflect nearby chromatin contacts, so not every peak is claimed as direct binding.
GO:0005694 chromosome	IEA GO_REF:0000044	ACCEPT	Summary: Chromosome association is consistent with the DNA-binding transcriptional role. Reason: Retain the curated UniProt location mapping, supported by human-cell chromatin occupancy and direct promoter footprints. Chromosome association does not imply a structural centromere or chromosome-segregation function.
GO:0005737 cytoplasm	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: Cytoplasmic localization occurs for particular BCL11A isoforms and conditions. Reason: PMID16704730 reports predominantly cytoplasmic GFP-BCL11A-S and its relocalization to nuclear paraspeckles when coexpressed with Gal4DBD-fused XL or L in COS7 cells. The general source location is preserved with this isoform and experimental-construct limit; it is not the principal site of transcriptional regulation.
GO:0005829 cytosol	TAS Reactome:R-HSA-9700131	MARK AS OVER ANNOTATED	Summary: The fusion-specific cytosol assertion is overextended to native BCL11A. Reason: The complete Reactome summary names BCL11A residues 1–219 fused to ALK residues 1058–1620 among ALK mutants that bind type I inhibitors. The source concerns this pathological fusion, not an independently established cytosolic location of native BCL11A. Preserve the exact TAS assertion but mark its transfer to the native gene product as over-annotation. This does not invalidate the separate cytoplasm annotation supported by isoform- and construct-specific localization experiments. Supporting Evidence: Reactome:R-HSA-9700131 BCL11A(1-219)InsDHPPA-ALK(1058-1620)
GO:0006357 regulation of transcription by RNA polymerase II	IBA GO_REF:0000033	ACCEPT	Summary: BCL11A regulates RNA polymerase II transcription. Reason: Direct repression of gamma-globin and context-dependent activation of RAG transcription support the direction-neutral process. Narrowing every source row to negative regulation would discard the reported positive regulatory context. The PAINT and ARBA assertions retain their distinct evidence provenance.
GO:0006357 regulation of transcription by RNA polymerase II	IEA GO_REF:0000117	ACCEPT	Summary: BCL11A regulates RNA polymerase II transcription. Reason: Direct repression of gamma-globin and context-dependent activation of RAG transcription support the direction-neutral process. Narrowing every source row to negative regulation would discard the reported positive regulatory context. The PAINT and ARBA assertions retain their distinct evidence provenance.
GO:0010628 positive regulation of gene expression	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: BCL11A can positively regulate gene expression in defined cellular contexts. Reason: The corrected and republished PMID29038163 reports XL binding and RAG transcriptional activation in pro- and pre-B cells. This supports a contextual positive role alongside the prominent repressor function. The exact original rat electronic donor chain was not reconstructed; no result from the retracted original version is treated as standalone evidence.
GO:0016363 nuclear matrix	EXP PMID:16704730 Functional studies of BCL11A: characterization of the conser...	ACCEPT	Summary: BCL11A-XL associates with the nuclear matrix in human cells. Reason: PMID16704730 fractionates Granta-452 and Namalwa cells and reports predominant XL nuclear-matrix partition; L also partitions with chromatin. Endogenous HEK293 protein shows similar enrichment. Retain the experimental and mapping records without extending the XL distribution to every isoform.
GO:0016363 nuclear matrix	IEA GO_REF:0000044	ACCEPT	Summary: BCL11A-XL associates with the nuclear matrix in human cells. Reason: PMID16704730 fractionates Granta-452 and Namalwa cells and reports predominant XL nuclear-matrix partition; L also partitions with chromatin. Endogenous HEK293 protein shows similar enrichment. Retain the experimental and mapping records without extending the XL distribution to every isoform.
GO:0016514 SWI/SNF complex	IDA PMID:23644491 Proteomic and bioinformatic analysis of mammalian SWI/SNF co...	ACCEPT	Summary: BCL11A is a component of mammalian BAF/SWI-SNF complexes. Reason: PMID23644491 identifies BCL11A/B in complex purifications and demonstrates stable association in human T-cell nuclear extracts by sedimentation, urea challenge and reciprocal immunoprecipitation. Membership is supported independently of the ARBA prediction. BCL11A is not assigned the ATPase chemistry of SMARCA4.
GO:0016514 SWI/SNF complex	IEA GO_REF:0000117	ACCEPT	Summary: BCL11A is a component of mammalian BAF/SWI-SNF complexes. Reason: PMID23644491 identifies BCL11A/B in complex purifications and demonstrates stable association in human T-cell nuclear extracts by sedimentation, urea challenge and reciprocal immunoprecipitation. Membership is supported independently of the ARBA prediction. BCL11A is not assigned the ATPase chemistry of SMARCA4.
GO:0016604 nuclear body	IDA GO_REF:0000052	ACCEPT	Summary: BCL11A is detected in nuclear bodies. Reason: The imaging assertion agrees with independently described XL nuclear dots and paraspeckle-marker colocalization. The exact source imaging record was not rederived, so its broad nuclear-body term is retained without assigning every observed body or isoform to a single subtype.
GO:0016925 protein sumoylation	ISS GO_REF:0000024	UNDECIDED	Summary: The inherited protein-sumoylation process requires clarification of BCL11A participation. Reason: PMID18681895 reports BCL11A sumoylation, UBC9 interaction and recruitment of SUMO1 and SENP2 to nuclear bodies. Being modified is insufficient to establish participation in the modifying process, while recruitment could provide a distinct organizing role. The complete relevant experiment and ortholog-source transfer were not inspected; retain uncertainty without assigning intrinsic SUMO ligase activity.
GO:0019901 protein kinase binding	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CASK interaction supplies a context for the kinase-binding annotation. Reason: PMID20623620 identifies association of CASK with Bcl11A-L and S in transfected COS cells and brain. Retain the ortholog-derived partner interaction in its neuronal context; CASK association neither transfers kinase activity to BCL11A nor establishes postsynaptic localization.
GO:0098794 postsynapse	IEA GO_REF:0000107	UNDECIDED	Summary: A postsynaptic BCL11A location requires target-specific evidence. Reason: The accessible CASK interaction study describes nuclear neuronal colocalization, although CASK has other synaptic functions. This does not independently substantiate or refute the postsynaptic source assertion. The exact rat donor experiment was not located; retain the electronic assertion unresolved instead of inferring its location from the partner.
GO:1903860 negative regulation of dendrite extension	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Bcl11A can restrict dendrite development in a neuronal transcriptional context. Reason: The original neuronal work reports cultured hippocampal responses to glutamate/NMDA and Bcl11A-L/DCC perturbation, including dendrite outgrowth. Retain the ortholog and phylogenetic developmental assertions with the experimental species, isoform and culture context. This is a transcription-dependent neuronal output, not direct actin or microtubule enzymatic activity.
GO:1904800 negative regulation of neuron remodeling	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Negative regulation of neuronal remodeling is a contextual developmental output. Reason: The neuronal studies connect Bcl11A-L and CASK/DCC pathways to restriction of neurite arborization. Preserve the broad inherited remodeling annotation without presenting this culture phenotype as an additional autonomous molecular activity. The original rat donor record was not independently reconstructed.
GO:1905232 cellular response to L-glutamate	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Bcl11A participates in the response of cultured neurons to glutamate. Reason: PMID20534004 reports reduced Bcl11A-L after glutamate stimulation and modulation of glutamate/NMDA-driven arborization by Bcl11A-L or DCC overexpression. This is a stimulus-dependent transcriptional response; BCL11A is not a glutamate receptor.
GO:2000171 negative regulation of dendrite development	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Bcl11A can restrict dendrite development in a neuronal transcriptional context. Reason: The original neuronal work reports cultured hippocampal responses to glutamate/NMDA and Bcl11A-L/DCC perturbation, including dendrite outgrowth. Retain the ortholog and phylogenetic developmental assertions with the experimental species, isoform and culture context. This is a transcription-dependent neuronal output, not direct actin or microtubule enzymatic activity.
GO:2000171 negative regulation of dendrite development	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Bcl11A can restrict dendrite development in a neuronal transcriptional context. Reason: The original neuronal work reports cultured hippocampal responses to glutamate/NMDA and Bcl11A-L/DCC perturbation, including dendrite outgrowth. Retain the ortholog and phylogenetic developmental assertions with the experimental species, isoform and culture context. This is a transcription-dependent neuronal output, not direct actin or microtubule enzymatic activity.
GO:2000173 negative regulation of branching morphogenesis of a nerve	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Bcl11A-L restricts axon branching in cultured neuronal systems. Reason: The CASK and glutamate studies report changes in axon branching after Bcl11A-L pathway perturbation. Retain the inherited morphological process with its developmental context and distinguish it from the molecular DNA-binding activity.

Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

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