cep-1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003677 DNA binding	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: CEP-1 is a bona fide DNA-binding protein, so this is not wrong, but DNA binding is a generic parent term. The more specific and informative molecular functions (sequence-specific DNA binding and DNA-binding transcription factor activity) are separately annotated and better capture the function.
GO:0003700 DNA-binding transcription factor activity	IEA GO_REF:0000120	MODIFY	Summary: CEP-1 is the worm p53-family transcription factor and binds a p53-like DNA consensus to activate transcription of target genes. This is a core molecular function. I propose a more specific RNA polymerase II-specific term as the core function, but the general term is correct. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0005634 nucleus	IEA GO_REF:0000120	ACCEPT	Summary: As a transcription factor, CEP-1 acts in the nucleus; UniProt records nuclear localization by similarity to the C. elegans ortholog. Core cellular component for a transcription factor.
GO:0006355 regulation of DNA-templated transcription	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: CEP-1 regulates transcription of target genes. This is correct but very general; the RNA polymerase II-specific positive-regulation term better reflects its activator role. Retained as a non-core, broader process annotation.
GO:0001666 response to hypoxia	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CEP-1 promotes apoptosis under hypoxic and other stress conditions (UniProt FUNCTION). This is a peripheral stress-response process for a pleiotropic transcription factor, kept as non-core.
GO:0005654 nucleoplasm	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Consistent with nuclear localization of a transcription factor. Reasonable but more granular than needed; subsumed by the nucleus annotation, kept as non-core.
GO:0005730 nucleolus	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Nucleolar localization is not part of the established function of worm p53/CEP-1, which acts as a sequence-specific transcription factor in the nucleoplasm. This electronically propagated component looks like an over-reach not supported by CEP-1 biology.
GO:0006979 response to oxidative stress	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CEP-1 promotes apoptosis under conditions of cellular and genotoxic stress, consistent with a role in oxidative-stress responses. Peripheral process for this pleiotropic TF, kept as non-core.
GO:0008270 zinc ion binding	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: The p53-like DNA-binding domain coordinates one zinc ion per subunit (UniProt COFACTOR and BINDING sites at residues 319, 322, 375, 379). Correct and structurally supported, though it is an accessory binding function supporting DNA binding rather than the core function.
GO:0008340 determination of adult lifespan	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CEP-1 negatively regulates lifespan (UniProt FUNCTION). A genuine but peripheral organismal-level role for this pleiotropic transcription factor, kept as non-core.
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage	IEA GO_REF:0000107	ACCEPT	Summary: CEP-1 is the central mediator of DNA-damage-induced germline apoptosis, acting downstream of DNA-damage signaling to induce egl-1 and ced-13. This is a core biological process. The p53-class-mediator child term is the most specific representation.
GO:0017053 transcription repressor complex	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: CEP-1 functions predominantly as a transcriptional activator of pro-apoptotic targets. While it interacts with the prmt-5/cbp-1 complex (which can inhibit its activity), placement in a transcription repressor complex mischaracterizes its primary role and is an over-reach of an electronically propagated component annotation.
GO:0042594 response to starvation	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CEP-1 promotes apoptosis under starvation among other stress conditions (UniProt FUNCTION). Peripheral stress-response process for this pleiotropic TF, kept as non-core.
GO:0042770 signal transduction in response to DNA damage	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CEP-1 acts in the DNA-damage response and is itself induced and phosphorylated following DNA damage. It functions as the transcriptional effector at the end of the pathway; the DNA-damage apoptotic-signaling terms capture this best. Kept as a non-core supporting process.
GO:0042771 intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	IEA GO_REF:0000107	ACCEPT	Summary: This is the single most specific and accurate process term for CEP-1, the worm p53-class mediator of DNA-damage-induced germline apoptosis (inducing egl-1/ced-13). Core biological process.
GO:0042803 protein homodimerization activity	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CEP-1 functions as a homodimer (UniProt SUBUNIT), consistent with p53-family DNA binding. Correct accessory molecular function supporting DNA binding; kept as non-core.
GO:0043565 sequence-specific DNA binding	IEA GO_REF:0000107	ACCEPT	Summary: CEP-1 binds the same DNA consensus sequence as p53 (UniProt FUNCTION) via its p53-like DNA-binding domain. This is a core molecular function underpinning its activity as a sequence-specific transcription factor.
GO:0045132 meiotic chromosome segregation	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CEP-1 has a normal developmental role ensuring proper meiotic chromosome segregation (UniProt FUNCTION). A genuine but non-core developmental process distinct from its DNA-damage apoptotic role.
GO:0045944 positive regulation of transcription by RNA polymerase II	IEA GO_REF:0000107	ACCEPT	Summary: CEP-1 is primarily a transcriptional activator, directly inducing target genes (egl-1, ced-13, phg-1) via RNA polymerase II. This accurately captures its mode of action as an activator and is treated as core together with the DNA-damage apoptosis role.
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Correct parent term describing CEP-1 as a p53-class mediator of intrinsic apoptosis. The DNA-damage-specific child (GO:0042771) is more precise and treated as core; this broader term is retained as non-core.
GO:0005634 nucleus	ISS GO_REF:0000024	ACCEPT	Summary: Duplicate of the nucleus localization (here by ISS from the C. elegans ortholog). CEP-1 acts in the nucleus; core component for a transcription factor.
GO:0001666 response to hypoxia	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS duplicate of the hypoxia-response annotation. CEP-1 promotes apoptosis under hypoxic stress; peripheral process, kept as non-core.
GO:0003700 DNA-binding transcription factor activity	ISS GO_REF:0000024	MODIFY	Summary: ISS transfer of the core transcription factor activity from the C. elegans ortholog. Correct; the RNA polymerase II-specific term is proposed as the most precise core molecular function. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0006355 regulation of DNA-templated transcription	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS duplicate. Correct but very general regulation-of-transcription term; retained as non-core in favor of the RNA polymerase II-specific positive regulation term.
GO:0006979 response to oxidative stress	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS duplicate of the oxidative-stress response. Peripheral stress process for this pleiotropic TF, kept as non-core.
GO:0008270 zinc ion binding	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS duplicate. The DNA-binding domain coordinates one zinc ion per subunit; accessory binding function supporting DNA binding, kept as non-core.
GO:0008340 determination of adult lifespan	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS duplicate. CEP-1 negatively regulates lifespan; peripheral organismal role, kept as non-core.
GO:0042771 intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	ISS GO_REF:0000024	ACCEPT	Summary: ISS transfer of the most specific and accurate process term: CEP-1 as the worm p53-class mediator of DNA-damage-induced germline apoptosis. Core biological process.
GO:0042803 protein homodimerization activity	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS duplicate. CEP-1 acts as a homodimer; accessory molecular function supporting DNA binding, kept as non-core.
GO:0043565 sequence-specific DNA binding	ISS GO_REF:0000024	ACCEPT	Summary: ISS transfer of sequence-specific DNA binding, a core molecular function. CEP-1 binds a p53-like consensus via its DNA-binding domain.
GO:0045132 meiotic chromosome segregation	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS duplicate. Genuine developmental role ensuring proper meiotic chromosome segregation, distinct from the core DNA-damage apoptosis function; kept as non-core.

Gene Description

Existing Annotations Review

Core Functions

Sequence-specific RNA polymerase II DNA-binding transcription factor that binds a p53-like DNA consensus element and activates transcription of target genes.

As the worm p53-class mediator, drives the intrinsic apoptotic response to DNA damage by transactivating pro-apoptotic BH3-only target genes (egl-1, ced-13) to trigger germline apoptosis after genotoxic stress.

References

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