From GO Public
BACKGROUND TO NOTCH SIGNALING
- Maturation of the notch receptor involves cleavage at the prospective extracellular side during intracellular trafficking in the Golgi complex.
- This results in a bipartite protein, composed of a large extracellular domain linked to the smaller transmembrane and intracellular domain (NICD).
- Binding of ligand promotes two proteolytic processing events; as a result of proteolysis, the intracellular domain is liberated and can enter the nucleus to engage other DNA-binding proteins and regulate gene expression.
Both Susan and Peter D'E have queried the Notch signaling terms.
- Where does the Notch signaling pathway end, given that it's such a short pathway.
- Are the co-activators/repressors that regulate transcription with Notch PART OF the pathway, or do they regulate the pathway?
- What do we mean by 'positive regulation of transcription of Notch receptor target GO:0007221' ?
[Term] id: GO:0007221 name: positive regulation of transcription of Notch receptor target namespace: biological_process def: "The activation of transcription of specific genes as a result of Notch signaling, mediated by the Notch intracellular domain." [PMID:12651094] synonym: "N receptor target transcription factor activation" RELATED  synonym: "Notch receptor target transcription factor activation" RELATED  is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter relationship: part_of GO:0007219 ! Notch signaling pathway
- Annotations to GO:0007221 are mainly to:
- RBPJ (part of the transcriptional activation complex that binds NICD to promote transcription of target genes).
- The whole pathway (ligand->Notch->nuclear TF/cofactors) is involved in regulation of transcription so having this term as part of the pathway is misleading. I believe the term is meant to represent the nuclear events that up-regulate transcription of target genes.
- We could rename GO:0007221 so that it points to nuclear events (occurs_in: nucleus)
- Or divide it up into the functions of the individual GPs.
E.g. RNA polymerase II transcription factor binding transcription factor activity involved in Notch signaling pathway --[isa]RNA polymerase II transcription coactivator activity involved in Notch signaling pathway sequence-specific DNA binding RNA polymerase II transcription factor activity involved in Notch signaling pathway