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THAP family remove annotations #3125

Closed RLovering closed 4 years ago

RLovering commented 4 years ago

Hi

I have looked in PubMed and some THAP reviews for confirmation that these proteins bind DNA and there is very little evidence of this. The best is for THAP1 and THAP11. But even though a few papers comment on THAP7 and THAP5 binding DNA the evidence just isn't there. For THAP5 they rely on identification of DNA motif and based on nuclear extracts PMID:21110952. The THAP7 papers don't have DNA binding evidence either.

THAP4 is involved in heme binding.

THAP9 does bind DNA but is shown to be an active DNA transposase PMID: 23349291 with DNA binding discussed in PMID: 20010837 (THAP Proteins Target Specific DNA Sites Through Bipartite Recognition of Adjacent Major and Minor Grooves).

Summary:

THAP1 dbTF
THAP2 no data
THAP3 reg Tx but no DNA binding confirmed
THAP4 heme binding
THAP5 PMID 21110952: DNA motif identified using MeWo nuclear extract and the THAP5/dsDNA complex Ippt, then EMSA with nuclear extract
THAP6 only 1 paper with THAP6 and no mention of DNA binding
THAP7 THAP7 (2 above) PMID:15561719 paper does not show DNA binding, but does show Tx regulation, annotated this as shows histone tail binding associated with C-terminal 77 amino acids of THAP7. HDAC3 bound specifically to a GST fusion of the THAP domain (amino acids 1–100), but not the central region of the protein (101–231). Some residual binding was also observed with the HID domain (232–309). Subsequent paper PMIDF:16195249 still not showing DNA binding although other papers claim this does
THAP8 no papers
THAP9 PMID:23349291 an active P-element DNA transposase. PMID:20010837 DNA binding
THAP10 no papers
THAP11/Ronin several papers confirm this is a dbTF PMID: 20581084 PMID:20581084 PMID:19008924 PMID:18585351 THAP11 ChIP data localises this protein to the promoter
THAP12/THAP0/DAP4 PMID: 7828849 THAP12 but no DNA binding data, proposed as serine/threonine kinase
RLovering commented 4 years ago

Because of the information above this family should not be annotated as dbTF unless expt evidence is available. Please remove the following annotations: Note that the InterPro IPR006612 domain does not support these annotations:

GENE PRODUCT ID SYMBOL QUALIFIER GO TERM GO NAME ECO ID GO EVIDENCE CODE REFERENCE WITH/FROM TAXON ID ASSIGNED BY ANNOTATION EXTENSION GO ASPECT
Q7Z6K1 THAP5 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q7Z6K1 THAP5 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
Q8WTV1 THAP3 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q8WTV1 THAP3 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
Q9BT49 THAP7 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q9BT49 THAP7 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
Q9P2Z0 THAP10 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q9P2Z0 THAP10 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
O43422 THAP12 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
O43422 THAP12 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
Q9H0W7 THAP2 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q9H0W7 THAP2 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
Q8WY91 THAP4 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q8WY91 THAP4 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
Q8TBB0 THAP6 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q8TBB0 THAP6 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
Q8NA92 THAP8 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q8NA92 THAP8 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
Q9H5L6 THAP9 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0000255 ISM PMID:19274049 InterPro:IPR006612 9606 NTNU_SB   F
Q9H5L6 THAP9 enables GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ECO:0005556 ISA GO_REF:0000113 tfclass:2.9.1 9606 NTNU_SB   F
mlacencio commented 4 years ago

Dear @RLovering and @pgaudet

I have removed the annotations!

Best,

Marcio

pgaudet commented 4 years ago

Thanks !