Merge 'transcription regulatory region DNA binding' into 'transcription regulatory region sequence-specific DNA binding' - & children

[pgaudet]

All binding is specific - for binding to produce a biological effect, the binding must be specific.

So I will merge:

• 'transcription regulatory region DNA binding' into 'transcription regulatory region sequence-specific DNA binding'

• same for all similar children

[ValWood]

These terms have different meanings.

The sequence specific one means that it binds to a defined motif or sequence. The parent is not necessarily at a specific motif or sequence.

This might include DNA break points of other structures (Holliday junctions for example)

[ValWood]

Condensin, DNA replication machinery outside of origins, endonucleases, histones not sequence specific

[pgaudet]

But then the fact that they bind regulatory regions is meaningless ! Those should be annotated to either DNA binding or some descendant. I think those bind specific conformations, so terms such as those might be more appropriate:

'DNA secondary structure binding' 'bubble DNA binding' 'D-loop DNA binding' 'DNA hairpin binding' 'double-strand/single-strand DNA junction binding' 'four-way junction DNA binding' 'heteroduplex DNA loop binding' 'Y-form DNA binding' 'G-quadruplex DNA binding'

Would that work ?

Thanks, Pascale

[ValWood]

I was confused. SOrry!

This merge seems OK

'transcription regulatory region DNA binding' into 'transcription regulatory region sequence-specific DNA binding'

I had read that 'xx DNA binding' into 'xx sequence-specific DNA binding'

so I thought that you wanted to merge GO:0043565 sequence-specific DNA binding into DNA binding

from the title

[pgaudet]

PR https://github.com/geneontology/go-ontology/pull/19339