#11760 new term: double-stranded/single-stranded junction telomeric DNA binding

[Nancy Campbell]

Hi,

new term request: double-stranded/single-stranded junction telomeric DNA binding

suggested ancestory:

child of: GO:0003691 double-stranded telomeric DNA binding

child of: GO:0098505 G-rich strand telomeric DNA binding

PMID:21852327

Aim: to annotate the IntAct complex Shelterin/Telosome in human to this new term.

GOC:nc
GOC:bhf
GOC:BHM

Thanks

Nancy & Birgit

[Tanya Berardini]

Can you please also suggest a definition? Is the binding to either ds telomeric DNA or ss telomeric DNA or is there a junction composed of both ds and ss DNA and it is that junction that is bound?

Thanks for the clarification.

[Nancy Campbell]

Suggested Definition:
Interacting selectively and non-covalently with double-stranded/single-stranded telomeric DNA junctions.

clarification:
The shelterin complex binds at the junction formed where ds (double-stranded) and ss (single-stranded) telomeric DNA meet i.e. double-stranded telomeric DNA is connected to/becomes single-stranded G-rich telomeric DNA 3' overhang. The shelterin complex has components that bind to single-stranded telomeric DNA and components that bind to double-stranded telomeric DNA, hence it is able to bind to this junction.

Does this help?

Thanks

[Tanya Berardini]

Revised definition:

Interacting selectively and non-covalently with the junction formed at the point where double-stranded telomeric DNA becomes a single-stranded G-rich telomeric DNA 3' overhang.

What do you think?

[Nancy Campbell]

Very good. Thanks.

[Tanya Berardini]

After thinking about this some more, I decided to add this term as a direct child of 'structure-specific DNA binding' instead of as both is_a
child of: GO:0003691 double-stranded telomeric DNA binding
child of: GO:0098505 G-rich strand telomeric DNA binding

Reasoning: The defs of both the telomeric DNA binding terms refer to interacting selectively with ds or G-rich strand DNA. The new term refers to interacting with the junction which is neither ds only or G-rich ss only, but both.

[Tanya Berardini]

[Term]
+id: GO:0090655
+name: double-stranded/single-stranded junction telomeric DNA binding
+namespace: molecular_function
+def: "Interacting selectively and non-covalently with the junction formed at the point where double-stranded telomeric DNA becomes a single-stranded G-rich telomeric DNA 3' overhang." [GOC:BHF, GOC:bhm, GOC:nc, PMID:21852327]
+is_a: GO:0043566 ! structure-specific DNA binding
+created_by: tanyaberardini
+creation_date: 2015-07-02T11:33:39Z
+

[Nancy Campbell]

Thanks. great. That makes perfect sense.

as the jucntion is formed of telomeric DNA, might linking to telomere related term be appropriate such as

telomeric DNA binding
Ontology Molecular Function
Definition Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.

Would you like me to open a new ticket for this?

Thanks.

[Tanya Berardini]

I'll just add that new parent next week. Today is a holiday here in the US!

[Nancy Campbell]

Hi,

Thanks Tanya. Great.

maybe also (?) go as child of more granular term of GO:0043566 structure-specific DNA binding such as:
GO:0000406
Name double-strand/single-strand DNA junction binding
Ontology Molecular Function
Definition Interacting selectively and non-covalently with a region of DNA that contains double-stranded DNA flanked by a region of single-stranded DNA.

Thanks

Nancy

[Tanya Berardini]

Changes:

-is_a: GO:0043566 ! structure-specific DNA binding
+is_a: GO:0000406 ! double-strand/single-strand DNA junction binding
+is_a: GO:0042162 ! telomeric DNA binding