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[go-friends] Obsoletion notice: GO:0090579 dsDNA loop formation & children

Pascale Gaudet Pascale.Gaudet at sib.swiss
Thu Feb 4 08:35:18 PST 2021


Dear all,

The proposal has been made to obsolete

- GO:0090579 dsDNA loop formation
-  GO:0090202 gene looping
- GO:0071733 transcriptional activation by promoter-enhancer looping
- GO:0090203 transcriptional activation by promoter-terminator looping

The reason for obsoletion is that the way those terms are defined, they are better represented by molecular functions. We have created 3 functions to replace those terms:

GO:0140587  chromatin loop anchoring activity
GO:0140585  promoter-enhancer loop anchoring activity
GO:0140586  promoter-terminator loop anchoring activity

and a more general function: GO:0140588 chromatin looping

The concepts of transcription regulation should be captured with 'GO:0006355 regulation of transcription, DNA-templated' or a child term.

There are 25 EXP annotations to those 4 terms. @ValWood and @colinlog have made suggestions for reannotation, see https://github.com/geneontology/go-annotation/issues/3610 (it may be a couple of days until the new terms are available).

We are opening a comment period for this proposed obsoletion. We’d like to proceed and obsolete this term on February 18th, leaving some time to make the corrections. Unless objections are received by February 18th, 2021, we will assume that you agree to this change.
You can comment on the ticket here: https://github.com/geneontology/go-ontology/issues/20204

Thanks, Pascale



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