ValWood
commented
3 years ago To clarify
and a more general function: GO:0140588 chromatin looping
is a new/biological process/ term. This is the only looping which was clearly multi-step, and therefore the only one retained in BP.
Obsoletion of existing terms was required because the were ambiguous (represented multiple activities, and this BP).
The new "chromatin looping" BP term is defined: A chromatin organization process that starts with the loading of an extrusion motor (SMC family complex) onto the chromatin, followed by chromatin extrusion that stops at loop anchoring sites on the chromosome.
So it's very specific for looping by extrusion, via SMC motors.
v
On 04/02/2021 16:35, pgaudet wrote:
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 https://github.com/ValWood and @colinlog https://github.com/colinlog have made suggestions for reannotation, see geneontology/go-annotation#3610 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: geneontology/go-ontology#19334 https://github.com/geneontology/go-ontology/issues/19334
Thanks, Pascale
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Dear all,
The proposal has been made to obsolete
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~ biological process: 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