Heterochromatin assembly vs. formation

[pgaudet]

During the transcription group discussion, the issue was raised that 'heterochromatin formation' is a more common term in the literature than 'heterochromatin assembly'. Moreover the LD caused issues, because heterochromatin assembly is not a type of chromatin assembly, although heterochromatin is a type of chromatin.

So, I removed the logical definitons, and changed 'GO:0031507 heterochromatin assembly' to 'heterochromatin formation', and changed definition from -def: "An epigenetic gene silencing mechanism that involves the assembly of chromatin into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation." [GOC:mah, PMID:25192661, PMID:33827924] to: "An epigenetic gene silencing mechanism in which chromatin is compacted into heterochromatin, resulting in a chromatin conformation refractory to transcription. This process starts with heterochromatin nucleation, its spreading, and ends with heterochromatin boundary formation." [PMID:25192661, PMID:33827924]

@colinlog @ValWood @hattrill @RLovering

[pgaudet]

The question is, should the children also be changed:

• 'constitutive heterochromatin assembly' -> 'constitutive heterochromatin formation'
• 'facultative heterochromatin assembly' -> 'facultative heterochromatin formation'
• 'heterochromatin assembly by small RNA' -> 'heterochromatin formation by small RNA' and likewise for
• 'subtelomeric heterochromatin assembly'
• 'pericentric heterochromatin assembly'
• 'inactivation of X chromosome by heterochromatin assembly'
• 'DNA methylation-dependent heterochromatin assembly'
• 'rDNA heterochromatin assembly'
• 'siRNA-independent facultative heterochromatin assembly'

Thanks, Pascale

[hattrill]

I think yes - that would be consistent with yesterday's discussion.

[ValWood]

me too.

[pgaudet]

• [x] standardized definitions
• [x] merged -id: GO:0140458 pre-transcriptional gene silencing by RNA into GO:0031048 small non-coding RNA-dependent heterochromatin formation

[pgaudet]

Changed definitions:

GO:0006346 DNA methylation-dependent heterochromatin formation -old def: "Repression of transcription by methylation of DNA, leading to the formation of heterochromatin." [GOC:mah] +new def: "Formation of constitutive heterochromatin by a pathway that includes methylation of genomic DNA such as CpG islands." [GOC:mah]

Change parent: from GO:0140718 ! facultative heterochromatin formation to GO:0140719 ! constitutive heterochromatin formation and remove has_part GO:0009008 ! DNA-methyltransferase activity

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Change definition GO:0140718 facultative heterochromatin formation -old def: "The compaction of chromatin into a conformation that is refactory to transcription but that be converted to euchromatin and allow transcription in specific contexts. These can be temporal (e.g., developmental states or specific cell-cycle stages), spatial (e.g., nuclear localization changes from the center to the periphery or vice versa due to exogenous factors/signals), or parental/heritable (e.g., monoallelic gene expression)." [PMID:17936700] +new def: "The compaction of chromatin into a conformation that is refactory to transcription but that can be converted to euchromatin and allow transcription in specific contexts. These can be temporal (e.g., developmental states or specific cell-cycle stages), spatial (e.g., nuclear localization changes from the center to the periphery or vice versa due to exogenous factors/signals), or parental/heritable (e.g., monoallelic gene expression). In metazoa, this involves the methylation of histone H3K27." [PMID:17936700]

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Change definition GO:0140719 constitutive heterochromatin formation -old def: "The compaction of chromatin into a conformation that is refractory to transcription." [PMID:17936700] -comment: Note that constitutive heterochromatin indicates that it usually cannot be reprogrammed to a transcriptionally-competent state, as opposed to facultative heterochromatin, which can be reprogrammed. +new def: "The compaction of chromatin into heterochromatin, a conformation that is refractory to transcription. Constitutive heterochromatin cannot be converted back to euchromatin, the transcriptionally-active conformation. In metazoa, this involves the methylation of histone H3K9." [PMID:17936700]

[pgaudet]

For consistency: we had changed the parent of 'GO:0006346 DNA methylation-dependent heterochromatin formation' from 'GO:0140718 ! facultative heterochromatin formation' to 'GO:0140719 ! constitutive heterochromatin'; we have now renamed it DNA methylation-dependent constitutive heterochromatin formation, even though this was in the parent term, but it was confusing not to have it in the term label.

[pgaudet]

Also, added comment to facultative heterochromatin formation:

Note also that facultative heterochromatin formation does not usually involve DNA methylation, while constitutive heterochromatin formation does.

and to GO:0140719 constitutive heterochromatin formation:

Note also that constitutive usually involves DNA methylation, while facultative heterochromatin formation does not.

[ValWood]

"Note also that constitutive usually involves DNA methylation, while facultative heterochromatin formation does not."

this isn't true for yeast which don't have DNA methylation so I'm not sure that this comment is super helpful for al curators, maybe you could qualify (I know it says usually, not always, but in yeast it is never)