PMID:25356590

[PCarme]

• [ ] New term : normal cenH-derived RNA level A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of RNA transcribed from cenH measured in a cell is normal. cenH is a region located between mat2-P and mat3-M that is homologous to centromeric repeats, and that produces non-coding RNAs and small interfering RNAs.

• [x] New term : decreased subtelomeric heterochromatin RNA level A cell phenotype in which the amount of RNA derived from subtelomeric heterochromatin regions is lower than normal. Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected.

• [x] New term : decreased LTR-derived RNA level A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from long terminal repeat elements (LTRs) measured in a cell is lower than normal.

• [x] New term : decreased protein localization to chromatin at protein coding gene A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to chromatin at one or more protein-coding genes is decreased.

• [x] New term : normal protein localization to chromatin at protein coding gene A cell phenotype observed in the vegetative growth phase of the life cycle in which the localization of a protein to chromatin at one or more protein-coding genes is normal (i.e. indistinguishable from wild type).

• [ ] New term : normal protein localization to pericentric heterochromatin during vegetative growth A cell phenotype observed during the vegetative growth phase of the life cycle in which the localization of a protein to chromatin at the pericentric regions is normal (i.e. indistinguishable from wild type).

• [x] New term : decreased cenH-derived RNA level A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of RNA transcribed from cenH measured in a cell is lower than normal. cenH is a region located between mat2-P and mat3-M that is homologous to centromeric repeats, and that produces non-coding RNAs and small interfering RNAs.

• [x] New term : normal LTR-derived RNA level A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from long terminal repeat elements (LTRs) measured in a cell is normal (i.e. indistinguishable from wild type).

• [x] New term : normal subtelomeric heterochromatin RNA level A cell phenotype in which the amount of RNA derived from subtelomeric heterochromatin regions is normal (i.e. indistinguishable from wild type). Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected.

• [x] New term : increased histone H3-K4 acetylation at protein coding gene during vegetative growth A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 4 of histone H3 occurs to a greater extent than normal in regions containing protein-coding genes.

• [x] New term : decreased histone H3-K4 acetylation at protein coding gene during vegetative growth A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 4 of histone H3 occurs to a lower extent than normal in regions containing protein-coding genes.

• [x] New term : increased histone H3-K4 acetylation at LTR during vegetative growth A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 4 of histone H3 occurs to a greater extent than normal at long terminal repeat (LTR) regions.

• [x] New term : decreased histone H3-K4 acetylation at LTR during vegetative growth A cellular process phenotype observed in the vegetative growth phase of the life cycle in which acetylation of lysine at position 4 of histone H3 occurs to a lower extent than normal at long terminal repeat (LTR) regions.

• [x] normal telomere repeat region derived RNA level

[ValWood]

For normal protein localization to pericentric heterochromatin during vegetative growth

we currently have:

Since the pericentromere is the region either side of the central core (which is CENP-A), I think we should just rename normal protein localization to pericentric heterochromatin during vegetative growth (it only has one direct annotation, which is presumably pericentromeric)

[ValWood]

do you agree?

[ValWood]

normal subtelomeric heterochromatin RNA level

problem. we have normal subtelomere-derived RNA level

A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from sub-telomeric regions measured in a cell is normal (i.e. indistinguishable from wild type).

so, I was going to change this to normal subtelomeric heterochromatin RNA level because, the subtelomere is heterochromatin.

BUT, it has some annotations to ARRET, which it really telomere. I will rename

normal subtelomere-derived RNA level and create a new term normal telomere-derived RNA level to migrate the ARRET annotation to

[ValWood]

I made the definition

"A cell phenotype in which the amount of RNA derived from subtelomeric heterochromatin forming regions is normal (i.e. indistinguishable from wild type). Total RNA or a specific RNA, such as the mRNA transcribed from a gene of interest, may be affected." To cover all bases (excuse the pun!)

[PCarme]

For normal protein localization to pericentric heterochromatin during vegetative growth

we currently have:

Since the pericentromere is the region either side of the central core (which is CENP-A), I think we should just rename normal protein localization to pericentric heterochromatin during vegetative growth (it only has one direct annotation, which is presumably pericentromeric)

Alright, makes sense !

[PCarme]

normal subtelomeric heterochromatin RNA level

problem. we have normal subtelomere-derived RNA level

A cell phenotype observed in the vegetative growth phase of the life cycle in which the amount of any RNA transcribed from sub-telomeric regions measured in a cell is normal (i.e. indistinguishable from wild type).

so, I was going to change this to normal subtelomeric heterochromatin RNA level because, the subtelomere is heterochromatin.

BUT, it has some annotations to ARRET, which it really telomere. I will rename

normal subtelomere-derived RNA level and create a new term normal telomere-derived RNA level to migrate the ARRET annotation to

And that solves the issue.

[PCarme]

While making the changes in the session, I noticed it is not possible to add an assayed gene as an extension to the new term "increased histone H3-K4 acetylation at protein coding gene during vegetative growth" (FYPO:0008254).

It would make sense to be able to enter specific genes for this term. Same thing for the "decreased" version of this term.

[ValWood]

@kimrutherford should a configuration issue go on Canto tracker or config tracker?

[kimrutherford]

should a configuration issue go on Canto tracker or config tracker?

We have been putting them on the config tracker but it doesn't matter too much. I'm subscribed to all the trackers (except for curation) so I'll see issues wherever they go.