phenotypes at outer centromeric repeats (this is messy)

[fypoadmin]

quite often you see experiments with phenotypes which show things like

decreased histone H3-K9 dimethylation at centromere outer repeat
this is refering to the endogenous repeat dg.

However, you see abolished histone methylation at the inserted marker gene at this locus

would this make sense: abolished histone H3-K9 dimethylation at centromere outer repeat exogenous pol II transcribed marker gene (and restrict the other term to the endogenous repeats?)

from PMID:20211136 Anti-H3K9me2 chromatin immuno- precipitation (ChIP) on stc1D cells indicates that, as in dcr1D cells, H3K9me2 is only partially reduced on centromeric outer repeats (cen-dg) but is completely lost from the cen1:ura4+ marker gene. Consistent with this, a reduced level of Swi6 remains associated with outer repeats, but not with cen1:ura4+ (Figure 1E).

(we need some way to distinguish the exogenous from the endogenous transcripts)

Original comment by: ValWood

[fypoadmin]

that would be one fugly term name (or more?), but I think I see what you're trying to do ...

and ouch, I wonder if I've done annotations the wrong way, and if so, how many ...

anyway, more FYPO tomorrow :D

Original comment by: mah11

[fypoadmin]

I always thought the marker would reflect what happens with the endogenous transcripts

Original comment by: Antonialock

[fypoadmin]

So what happens (based on my limited understanding) is that the repetative nature of the repeats triggers dsRNA-> siRNA-> RNAi -> heterochromatin assembly.

So to get heterochromatin assembly (probably to start), you need some transcription of the repeats.

Inserting a reporter gene into the dg repeats is to show something else. This just shows that silencing is derepressed. The gene is deleted at its normal chromatin location and then inserted into the centromere. Cells can only grow if the silencing isn't happening (even though the inserted gene isn't a repeat (and as far as I know doesn't generate siRNAs, once the heterochromatin forms it spreads to the boundary elements)

So these 2 types of transcription in the outer repeat region have opposite meaning. The reporter gene indicates no silencing. The endogenous RNAi detection means that RNAi is working and silencing can occur (provided nothing else downstream is mutated).

Possibly if there was a single parent term with children for these 2 scenarios, we could make the parent "not for direct annotation" and migrate the remaining annotations to the children on a case by cases basis?

(this comment applies to all of the outer repeat terms, transcription, methylation etc)

Original comment by: ValWood

[fypoadmin]

No hurry for this, we can try to figure it out at curator meeting if you prefer. Just bear in mind when making annotations around this process.

v

Original comment by: ValWood

[fypoadmin]

ah yeah, I think I'm with you. I haven't done papers on silencing for eons, but I think I've been using the eg. abnormal chromatin silencing at centromere outer repeat region for the reporter gene growth assays is that ok

not sure I have seen this phenotype..at least not that I can remember on top of my head, abolished histone methylation at the inserted marker gene at this locus

Original comment by: Antonialock

[fypoadmin]

That would make sense. I don't think it is usual to test the methylation patter of the reporter gene.

Original comment by: ValWood

[fypoadmin]

OK. The common-parent angle makes it worth tackling at a meeting -- it'd probably be straightforward enough to add terms to distinguish levels of exogenous vs. endogenous transcripts, but most of the "silencing" is what you infer from the transcript levels you observe.

I haven't done a huge amount of annotation in this area, but I'm confident that I wouldn't have annotated exogenous transcript levels with the "outer repeat transcript level" terms. I'm not sure I remember seeing much to distinguish exogenous vs. endogenous for histone modifications.

Original comment by: mah11

[fypoadmin]

note to self: have added comments to the "cen outer repeat transcript" level terms. edit the comments to add name & ID of appropriate "exogenous transcript" terms if & when added.

Original comment by: mah11

[mah11]

closing because this is old and annotations haven't caused ructions in the meantime but reopen (or start a new ticket) if you spot problems