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Fission Yeast Phenotype Ontology
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Ringlike nuclear chromatin #40

Closed fypoadmin closed 9 years ago

fypoadmin commented 13 years ago

Hi Midori,

I'd like to request a term for "ringlike nuclear chromatin"

Thanks, Antonia.

Original comment by: Antonialock

fypoadmin commented 13 years ago

Hi Antonia,

Midori is at a seminar this afternoon, but I think she will need more info for this one.

What is is? do you have a PMID?

Val

Original comment by: ValWood

fypoadmin commented 13 years ago

Original comment by: Antonialock

fypoadmin commented 13 years ago

Hi Val,

it's in a paper by Yanagida (18362178). You have curated it already but it was on the ref genome list so I thought I'd add the phenotypes. The mutants in question are shown in figure 6A page 1124

Antonia.

Original comment by: Antonialock

fypoadmin commented 13 years ago

Do you know if the marker is for all heterochromatin or rDNA heterochromatin? They also describe this as "nucleolar collapse" so it appears to be some sort of chromatin misorganization phenotype which results from nuleolar collapse? v

Original comment by: ValWood

fypoadmin commented 13 years ago

Both DAPI (fig 6A) and that Hoechst dye (fig 6B) stain all DNA; I don't even think they're particularly specific for chromatin, so the figure is certainly not specifically showing rDNA. (I do think it's reasonable to conclude that the DNA in the cell is still in some form of chromatin.)

I'd be inclined to annotate arc1-936 to "abnormal chromosome organization" (which I can add). The reasons are that they're looking at nuclear DNA (actually, theoretically all cellular DNA; the mitochondrial signal is probably just too faint to detect) and seeing that it doesn't end up in the same place as in wild type, on a scale that suggests that whole chromosomes or at least big parts/regions of chromosomes are abnormally located. Maybe you could use "abnormal chromatin organization" (which would be another new fypo term, and probably useful for other mutants anyway), but I'm not sure fig 6 provides direct evidence for an effect on chromatin structure.

How important is the ringlike appearance? If it's a big deal we could include a child term ...

hope this helps, m

Original comment by: mah11

fypoadmin commented 13 years ago

probably abnormal chromatin organization (or location?) would be best...

Original comment by: ValWood

fypoadmin commented 13 years ago

I've added these to FYPO:

abnormal chromosome organization FYPO:0000641 abnormal chromatin organization FYPO:0000642

Original comment by: mah11

fypoadmin commented 13 years ago

I'm going to close this since there haven't been any further comments (here, in email or in person). Easy enough to reopen or create a new item if anything else needs to be done.

m

Original comment by: mah11

fypoadmin commented 13 years ago

Original comment by: mah11