Different treatment of 'repressing RNAs'

[ValWood]

We have

https://www.pombase.org/gene/SPNCRNA.9001 repressing RNA for https://www.pombase.org/gene/SPBC8E4.01c

https://www.pombase.org/gene/SPNCRNA.1712 for https://www.pombase.org/gene/SPBP4G3.02

but for tco1 we have treated as alternative transcripts translationally silent transcript from tco1 locus https://www.pombase.org/gene/SPAC17G6.02c

I think treating as an independent ncRNA is perhaps clearer?

(need to check this is the same situation but at first glance it seems to be)

[mah11]

This looks like a curation issue.

The only reason tco1 has been done as alternative transcripts is that you put it on the list in https://github.com/pombase/curation/issues/61 (and I tried it first because having the RNA annotated meant the coordinates were available).

[kimrutherford]

I think treating as an independent ncRNA is perhaps clearer?

Does that mean that the non-coding transcript would be treated as a different gene?

[ValWood]

Yes, there is a precedent for this: here https://www.pombase.org/gene/SPNCRNA.9001 repressing RNA for https://www.pombase.org/gene/SPBC8E4.01c

and here https://www.pombase.org/gene/SPNCRNA.1712

I suspect the way they were created was based on how they were described in the publications.

@juanmatacambridge @bahler what do you think is the best way to represent these 'same strand non-coding alternative transcripts' ?

[bahler]

I would show these the same way as all other ncRNAs: a thin grey arrow indicating transcript length and direction

Cheers,

• Jurg

[ValWood]

that wasn't quite the question. It was whether these "alternative transcripts' in the same strand as a protein coding gene should be classified as alternative transcripts of the locus (i.e 'independent' non coding RNAs). But

i.e as for tco1 https://www.pombase.org/gene/SPAC17G6.02c SPAC17G6.02c.1 SPAC17G6.02c.2

or as independent non coding RNA's ?

Actually, I'm answering the question. I think it makes more sense to change this feature to an independent RNA. ...and we only have one to fix.

Is there a specific classification for this type of regulatory RNA on the same strand as the coding gene?

[juanmatacambridge]

Agree

[bahler]

Without any additional data, there's no specific classification for such ncRNAs

Cheers, -Jürg

[ValWood]

There is data:

tco1 translationally silent transcript from tco1 locus https://pubmed.ncbi.nlm.nih.gov/18276645/

prt2 repressing sense RNA Prt2 https://www.pombase.org/reference/PMID:29414789 pho84

nc-pho1 translationally silent transcript from pho1 locus https://www.pombase.org/reference/PMID:24493644

something like: x repressing translationally silent sense transcript ? (a bit redundant?) x repressing sense transcript ? translationally silent sense transcript ?

(In the absence of any more 'official' classifier, I would like to standardise)

[juanmatacambridge]

In the case of tco1 there is no independent ncRNA. There is a change in promoter (TSS) that creates an mRNA with a longer 5'UTR, which then represses translation.

I would say it is an alternative transcript of the tco1 gene.  I haven't looked at the others

It's  common in cerevisiae (PMID: 29474919 https://www.ncbi.nlm.nih.gov/pubmed/29474919) and we have seen some examples in meiosis in pombe.

Juan

[ValWood]

OK so if the transcript contains an orf, even if it isn't translated its an mRNA, but with no product?

So, that would make nc-pho1 which is described as an lncRNA in the manuscript also an alternative transcript, since the transcript is on the sense strand and contains the orf. It seems the same (i.e. different TSS, longer 5' UTR). Or is there additional criteria?

"The expression of the phosphate transporter Pho84 in fission yeast Schizosaccharomyces pombe is repressed in phosphate-rich medium and induced during phosphate starvation. Two other phosphate-responsive genes in S. pombe ( pho1 and tgp1 ) had been shown to be repressed in cis by transcription of a long noncoding (lnc) RNA from the upstream flanking gene, but whether pho84 expression is regulated in this manner is unclear. Here, we show that repression of pho84 is enforced by transcription of the SPBC8E4.02c locus upstream of pho84 to produce a lncRNA that we name prt2 ( p ho - r epressive t ranscript 2). We identify two essential elements of the prt2 promoter, a HomolD box and a TATA box, mutations of which inactivate the prt2 promoter and de-repress the downstream pho84 promoter under phosphate-replete conditions. We find that prt2 promoter inactivation also elicits a cascade effect on the adjacent downstream prt (lncRNA) and pho1 (acid phosphatase) genes, whereby increased pho84 transcription down-regulates prt lncRNA transcription and thereby de-represses pho1 Our results establish a unified model for the repressive arm of fission yeast phosphate homeostasis, in which transcription of prt2 , prt , and nc-tgp1 lncRNAs interferes with the promoters of the flanking pho84 , pho1 , and tgp1 genes, respectively. "

[ValWood]

Penny dropping.....

So these are trancripts with uORFs:

The poor translation of Ndc80 protein from the long transcript led to it being named a “LUTI” or “Long Undecoded Transcript Isoform”, and depends on the translation of AUG-initiated uORFs.

Perhaps I request a SO term for “Long Undecoded Transcript Isoform”. We need some way to indicate that the large orf is not translated from this transcript

[ValWood]

See what happens in the contig map with tco1 https://www.pombase.org/gene/SPAC17G6.02c it's confusing....

It might work if these are curated as mRNAs without the orf coordinates. I will try that.

[juanmatacambridge]

I would think this is correct?

What do they call them in the Brar paper?

[kimrutherford]

It might work if these are curated as mRNAs without the orf coordinates. I will try that.

I'm not sure that will work. Could you let me know when you make that change so I can keep an eye on things?

[ValWood]

https://github.com/pombase/curation/issues/3386