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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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polyadenylation-dependent snoRNA 3'-end processing #27068

Closed ValWood closed 4 months ago

ValWood commented 6 months ago

The term polyadenylation-dependent snoRNA 3'-end processing is a conflation of different pathways:

Ask about sno

Need to find a good review for snoRNA processing Considerations i) intronic snoRNAs ii) tandemly expressed snoRNAs (there is a pathway involving a stem loop which might be for separation of tandem snoRNA?) (presumably processing is different for these) iv) Are CD box and H/ACA box processed differently

In human a complex called "Integrator" which is absent from yeast is involved.

ValWood commented 6 months ago

Some papers:

The 3′ End Formation in Small RNAs https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977532/

Functional analysis of yeast snoRNA and snRNA 3'-end formation mediated by uncoupling of cleavage and polyadenylation https://pubmed.ncbi.nlm.nih.gov/11839805/

Human is different, integrator complex https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3969742/

Yeast, tramp /exosome and CPF https://pubmed.ncbi.nlm.nih.gov/18951092/

ValWood commented 6 months ago

This is a useful, more recent review which shows the genomic context dependent differences , and diffences between CD box and H/ACA for some contexts (but mainly assembly?) https://www.tandfonline.com/doi/full/10.1080/15476286.2023.2254540

Screenshot 2024-02-15 at 17 06 28 Screenshot 2024-02-15 at 17 06 51
ValWood commented 6 months ago

A good fist move here would be to merge polyadenylation-dependent snoRNA 3'-end processing into the parent "snoRNA 3'-end processing"

ValWood commented 6 months ago

also based on this:

In S. cerevisiae, termination of transcription of short noncoding RNAs, including snoRNAs, is facilitated by the Nrd1-Nab3-Sen1 (NNS) complex and Pcf11, a component of the cleavage and polyadenylation complex [Citation69,Citation70]. The NNS complex is recruited to specific residues on the C-terminal domain of RNA Pol II where it binds the RNA through the RNA binding protein subunits, Nrd1 and Nab3. The helicase Sen1 then interacts with RNA Pol II to terminate transcription of the nascent RNA and the elongation complex dissociates [Citation71–73]. In humans, the NNS is replaced by the Cap-binding complex (CBC) and Arsenic resistance protein 2 (ARS2), which interact to terminate transcription of independently transcribed snoRNAs or those that are capped [Citation74,Citation75]

I could create the term:

co-transcriptional monocistronic snoRNA 3'-end processing, cleavage and polyadenylation pathway

(the intron embedded snoRNAs are processed by 2 different pathways, but are not polyadenylated by CPF pathway)

I can also add capping as a dependency in the definition or comment of co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway (GO:0180012) and descendants.

ValWood commented 4 months ago

Tickets opened. will disambiguate existing structure. Can add more terms as requested.