histone mRNA 3'-end processing comment

[gocentral]

Hi,

This original set term "histone mRNA 3'-end processing ; GO:0006398" and its histone mRNA specific parent term (histone mRNA metabolic process ; GO:0008334) were probably made based on the fact that in higher eukaryotes, histone mRNAs are not polyAdenylated, and thus have a different form of 3'-end regulation than other mRNAs. However, the term names and definitions are very general and may not be specific enough because it seems that histone mRNAs are pA's in lower euks.

See PMID: 17855393 Quotes: "In higher eukaryotes, replication-dependent histone mRNAs are non-polyadenylated and the formation of the 3'-ends of the mRNAs contributes to their accumulation during the S-phase of the cell cycle. The 3'-ends of the mRNAs are defined by a highly conserved stem-loop (S-L) structure (6) and a loosely defined purine-rich element (7) that lie immediately upstream and downstream of the 3'-end cleavage sites, respectively. "

"Histone mRNA biogenesis is also cell cycle regulated in lower eukaryotes, such as fungi and protozoans, however, here the 3'-ends of histone mRNAs are polyadenylated"

-Karen

Reported by: krchristie

Original Ticket: geneontology/ontology-requests/6321

[gocentral]

Good to know. At present neither term is used for very many annotations (fly and human, plus mouse and rat for the child term), and all are either U7 constituents or stem-loop binding proteins, so we're pretty much free to make the names and definitions completely specific for the metazoan processing.

Do you have anything specific in mind? Let me know if you want me to do the editing.

It might not be a bad idea to include a comment anyway, even after revising the names and defs. m

Original comment by: mah11

[gocentral]

I don't have anything in mind. I just went ahead and made the SF item to note the issue.

From the paper I cited, it seems like there's some interesting regulation specific to histone mRNAs even in lower euk's, but different than in higher euk's. So, it seems that the higher level term "histone mRNA metabolic process" might really be best as a general term, with multiple child terms to represent the various different processes that occur.

-Karen

Original comment by: krchristie

[gocentral]

OK, fine to leave the parent as is; I'll assume you'll add (or request) child terms for smaller euks as and when you figure out good names.

For GO:0006398, we could either leave it as a generic term for any histone mRNA 3'-end processing or rename it to be specific for the bigger-euk processing -- e.g. "stem-loop-containing histone mRNA 3'-end processing". Def changes to match, of course. Any preference?

m

Original comment by: mah11

[gocentral]

Hi Karen,

Would you wish to implement this, or close it as out-of-date?

Thanks, J, B, P

Original comment by: paolaroncaglia

[gocentral]

• labels: 397373 --> RNA processes
• assigned_to: nobody --> kchris

Original comment by: paolaroncaglia

[gocentral]

This comment is still true, so I've transferred it to Becky to decide upon action on it.

-Karen

Original comment by: krchristie

[gocentral]

• assigned_to: kchris --> rfoulger

Original comment by: krchristie

[gocentral]

Left GO:0006398 as it is, but added a comment; Comment: In higher Eukaryotes, histone mRNAs (stem-loop containing) are non-polyadenylated and thus have a different form of 3'-end regulation to other mRNAs. In lower Eukaryotes, the 3'-ends of histone mRNAs are polyadenylated.

and synonym: narrow synonym: stem-loop-containing histone mRNA 3'-end processing

Can add in terms for specific mechanisms underneath, as required.

thanks Becky

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-works-for-me

Original comment by: rebeccafoulger