Talk:Polyadenylation/GA1

GA Review

This is a very well written article, polished, well illustrated, and the references are great. It's great that a lot of the refs are reviews in well-respected journals and a lot have free full text. However, I do not believe it covers the subject in enough depth, so I'm failing it for now. Here are some specific suggestions:

How about sections such as Evolution, and History and discovery? Are there any technological applications? If so, that might make a good section.
How about more detail on the differences between procaryotes and eucaryotes? There could be separate sections on each, and I think a further explanation of why it promotes degradation in some cases and inhibits it in others would be good.
In addition to wikilinks, it would be good to provide short parenthetical explanations for unfamiliar words and concepts like exosome, degradosome, Xist, UTR. Similarly, it's worth explaining what is meant by concepts like AAUAAA and GU-rich region, since the reader might not be familiar with the subject. This is taught in intro-level biology classes, so the article shouldn't assume any familiarity with the subject area.

GU-rich should be easy enough, but explaining AAUAAA further will be hard, maybe creaing a stub on RNA sequence.Narayanese (talk) 05:53, 30 August 2008 (UTC)[reply]

Oh, I just meant explaining the general concept that each nucleotide has an abbreviation and what the abbreviation for each one you use is. delldot talk 22:19, 30 August 2008 (UTC)[reply]

I think a lot of the concepts could be expanded on for understandability. For example, for "The reaction is RNA + n MgATP → RNA–(A)n + n MgPPi" you could explain this reaction in words in addition or instead. Also, I don't think wikilinks are enough for explaining what the components are, I recommend an explanation of each. I'd also recommend a short explanation of each protein in the text under Mechanism (although the legend box at right works very well and I recommend keeping it).

They're all explained in the text... or you mean writing out the abbreviations in the text (I don't think that wil help, protein names aren't very informative)?Narayanese (talk) 05:53, 30 August 2008 (UTC)[reply]

The concern about expanding unfamiliar concepts applies throughout a lot of the article.
The Mechanism section only has one sentence about prokaryotes. Perhaps a separate section or a subsection on their mechanism?

The protein-protein interactions and RNA recognition parts don't seem to be known, plus there are one or a few poly(A) polymerases that are still unknown, but I found a paper recently discussing the interplay between the polymerase and the degrading enzymes.Narayanese (talk) 05:53, 30 August 2008 (UTC)[reply]

Sure, just explaining what is and is not known should be fine. delldot talk 22:19, 30 August 2008 (UTC)[reply]

This sentence is hard to understand: The differing 3'UTRs resulting from alternative polyadenylation can cause different regulation for different polyadenylation variants, since it can change which binding sites for microRNAs the 3'UTR contains.

Hopefully adding a description of microRNAs' functions is enough.Narayanese (talk) 05:53, 30 August 2008 (UTC)[reply]

Sure, and maybe reword for fewer uses of 'different'. delldot talk 22:19, 30 August 2008 (UTC)[reply]

I think the article needs more explanation of the purpose served by the poly(A) tail. The function section doesn't go into much detail. For example, in eukaryotic somatic cells, and mRNAs with shorter poly(A) tail are translated less and degraded sooner. Why are they translated less? Why are they degraded sooner? What's the mechanism?
Along those same lines, I think it would be helpful to place this subject in context with a summary of what's going on in the cell that causes RNA to be degraded without the poly(A) tail (or not to be, in those cases).
Similarly, I think a lot more info could be provided about how they get shorter. What's the mechanism for that? How long does it usually take? Is it different in different organisms?
Sentences like this should be placed in context: Deadenylases include CCR4-NOT, PAN2-PAN3 and PARN are these eukaryotic proteins? Humans only?

There's loads more info out there and I think this article would benefit from significant expansion. I think it would be especially helpful to expand on the differences in prokaryotes and eukaryotes and maybe have separate sections for each. I hope this isn't discouraging, it really is very well done and will certainly merit GA or FA status with some work. Definitely let me know if you would like to discuss anything or would like any further input. delldot talk 05:25, 29 August 2008 (UTC)[reply]

I should be able to find enough to write about the evolution and the downstream stuff like translation regulation. But discovery and technology (oligo-T selection of cDNA is the only thing that comes to mind) would likely be extremely short sections.

Thanks for the review! Narayanese (talk) 05:53, 30 August 2008 (UTC)[reply]

Sounds good. Like I said, what you have is high quality, so I look forward to seeing what else you bring. Definitely let me know if you want any input or anything. The discovery and technology sections were just suggestions, no need for those per se. But isn't it used in labs when working with RNA because the RNA is degraded so quickly otherwise? Anyway, I'm not asking for more info than what you'd find in an average textbook chapter or lit review on the subject, just a general survey of what's out there. In other words, the article should give a good overview of the info that is available; it would be unrealistic to expect more. I hope I'm making sense. Anyway, let me know if there's anything I can do to help! delldot talk 22:19, 30 August 2008 (UTC)[reply]

GA Review

This review is transcluded from Talk:Polyadenylation/GA2. The edit link for this section can be used to add comments to the review.

Well written?

RNAs are a type of DNA-like molecules. - A bit vague maybe say "Like DNA, ...."
"Nucleotides are the individual units that make up RNA." - Seems out of sequence, deal with structure first and types later?
"transcription is the synthesis of RNA from a DNA template" - also needs to be earlier, an explanation with another explanation nested within it is confusing.

Starting the section on "Nuclear polyadenylation" with the sentence "The poly(A) tail protects the mRNA molecule from enzymatic degradation in the cytoplasm" is confusing. You need to state at the start of each section what the subject is - expand and explain the section title.
"Failure of polyadenylation can result in human disease" - if you are going to mention this, it needs to be an independent subsection.

I'll rearrage the primer section. The history section looks good. I don't like your changes to the evolution section, PNPase doesn't really create polyA tails nor is an integral part of the mechanism (only in some of the cases). And all domains of life don't have polyadenylation, not even all have PNPase. And the additions to the lead don't increases the understanding of polyA much imo (the rewordings are good though) I didn't add "Failure of polyadenylation can result in human disease", though I like the ref. The subject is too broad though for inclusion, there'd be a large mix of genetic diseases with little to do with each other and not really having much to do with polyadenylation. Maybe make a further reading section instead. Narayanese (talk) 05:54, 13 February 2009 (UTC)[reply]

OK, please see all my edits as suggestions - I'm much more of a biochemist than a molecular biologist! I've reworded the first sentence of the evolution section a bit more and added PMID 9242905 to give a better review of the instances of poly(A) in prokaryotes. I was trying to edit the evolution section so that the connections between the facts were more apparent, but if I didn't quite hit on what these were please revise it some more. Tim Vickers (talk) 18:25, 13 February 2009 (UTC)[reply]

The problem is semantics and scope more than facts. A solution would for me to add a little section on heteropoymeric tails. Though "component of polyadenylation system" doesn't seem quite right. Narayanese (talk) 11:50, 14 February 2009 (UTC)[reply]

OK, that seems a good solution. Tim Vickers (talk) 21:47, 14 February 2009 (UTC)[reply]

endonucleolytic cleavage, used without definition.
The protein CFII is also involved in cleavage somehow - a weak statement. The protein CFII is needed for the cleavage reaction, but its role is not yet known?
and promotes it to terminate transcription - poor wording

Factually accurate?: Pass
Broad in coverage?: Pass
Neutral point of view?: Pass
Article stability?: Pass
Images?: Pass

Tim Vickers (talk) 00:13, 17 February 2009 (UTC)[reply]

Nice of you to review it, and thanks for the history and occurrence additions.

I'd rather keep mitochondria out of the lead, those that have been studied are so diverse that little can be generalised. Narayanese (talk) 13:08, 20 February 2009 (UTC)[reply]