Talk:RNA polymerase II

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This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Peer reviewers: Lovinne, CraigClark.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 07:39, 17 January 2022 (UTC)

Confused by the elongation part
I am confused by the elongation part of this article and I see no citations or references that would allow the text to be verifiable.
 * Did you read the recent review by one of the experts on transcription regulation: Danny Reinberg? I think this would help the entire article a lot, especially the elongation part could be revised thoroughly.
 * I don't understand the classification of elongation promoters?? Even if these are rather factors I don't follow it. Why did you make this division? What means Drug/sequence-dependent arrest affected factors? Why would factors that are affected by drugs be different from the ones that affect the catalytic activity of the RNA polymerase?
 * What is the reference of There is, however, a change in methylation of the polymerase, midway through elongation the phosphorylation location changes slightly under the influence of Ctk1.? What is meant by the phosphorylation location? Do you mean a site on the CTD of the polymerase? --AAM 22:19, 19 February 2006 (UTC)

I removed the part on the methylation by Ctk1. Ctk1 is a kinase and these do not methylate. There might have been some confusion as phosphorylation of PolII by Ctk1 could affect the Set2 mediated histone methylation (see Genes Dev. 2003 Mar 1;17(5):654-63. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast.) If anybody comes with a reference proving that I was wrong in removing this text we can discuss. --User:AAM | Talk 16:08, 1 March 2006 (UTC)

Role of TATA box
The role of the TATA box is somewhat overestimated here. Relatively recent genome-scale studies in Homo sapiens and other species indicate that TATA boxes are NOT present in a majority of active promoters; e.g. see Bing Ren paper in Nature 2005. This is also, of course, supported by computational studies (i.e. searching for TATA boxes, not finding them...)

So... what is it?
This article tells me what RNA polymerase II does, but it doesn't say what it is - is it a kind of RNA? An organic chemical? An organelle? Same complaint for RNA polymerase I and RNA polymerase III. This is like writing an article on horse saying that a horse is ridden and used for farm work without ever saying that it is an animal! bd2412 T 18:28, 15 December 2006 (UTC)

I think the first sentence would be improved were it to read: "RNA polymerase II (also called RNAP II and Pol II) is an enzyme found in eukaryotic cells which transcribes DNA to synthesize precursors of mRNA and most hnRNA." This takes care of the essential basics which I feel are missing from this page.

It might also be useful to explain some of the abbreviations - for example hnRNA stands for 'histonal RNA'. 163.1.236.79 13:56, 10 February 2007 (UTC)


 * Please note: hnRNA = heterogeneous nuclear RNA (the unspliced pre-mRNA is of very different size, only found in the nucleus, hence its name; see Alberts et al.) and likewise hnRNP = heterogenous nuclear ribonuclein protein (a protein associated with hnRNA). Wlanger (talk) 10:50, 16 January 2011 (UTC)

RNAPII is a protein/protein complex, not an organelle or a chemical. It is fairly clear what it is and RNAP is not an easy subject, so it is expected that it wouldn't be easy to understand. B —Preceding unsigned comment added by 146.115.19.108 (talk) 07:56, 20 December 2007 (UTC)

Picture?
I think this article would benefit from a picture/diagram of RNAP II. 203.160.122.99 21:26, 19 October 2007 (UTC)


 * We might try "RNA polymerase (1i6h).png" from Wikimedia Commons. I can look into it further, but I think it's an image of yeast RNA polymerase II.    Forluvoft 21:37, 19 October 2007 (UTC)

New category to replace DNA Replication category?
Shouldn't this article and others related to transcription be re-categorized to a new category, Category:DNA transcription? Category:DNA replication doesn't make sense to me. —Preceding unsigned comment added by Skoch3 (talk • contribs) 05:59, 11 January 2008 (UTC)

Possible revision of article
I find this article a bit confusing. RNA polymerase II is only a small part of it. Transcription of primarily mRNAs occurs after the RNA polymerase II holoenzyme has been assembled and in place on the promoters. May I suggest replacing the transcription sections with a short discussion of RNA polymerase II holoenzyme, and let the holoenzyme article begin the discussion of transcription.

Also, what do you think of additional sections here about transcription of the subunits of RNAP2? What causes its transcription? How many are made and incorporated into transcription factories?

And, perhaps a bit more on the assembly of RNAP2 would be good: parallel processing, concentration dependency, diffusion, or active diffusion?

How long do the components (subunits) last before the cell has to replace each. How is this done? Is the whole complex destroyed or is there part replacement? Marshallsumter (talk) 00:26, 14 February 2010 (UTC)

I have gone ahead and modified the article quite a bit. As indicated above I asked for some input beforehand and left a message on the discussion page of WikiProject Genetics at the same time as the above - also no feedback. No one home I guess. I believe I have answered the concerns of the refimprove box from June 2009 so I will remove it. Please feel free to criticize further, and of course with specificity. Marshallsumter (talk) 21:26, 19 February 2010 (UTC)

Additions to page
I am going to add a history/discovery section: One that talks about the discovery of the enzyme RNA Polymerase II. In this same section I will quickly summarize the other two RNA Polymerases (I,III) and possibly how to distinguish between them experimentally. This addition, not sure in the same section, I will emphasize that the three different polymerases play different roles in transcription. (All the enzymes will be linked to their corresponding wiki page). In the introduction: I am going to add the specific promoter the enzyme binds to (Class II Promoter), and a brief description of what that is. Also in the introduction I am going to mention the role it plays with other proteins to form the "pre-initiation complex" and what this is in terms of transcription. Jasper94574 (talk) 06:27, 21 February 2017 (UTC)

Kinetics
The section begins with a general paragraph about how RNA polymerase II is an enzyme and how they are like, but not the values of its $$K_m$$, $$k_\text{cat}$$ or $$V_\text{max}$$. Alfa-ketosav (talk) 07:20, 21 April 2024 (UTC)