Talk:Transcription (biology)

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This article was the subject of a Wiki Education Foundation-supported course assignment, between 9 January 2020 and 24 April 2020. Further details are available on the course page. Student editor(s): Charlov21. Peer reviewers: Magdala5.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 11:37, 17 January 2022 (UTC)

Lead section too long
The lead seems too long, and contains quite a few inaccuracies. A good lead should be brief and refer to the major sections of the article. This one is long and often too detailed. Some of the inaccuracies:
 * ...which produces a complementary, antiparallel RNA strand: RNA is mostly single-stranded, so it would be better to say that the RNA sequence is reverse complementary to the template strand of the DNA
 * Both RNA and DNA are nucleic acids, which use base pairs of nucleotides ...: Again, RNA usually does not contain base pairs. In double-stranded DNA, the information is stored twice (redundantly in the two strands), in RNA it is present once in a single strand.
 * Transcription proceeds in 5 or 6 steps, each moving like a wave along the DNA: This is a list that used to make sense, referring to steps in transcription elongation. In the current form, point 6 is the odd one out, certainly not moving like a wave along the DNA.
 * The other DNA strand is called the coding (lagging) strand...: One strand is called the template strand, and the other the non-template strand (or coding strand because its sequence, apart from the U vs T issue, is identical to that of the RNA). Why would it be called the lagging strand, though? This makes sense for replication, but not for transcription.

My suggestion would be to remove most of the material from the lead, especially the list of "5 or 6" steps. If the lead had brief explanations of DNA, RNA, RNA polymerase, the biological role of RNA, the steps of transcription and the importance of transcription regulation for gene expression, it could be concise and less riddled with errors or misleading statements.Theislikerice (talk) 04:23, 17 March 2013 (UTC)

Central Dogma
The "see also" section has a misstatement of the central dogma (as stated by Crick). In papers in both 1958 and 1970 he emphasized that it was "once information has got into a protein it can't get back out." The idea that we have DNA->RNA->protein and never the other way around seems to be due to Watson's misunderstanding of Crick's central dogma. So either don't call it Crick's central dogma or change it to what Crick meant when he said "the central dogma." —Preceding unsigned comment added by 67.180.16.146 (talk) 00:06, 22 May 2011 (UTC)

2008 Major upgrade?
New Article Hi i´m Lukas Müller and i´m coming from Köln in Germany. i´m Studying biology at the Heidelberg-University, one of the best universities in germany and i want to ask, if we can make the site "Transcription" new so we can get a perfect article.
 * Please see the page section called, below, for discussion of major changes. --JWSchmidt (talk) 21:18, 3 January 2008 (UTC)

Harvard Papers?
"By the late 1960s several papers that came out of the Harvard University Biological Laboratories established the basic mechanics of gene expression in bacteria."

This information is not related to this article in context and will be deleted. If you're going to include this you might as well include all the articles on pub med because the "basic mechanics of gene expression in bacteria" is a communitative effort not just exclusivly by faculty in Harvard. Although I presume they had made their contributions as well. It's just not correct to include one place that contributed to gene expression, so I assume the person who included this is maybe from the school itself.

Reverse transcriptase
According to the current article, transcription refers solely to DNA>RNA transcription, and even goes to far as to link to Crick's central dogma (DNA is transcribed to RNA which is translated to polypeptides, never the other way around). Someone should make it clear from the start that transcription, while usually used to refer to DNA>RNA transcription, might also refer to RNA>DNA transcription. -- Ec5618 23:3'''9, 4 December 2005 (UTC)

I added a beginning of informations plus a little scheme I made earlier ... I think it should be in another page, but I don't know how to do ;-P. Hope someone will ! -- Totophe64

Eukaryotic Transcription
Edit 4/2/06 explanation Most eukaryotes have 4 RNA polymerases, plants have 5. Although RNAP is a commonly used abbreviation for bacterial and bacteriophage RNA polymerases, it is almost never used for eukaryotic RNA polymerases. I have substituted Pol I, II and III. (This will also need to be done in the subsections.) I have also included Pol A, B, and C not only in recognition of the work of Pierre Chambon and Andre Sentenac (vs. the nomenclature of William Rutter and Robert Roeder), but at some point the gene names (eg., RPA1, RPB1, RPC1) will come up as this section expands, and this edit will help clarify this nomenclature. -opus118

Organization and additional items needed "Perhaps one way of organizing this section is to group the different RNA polymerases: Archaea, bacteria, chloroplast, and eukaryotic nuclear RNA polymerases form one related group.  Bacteriophage T7-like and mitochondrial RNA polymerases form a second, DNA polymerase I-derived group (does reverse transcriptase fall into this category?), and then a diverse mixture of bacteriophage and viral RNA polymerases that do not fall within the above two categories.  There should be some emphasis on common mechanisms and related subunits.  For example: 1) the β'βα2ω subunits of bacteral RNA polymerase have sequence-related homologs in chloroplast RNA polymerase, archaeal RNA polymerase and Pol I, II and III. 2) The 12 (?) subunits of archaeal RNA polymerase have homologs in Pol I, II and III (with Pol III containing 5 additional unique subunits); 3) TBP is a transcription factor for archaeal, Pol I, Pol II, and Pol III transcription. 4) A TFIIB-related factor is common for archaeal, Pol II and pol III transcription. 5)TFIIH functions for Pol I and II transcription. 6) Promoter opening occurs with an upstream to downstream polarity with all polymerases. 7) Stem-loop structures at sites of termination are common (with the possible exception of Pol III). 8) The mechanism of catalysis for RNA chain elongation is identical (the active site region is highly conserved). 9) bacterial GreA/GreB, TFIIS and Rpc11 all stimulate a 3' to 5' ribonucleolytic activity at the RNA polymerase active site by inserting a finger-like structure in the nucleotide substrate feeding pore of RNA polymerase to place a pair of acidic residues near the catalytic site that chelates an additional Mg2+ ion for hydrolysis. It is the polymerase-unique properties that might be best dealt with in subsections. -opus18

Termination

 * Garbeled section needs Editing. Something missing or duplicated etc in the "sentence(s)":
 * in the DNA template. or where a GC-rich inverted 
 * 4 A residues. the inverted repeat forms 
 * dissociate from the DNA template. where the -35 region

*Rho-dependent termination uses a termination factor called ρ factor(rho factor) to stop RNA synthesis at specific sites. This protein binds and runs along the mRNA towards the RNAP. When ρ-factor reaches the RNAP, it causes RNAP to dissociate from the DNA, terminating transcription.
 * See the following surround section.

Other termination mechanisms include where RNAP comes across a region with repetitious thymidine residues in the DNA template. or where a GC-rich inverted repeat followed by 4 A residues. the inverted repeat forms a stable stem loop structure in the Rna, which causes the RNA to dissociate from the DNA template.

where the -35 region and the -10 ("Pribnow box") region comprise the basic prokaryotic promoter, and |T| stands for the terminator. The DNA on the template strand between the +1 site and the terminator is transcribed into RNA, which is then translated into protein. DLH 17:37, 10 September 2006 (UTC)

category
Surely this article should be under Molecular Biology? answer: WHY? Where else should it be?

order?
Is there any reason why it shows "see also" and "external links" then more of the article, then another "external links" section? If I dont' get any replies within a week or so, I'll go ahead and move the rest of the article up, and combine the two "external links" sections. jf 22:20, 23 May 2006 (UTC)

Other
"For instance, in eukaryotes the genetic material (DNA), and therefore transcription, is primarily localized to the nucleus, where it is separated from the cytoplasm (where translation occurs) by the nuclear membrane." This sentence has a very unclear structure*.

I miss the pictures!!!
YES! I do!!!!!!! Somebody, add some, please, it would be VERY IMPORTANT!!! Myrmeleon formicarius 12:42, 12 March 2007 (UTC)

Contradictions in Direction
In transcription, DNA is read 3'-->5' and RNA is produced 5'-->3'.

So, in an image of DNA being read by RNA polymerase, short strands would be expected at the 3' end, and long strands at the 5' end. The first diagram has this backwards.

I can't see what I'm missing, and since this is marked as a high priority for improvement, I thought this could use clarification, but since I suspect some actual biologists edit this page, I won't do it myself.

(Didn't log on the first time I posted this.)

Triacylglyceride 17:46, 13 May 2007 (UTC)triacylglyceride


 * I believe the image is marked incorrectly. Where transcription started the transcripts will be longest; the picture indicates the opposite. BTW your username is kinda funny, since it's usually either triacylglycerol or triglyceride :P -Sakkura 19:27, 9 September 2007 (UTC)


 * I think Triacylglyceride is right. Short RNA strands will be found near the start of transcription (3' end on the template strand) and the longest RNA strands near the end.  Forluvoft 00:02, 10 September 2007 (UTC)


 * Aye, that was a brain fart by me. It certainly looks correct now, although maybe you shouldn't take my word for it :P Sakkura 00:54, 14 September 2007 (UTC)

Scientists Discover the Dynamics of Transcription
'''One surprising finding was how inefficient the transcription process really is, particularly during its first two stages,� says Dr. Singer. �It turns out that only one percent of polymerases that bind to the gene actually remain on to help in synthesizing an RNA molecule. Transcription is probably inefficient for a reason.''' Brian Pearson 02:10, 7 August 2007 (UTC)

5', 3', direction of transcription, etc....
We're making this much more complicated than it has to be. We're too fixated on the directionality from the point of view of the template strand (because it's the actual physical template for RNA). But in reality, when molecular biologists talk about gene regulation, they talk about directionality from the point of view of the coding (non-template) strand. Maybe this is because the coding strand has the sequence of the resulting protein in the correct orientation. Thus, to molecular biologists, the 5' end of a gene is always near the promoter.

Hopefully this will make things clearer (if I don't screw it up):

RNA is synthesized using the template strand of DNA. RNA is synthesized from the 5' end to the 3' end. On the DNA template strand, this is 3' to 5'.

On the coding strand, however, transcription proceeds from 5' to 3'. Although RNA might not even touch the coding strand, the RNA will be an exact replica of the coding strand. Since RNA translation into protein occurs from 5' to 3', the DNA coding strand also shows what the protein sequence will look like, in the correct orientation (no reverse complementation necessary). So scientists usually like to work with the coding strand. Forluvoft 01:31, 27 September 2007 (UTC)

Reverse transcription
I added reverse transcription to the "See also" list. Does it really need its own section in this article? Forluvoft 03:53, 27 September 2007 (UTC)


 * It's called reverse transcription for a reason, so yes, it should have its own section here since it is a form of transcription (albeit unusual) Sakkura 00:00, 7 October 2007 (UTC)


 * Ok. Forluvoft 00:48, 7 October 2007 (UTC)

Transcription cartoons
I made and added some transcription cartoons. Let me know if something needs to be tweaked. The cartoons are really simplistic and I would envision them instead on an "Introduction to Molecular Genetics" page instead of this one. If this page ever gets to FA status, it will need much more detailed and accurate diagrams. Forluvoft 18:03, 12 October 2007 (UTC)


 * Yeah, they are quite simplistic, but it's far better than nothing. Especially for laymen. The protein complex at the promoter does look more like a eukaryotic preinitiation complex than what typically goes on in prokaryotes, but at least enhancers and whatnot are excluded, so I think they can be used as a general illustration for both eukaryotes and prokaryotes. Sakkura 10:53, 17 October 2007 (UTC)

Major Edits - Procedure?
Hi, new here. I'm currently doing a great deal of study of the transcription / translation area as an undergraduate at Cambridge - not saying that my opinion is any more valid than the next undergraduate and it certainly isn't compared to a PHD student, but I noticed quite a few holes here. I wondered what the procedure would be if I wanted to perform some major edits, probably adding a great deal more about Eukaryotic transcription (basal transcription factors, pol I-III etc) and doing some major rearrangements. I don't want to step on anyone's toes, but I'd like to do something useful. Martyn Axon (talk) 16:27, 27 December 2007 (UTC)
 * It would be great if we could improve the Wikipedia transcription article to featured article quality. If you want to start from scratch, create a page called Martyn Axon/Transcription. Alternatively, we could just start making major changes to the current article. Examples of featured biology articles. --JWSchmidt (talk) 21:26, 3 January 2008 (UTC)

B-Class Quality?
The information provided here is good, it does provide a broad introduction to transcription, im not complaining there. However, reading through this article i find parts where i just skip over due to grammatical errors, or just stupidity (i am not trying to be rude here i just cannot think of another word to describe it at the moment). For instance, a line just before the contents reads "Enzyme is the start of transcription". What would that mean exactly? —Preceding unsigned comment added by 152.78.249.55 (talk) 15:58, 15 January 2009 (UTC)


 * This has been fixed. --Timemutt (talk) 17:44, 11 October 2009 (UTC)

Repetition
For example:

"A polymerase binds to the 3' end of a gene (promoter) on the DNA template strand and travels toward the 5' end."

&

"The DNA template strand is read 3' → 5' by RNA polymerase and the new RNA strand is synthesized in the 5'→ 3' direction."

as found in the much too long introduction.


 * I addressed the repetition and grammatical flaws of this article. The introduction could still be shortened by including the information elsewhere if someone is feeling ambitious. --Timemutt (talk) 17:44, 11 October 2009 (UTC)

Some thoughts from a layman
The whole 5->3, 3->5 thing caused me some trouble for a while. It wasn't until I realized that the two halves of a DNA strand are going in opposite directions that it made sense.

I also think that the article is fuzzy on what kinds of cells are being discussed at points. I had trouble during the pre-initiation section trying to parse out what would apply only to prokaryotes, what would apply to eurkaryotes, and what would apply to both. Also, information is scant on archea and the distinction between archea and prokaryotic bacteria is sometimes lost. As someone who is using wikipedia article on the topic as an introduction to the material, I'm hesitant to make significant edits. Mishlai (talk) 15:53, 24 June 2009 (UTC)


 * Ah, and to make it more confusing there's still disagreement over whether all bacteria are Prokaryotes, broken into Bacteria and Archea or whether there are just Prokaryotes and Archea. I prefer the latter, but I'm definitely not getting involved in that fight. Mishlai (talk) 15:57, 24 June 2009 (UTC)


 * Although not universally accepted, I believe the trend now is to separate archae from bacteria, with only bacteria considered prokaryotes now. I made these distinctions for the information already within the article but it would be best for someone to add information differentiating more between the 3 during each stage. --Timemutt (talk) 17:44, 11 October 2009 (UTC)

Grammatical Mistake in Introduction
Hello all,

I've noticed a small grammatical mistake in the introduction to this article and would like it fixed. However, since it is in the introduction, I can't fix it myself, so I would like someone with sufficient permissions to change it for me.

The fifth paragraph has within it a sentence reading "This means it's 5' end is created first in base pairing." This is an incorrect usage of the word "it's", which should be changed to "its" in this case.

My thanks to anyone who fixes this on my behalf. —Preceding unsigned comment added by Mnkyman (talk • contribs) 02:01, 11 October 2010 (UTC)

Promoter clearance
I note that the section on promoter clearance mentions that the sigma factor stays attached to the polymerase up to 80 bp after elongation starts. However I am not entirely certain this is an accurate assessment. According to Rodney Boyer's 'Concepts in Biochemistry' (third edition), chapter 11, page 339 it stays on for ten bp, and according to page 1004 in Lehninger's 'Principles of Biochemistry' 4th edition it can stay on for 8-9 bp.

The difference between 8-10 bp and 80 bp is hardly trivial. Is this a mistake in the article, or is the cited source credible? Elvegaro (talk) 14:32, 6 June 2011 (UTC)

Hello, This article claims that transcription is an energy-dependent process and so requires ATP. While transcription does require energy, my understanding is that this energy comes from hydrolysis of the triphosphate of the incorporated nucleotide, not specifically ATP. Perhaps this article should be modified. Molecular Biology of the Cell (4th edition) pg. 305 figure 6-8. — Preceding unsigned comment added by 169.230.76.4 (talk) 16:21, 13 July 2012 (UTC)

RNA Polymerase/Helicase Confusion
The page states, "1.Helicase unwinds/"unzips" the DNA by breaking the hydrogen bonds between complementary nucleotides". Yet on the Wikipedia page for RNA Polymerase, it states, "In contrast to DNA polymerase, RNAP includes helicase activity, therefore no separate enzyme is needed to unwind DNA."

Which is it--does helicase unwind the molecule or RNA polymerase? Or is there some confusion of the terms that would resolve this issue? — Preceding unsigned comment added by 74.51.196.146 (talk) 16:09, 28 November 2011 (UTC)

hello user above^ I am not sure how to reply to your comment, so am including my reply as an edit of your original comment. Your confusion about the perpetrator of this DNA helicase activity is understandable, and I think this article on DNA transcription is quite poorly written and should be entirely reformed with input from some academics or experts in the field of genetics. I am an undergraduate biology student and I immediately identified several erroneous claims and fuzzy descriptions of what I think are generally considered vitally important intracellular mechanisms involved in this process. The RNA polymerase RNA-P II- which is the one we're discussing if considering the transcription of mRNA- is a complex enzyme consisting of 10 subunits. The helicase activity is not catalyzed by the RNA-polymerase though, it's performed by a transcription factor (TF2H) that is bound to promotor region of the DNA, one of many co-factors that assembled on the promotor region, collectively forming the the activation complex (with the addition of the polymerase) before transcription can proceed. This transcription factor, TF2H (the 2 is normally designated with roman numerals) is the most complex of the several transcription factors that will bind to the polymerase during transcription, consisting of 9 subunits. One of these subunits is a DNA helicase, This subunit hydrolyzes ATP and 'unwinds' the helical structure of the DNA, exposing the template strand that will be read by the polymerase during the elongation phase of transcription. Hope this elucidates the topic somewhat for you. Someone should fix that damn article, it's an academic disgrace.

Renamed
This article was moved from 'Translation (genetics)' to 'Transcription (biology)' to match Translation (biology), based on discussion at WT:MCB. T.Shafee(Evo &#38; Evo)talk 00:01, 30 November 2016 (UTC)

Should RNA replication be splitted as an article?
Nowadays RNA replication is a redirect page to that article. I think that transcription and RNA replication could and should be splitted into two differenciate articles. As a key concept, trascription is a main goal in all DNA based genotypes. But in fact, at least exist some "organisms" commonly called RNA viruses (i.e.) o molecules called ribozymes, that uses and replicate RNA without transcribing it from DNA and does not use it at all (or not in a closed relation in cellullar machinery). Therefore I think that that splitting should involve at least these redirection pages: RNA synthesis, RNA replication, Template strand, Rna elongation, and RNA synthesis inhibitor. There is any volunteer to do that. I'm not a good writer in english language. Thanks and debate if you do not see it clear. --Bestiasonica (talk) 09:51, 13 December 2016 (UTC)
 * RNA "replication", by viruses and some organelles, is the copying of RNA by RNA. Terms such as RNA "transcription" and, usually at least, RNA "synthesis" refer to the copying of DNA code as RNA and typically results in the production of more RNA. They are pretty much unrelated topics. I have changed RNA replication to redirect to RNA-dependent RNA polymerase, which is a little more informative than the ribozyme article mentioned. But I agree, RNA replication does deserve a standalone article to organize the various metabolic processes that exist - ribosomal, viral, transcriptive and for all I know some other arcane corners of life. &mdash; Cheers, Steelpillow (Talk) 14:40, 11 May 2019 (UTC)


 * [Update] The article on RNA-dependent RNA polymerase, to which RNA replicase now redirects, directly contrasts RNA "replication" with DNA "transcription". The majority of sources appear to treat "RNA transcription" as the process of copying DNA code as RNA, i.e. a synonym for "DNA transcription". On that basis the viral material in the present article should simply be deleted and at best replaced by a hatnote or similar. I have tagged the article in a couple of places and if nobody comes up with a sensible alternative, I will go ahead with that. &mdash; Cheers, Steelpillow (Talk) 15:39, 12 May 2019 (UTC)

external link
these two links show 404 redirects ( not found) or Dead link '''Interactive Java simulation of transcription initiation. Interactive Java simulation of transcription interference--a game of promoter dominance in bacterial virus'''. when I try to remove it someone undoes my editing takes a look audit. thank you. Amitsabhadiyaj (Talk)

Delete figure?
The figure at the top of the page is labeled "RNA transcription" but most of it shows RNA processing, not transcription. Furthermore, it is very eukaryotic-centric and therefore not appropriate for a general article on transcription. In addition, the figure only shows RNA polymerase II transcription producing mRNA. There are a lot of noncoding genes transcribed in eukaryotes by RNA polymerases I and III.

I think we should remove this figure and replace it with one that just covers the basics of transcription in bacteria and eukaryotes.

What do others think? Genome42 (talk) 21:13, 5 June 2023 (UTC)