Talk:Eukaryotic transcription

Untitled

A paragraph about transcription termination should be added. Any expert around? Jullag 15:32, 26 June 2007 (UTC)

Ideas for how to expand the topic of Eukaryotic Transcription

Based on a class project for our Molecular Biology Class, our group (81B -user:Birdy0124 and user:Mtee87) came up with this outline+reference list. Please let us know if you want to work with us on this, or if you have suggestions about other subtopic that can be added

Eukaryotic Transcrion Outline

I. Making RNA replica of gene

II. Eukaryotic RNA polymerases

A. RNA polymerase I

B. RNA polymerase II

C. RNA polymerase III

III. Initiation

A. Eukaryotic promoters

B. Regulatory sequences beyond the core promoters

C. General transcription factors

D. Preinitiation complex

E. Promoter melting and close-to-open transition

F. Abortive initiation

G. Promoter escape

IV. Elongation

A. Elongation factors

B. Proofreading and transcription fidelity

C. RNA processing

V. Termination

A. Cleavage and 3'-end polyadenylation

B. Second RNA (Torpedo model)

VI. Transcription through nucleosomes

VII. Eukaryotic transcriptional control

A. Initiation (Mediator complex, etc)

B. Elongation

C. Termination

VIII. Comparisons between prokaryotic and eukaryotic transcription

IX. Comparisons to eukaryotic DNA replication

X. Transcription-coupled DNA repair

References

Suggestion for Exisiting Content edit

Hi! I wanted to make a suggestion to the current RNA polymerase table. Instead of having transcribed as indicating positions in the nucleus, I suggest that we change that section to position, add a section called RNA transcribed and go ahead to detail the products as the different RNA's transcribed. Also, I wanted to suggest we add an additional section with functions. This way we can detail functions of each of RNA's transcribed by the different polymerases. Look forward to hearing from you. Mtee87 (talk) 23:38, 29 October 2013 (UTC)

Also suggest the citing of the stated facts from the 2nd paragraph under initiation. If there is no citing information, then I suggest the removal of the information.Mtee87 (talk) 00:41, 30 October 2013 (UTC)

Comments from Klortho

• General:
  • I like your overall article structure, for the most part. But, it seems to me that the "Initiation", "Elongation", and "Termination" sections under Eukaryotic transcriptional control could be combined with the major sections of the same name, that appear earlier.
  • Most of the article has no wikilinks. Things like "eukaryotic", "DNA", "RNA", "prokaryotic", etc., should be linked to their respective Wikipedia articles
  • A lot of the content lacks any inline citations. These are very important. You should be adding citations at the same time as you are adding content, so that: A, you don't have to try to match up content to references later, and B, people can verify the material any time they want, as soon as it's on the page.
  • The paragraph Initiation, under Eukaryotic transcriptional control, is somewhat better, but you don't need to repeat the same citation for every sentence in the paragraph. If the whole para is from one reference, then one citation at the end will do.
• Lead:
  • "mosaic structure of the eukaryotic genes" - I wonder if you couldn't use simpler phrasing to describe what you mean here. I'm not sure what "mosaic structure" is, and suspect most people wouldn't know, either.
  • You definitely should have a link to Transcription_(genetics), and explain that eukaryotic transcription is a subset of this.
  • Why is eukaryotic transcription notable? You might describe how it fits into the larger scheme of biology and the "central dogma", written for a non-biologist. See the Transcription_(genetics) article -- but you'll want to make your description different from that one, and highlight areas where eukaryotic transcription is special. For another example, this article seems to be written at a very nice level, and gives a more gentle introduction to the topic. To understand what I mean, consider that your lead doesn't even mention genes until the phrase, "Due to the mosaic structure of the eukaryotic genes". If someone doesn't already know what transcription is, they would not be able to understand this.
  • You say, "eukaryotic transcription is more complex than prokaryotic transcription", but I don't see anywhere in the article where you make this explicit, even in the section near the end, Comparisons between prokaryotic and eukaryotic transcription. How exactly is transcription itself more complex?
• "Making RNA replica of gene in eukaryotic cells"
  • As it stands, this could be combined with the lead. Do you have plans to expand this section more?
• "RNA Polymerase"
  • Make sure (in general) that you link to the main articles for each of these subtopics. In this case, RNA_polymerase
  • In your table, is the header "Transcribed" correct? Shouldn't it be "location"?
• Other:
  • A lot of terms should be glossed when they are used. For example, "Pre-RNA molecules". What are these?
  • sometimes you have details that don't seem to be related to transcription. For example, "The pre-mRNA transcripts are capped at their 5′ ends and polyadenylated at their 3′ ends.". This detail doesn't seem to belong in this article.
  • It would be nice if you could find some images for this article.
  • I think the writing level is too technical in most places. Try to remember that you are targeting a bright high-school student or undergraduate, not a professional biologist.

Klortho (talk) 01:13, 3 November 2013 (UTC)

Comments from sefacci

Klortho covered a lot of the concerns I had; I will try to add to those comments.

Introduction: The introduction is very confusing right now-- consider starting out broad and narrowing down like you would in an outline. I also don't know what you mean by mosaic, so if you're going to use this term it should be explained. I would suggest giving a more comprehensive overview of the transcription process, in a chronological manner, in the introduction. Keep in mind a lot of people only read the introduction. I think this should evolve bit by bit as you add to the main article- consider checking that the introduction contains all the necessary information whenever you add to the body.

Content and Organization: Your outline seems overly complex. You discuss the molecules needed before explaining the process, which could be confusing to readers. I would even consider getting rid of the sections for the polymerases and incorporating the information into the other sections as necessary. Keep in mind that these also already exist as their own wikipedia pages, so it doesn't make a lot of sense to rewrite what other people have written. Think about linking to the other articles and summarizing the important facts in your text. I'd recommend expanding the initiation, elongation and termination sections with summaries before delving into subtopics. I'm also not sure if transcription-coupled DNA repair is in the scope of this article. You'll have to consider that carefully. It seems too early in the process to comment on what might be missing so we'll save that for later.

Tone: There is a lot of good information in the article so far, but I agree with Klortho that the tone should probably be simplified for the lay reader. I'd say you did a good job maintaining a neutral point of view. But I'd like to hear your voices come through a little bit as you explain.

Citations: I am concerned that there are whole sections missing citations. Perhaps focus on one section at a time instead of trying to fill in a little on each, then you can more easily add citations as you go. Some of the citations seem misplaced. For example, under Eukaryotic transcriptional control, the first sentence is very general and doesn't need a citation. Remember citations are to back up specific facts, not link readers to further information. It's great to start with our textbook, but recall that you should also have freely available articles and books according to the wikipedia mission statement. Try google books!

Metadata: You might want to consider adding some maintenance tags alerting the reader that this is an article in progress. There are also templates that you can insert in the text to mark the section for expansion-- it will look more professional than writing (under construction). I see that you have categories added at the bottom of the page, to give the reader some context.

Sarah Facci (talk) 02:39, 4 November 2013 (UTC)

I went ahead and added in some templates for you- I think it looks more professional and clearly indicates to any reader that you're still working on the article. Sarah Facci (talk) 22:04, 10 November 2013 (UTC)

Comments from AjoneWiki

Content Coverage

Overall, I like the layout of your article. Keeping details and scope of the main article in mind, I would consider expanding the introduction.

Wikilinking

Add Wiki-links to guide the reader to additional information rather than artificially expanding the scope of the article.For example, I am not sure if each factor has to be covered in such detail.

Referencing

You need to add citations to your article. I personally found adding citations during the writing process to be a lot easier than trying to add them later on.

Writing categories

Your terminology is a bit too specific/too technical and can get confusing. As a biologists, it gives me a good understanding transcription, however, it appears you are going into too much detail in terms of scope. You could add a wiki-link for topics like DNA repair. If you are using terms, add wiki-links to enable the interested reader.

Illustrations

You could add some illustration to help the reader visualize transcription.

AjoneWiki (talk) 18:47, 5 November 2013 (UTC)

Note: I found an article that might help you with the section "Comparisons between prokaryotic and eukaryotic transcription". AjoneWiki (talk) 04:02, 6 November 2013 (UTC)

I see several improvements from my review a month ago - good job. AjoneWiki (talk) 23:30, 14 December 2013 (UTC)

References

Comments from Harshil Patel

Your page is planned and well structured with relevant topics covered related to the topic of the article. I like the table you included in your content, however I think it would be good to see the heading of each column in your table to the centered position. Personally, I think having headers in the centre stands out visually and attracts reader to read the table. I noticed there is no pictures added in the article yet, I recommend you to adding pictures, it is to better illustrate the content.

One other thing I think needs attention is the referencing - there is no in-site referencing for the content under RNA Polymerase I , II and III, Subunit composition, Structure of eukaryotic RNA polymerases, and Carboxyl terminal domain of RNA polymerase II.

To better understand terminologies adding links to them would be helpful. You can link words by the clicking on the chain symbol on the top of your edit page.

I also suggest to have a consistent format in your headings, for instance some of you headings are in bold and some are not bold.

Igenes (talk) 03:58, 6 November 2013 (UTC)

Harshil, the formatting of the headings happens automatically according to wikipedia's built-in markup. I agree sometimes it looks a little confusing but I think also adding some illustrations and expanding the text will help with the appearance. Sarah Facci (talk) 22:02, 10 November 2013 (UTC)

Thank you so much Harshil and Sarah. We had definitely started wikilinking some of the common terms as suggested by Klortho. And by the end of the unit, we should have added wikilinks to all necessary parts of the article. I had no clue about the wiki's built-in markup, but it definitely will help especially from others who are willing to work on the article. Sincerely, Mtee87 (talk) 01:22, 11 November 2013 (UTC)

Comments from Dmille96

Your article appears to be coming along quite nicely in terms of information added. The outline looks great and you have a good bit in each section to give the general overview; moreover, the breakdown of the topic is done very well and you cover the topic in its entirety. While you appear to have the basics down-good wikilinking (albeit a bit inconsistent), bits about each topic-for the amount of writing that you have I was expecting more references. If you just wanted to get the basics down that's understandable, but I would focus over the next couple weeks on reinforcing the ideas you've put out there with any research that is available. Next, with such a large topic it is going to be very easy for the reader to get lost without visual aids. There are a lot of proteins mentioned and it would be good to have one picture or chart that helps people keep the topic straight in their head. Small suggestion: I think if you could use a chart for comparison of eukaryotic and prokaryotic transcription that would make the article really stand out.

Other than those thoughts, I think that you have a good article in the making. As long as you keep adding bits of information and attaching more and more references, it will end up great. Dmille96 (talk) 00:58, 20 November 2013 (UTC)

Comments from Oalnafo1

Nice work since the September 8th update. The page outline has been created and a lot of it has been filled in. There are a few things that I noticed could be improved:

1. The language is not as clear and concise as it could be, I believe this may be a fairly difficult read for a college undergraduate.
2. There are many terms that can be intralinked to outsource the problem of explaining all of the details included in the article. For instance, in the introductory paragraph eukaryote, prokaryote, nucleosome, transcription, mRNA, RNA splicing, etc can all be intralinked to facilitate the ease of information display and comprehension by the reader.
3. The page can use some images even if very simplified. Adding some colored schematics can help to both increase to aesthetics of the page and improve understanding of difficult to visualize concepts.
4. Inclusion of See Also and External Links subsections would seem helpful.

Other than that, just keep up the good work! — Preceding unsigned comment added by Oalnafo1 (talk • contribs) 09:04, 20 November 2013 (UTC)

Hi Oalnafo1 - thank you for your comments. In the last week, my partner and I are focused on completing the content and working our way to revising the text to improve clarity and readability. We are also generating figures ourselves to help understanding of the material as there are not many available which are appropriate for use here. Thanks for your encouragement.Birdy0124 (talk) 02:48, 28 November 2013 (UTC)

Comments from Keilana

Hi guys, great job so far. Here are my comments for you - please ask on my talk page if you have questions or need help!

• Check through for grammar and spelling mistakes - I saw several in the lead alone.
• The lead could do with expansion. This is a fairly long article and the lead is supposed to summarize the whole article.
• In general, this article is written at way too high a level for the usual readers of Wikipedia. The audience I like to think of is a smart 15-year-old who is interested in whatever I'm writing about. (For example, don't explain what a cell is but explain what a carboxy-terminus is.)
• "Transcription is the process of transcribing or copying genetic information stored in a DNA strand into a transportable complementary strand of RNA. Eukaryotic transcription takes place in the nucleus of the cell catalyzed by three RNA polymerases and proceeds in three sequential stages: initiation, elongation, and termination." - this needs a citation.
• SparkNotes is not an acceptable source for Wikipedia. Please remove it.
• The second source you give is a broken link. Remove or fix it.
• The Molecular biology of the cell source is malformatted, if you need help fixing it please let me know and I can help with the template syntax. :)
• The sections RNA Polymerase I, RNA Polymerase II, RNA Polymerase III, and Subunit composition all need citations.
• The whole article could do with more wikilinks to important concepts.
• "Long and structurally disordered, CTD contains multiple repeats of heptapeptide sequence YSPTSPS..." - this whole section needs citations.
• "Some genes also have enhancer elements that can be thousands of bases upstream or downstream of the transcription initiation site. Combinations of these upstream control elements and enhancers regulate and amplify the formation of the basal transcription complex." - this needs a citation.
• The Eukaryotic promoters, General transcription factors, Assembly of preinitiation complex, Promoter melting and close-to-open transition, Abortive initiation, Promoter escape, Elongation, Elongation factors, Proofreading and transcription fidelity, and RNA processing sections all need citations.
• The termination sections, Comparisons, and Transcription-coupled DNA repair need to be filled in.
• The first paragraph of Eukaryotic transcription control and the first paragraph of Comparisons need citations.

All the best, Keilana|^{Parlez ici} 03:07, 21 November 2013 (UTC)

Thank you for all your input! we have worked on the references you mentioned, and are slowly working our way up to adding the inline citations you suggested. The other sections have been filled in at this point. We will work on adding more content where necessary, and trying to make the language. The only thing we may have problems with is finding figures/diagrams that can be uploaded to wikimedia commons on our subject title. Although we were just going to use inkscape to create the images.Mtee87 (talk) 04:46, 27 November 2013 (UTC)

Hi Keilana - thanks for your comments. You posed some of the same concerns as

Oalnafo1. We are continuing to refine the content (including fixing typos and grammatical errors). We are continuing to integrate more references. This is such a big topic that we have been a bit overwhelmed by the amount of material. But we will try to adjust the "level" of writing during the final stages. Birdy0124 (talk) 02:54, 28 November 2013 (UTC)

Comments from R. Chappel

Just a few comments on the article. It's looking really good!

• In the first paragraph: There are a lot of locations to place useful Wiki links, such as translation, transcription, nucleus, nucleosome, chromatin
• Throughout the article I would add a lot more Wiki links on general subjects. Some more examples: mRNA, non-coding RNA, 18S, the different transcription factors, enhancers, silencers, isolators...just to name a few. The detail of the article is great. Adding some links to the specific details really makes the articles more readable to someone who is unfamiliar with the subject matter.
• I really like the Polymerase chart!
• The Structure of eukaryotic RNA polymerases section is a little hard to read. Maybe separate the examples of what the crystal show into more than one sentence.
• The "Promoter escape" section does not have a reference associated with it. Does it go with the next reference listed in the Elongation section?
• In the Elongation section - a quick explanation of what Ser2 is might help that paragraph make more sense.
• I'm sure we all have been having some trouble finding pictures - we had some luck searching through Wiki Commons. Have you tried looking there for some general pictures of these processes? Or one of the structures of the different polymerases?
• In the Transcription-coupled DNA repair - maybe one sentence about what a lesion is (as well as another great place for a Wiki link).
• In the subheadings of "Global control and epigentic regulation" and "Gene-specific activation" there are no references - I assume this is because they share the same reference as the next subheading (reference 39) but I would add that reference to the end of each subheading just to make sure every section has a reference.
• I like the addition of the paragraph comparing eukaryotic to prokaryotic transcription.

• I am not sure if "entaamoeboic" is a typo or something I don't know about - maybe an explanation about what this means.

• Overall:

• There are some minor typos / syntax stuff which should be an easy fix after another read through.

• The biggest one I noticed was in one of the main headings: "Global control and epigentic regulation" - just because it also is shown in the Contents box this one is more obvious.

• I would make sure there is at least one reference per subsection listed.

• The article looks really great! There is a ton of information on there about all aspects of transcription. Great job!

Rebeccachappel (talk) 17:53, 3 December 2013 (UTC)

Thank you for your detailed review of this article Rebeccachappel. We will be sure to take a look at your corrections and make them as they apply to the article. Sincerely Mtee87 (talk) 04:07, 8 December 2013 (UTC)

Comments from Seanmcaruthers

Hi all – You’ve made quite a contribution since the beginning of class. You have really pulled through on getting almost everything cited it looks like. But there are some whole sections (Promoter escape, Global control and epigentic regulation, Gene-specific activation) with no citations that really need at least one. Additionally, I think you mean epigenetic regulation, but it is used as epigentic and epigenic in the article. At this point, not a whole lot I can suggest changing. Your overall structure is coherent, but this is such a big topic, you have to be careful about digging into too much detail rather than just explaining. Some parts are very technically heavy. For example, the “Elongation factors” section is very hard to read and think is above the level of what we are shooting for. I would try to add more wiki links. Things such as “elongation factor” and all the transcription factors (TFIIA, TFIID, etc.) all have pages. It seems to me, in the lead there should be just a little more mention of why this is important. Klortho had mentioned about the “central dogma” of biology. It wouldn’t hurt to include mention of polymerase, the three stages (initiation, elongation, termination) to give a feel of what you cover in the article. I’m left a little wondering what all is in the article when just reading the lead, and there is so much good information you have put in. As others have said, a picture or two would really polish things up. All in all very good work.Seanmcaruthers (talk) 09:52, 7 December 2013 (UTC)

Thank you, Seanmcaruthers. Thanks for pointing out the lack of citations in Global Control and Epigenetic regulation. I will add citations as well as correct the typo in the next few days. It's been a challenge, figuring out what level of detail is sufficient with a topic so large as you considerately mentioned. I will do my best to integrate your suggestions in the time we have left in the course.

Birdy0124 (talk) 17:26, 10 December 2013 (UTC)

Some more comments from Klortho

Hi, I can see that you've put a lot of work into this article, and it is very much improved over the last time I looked at it. Great job! There are still a few more things that could be improved, so here are a couple of comments. Note that this list isn't meant to be exhaustive -- please also, if you have time, revisit Keilana's suggestions above, and those of your classmates, to make sure you've addressed the most pressing concerns.

• General
  • I think you maybe you could "flatten" some of the subsections. In other words, just do away with the subsection headers. For example, under "RNA Polymerase, you could do away with the subsection headings RNA polymerase I/II/III. Each subsection is very short, and if the extra headings are just distracting, and don't add any value, IMO. There are several other places in the article where this is also true.
  • One question I had while reading the article was, how much difference is there among all the various eukaryotic species? The text of the article doesn't address this question, but I find that hard to believe that there isn't a good deal of variation. For example, are there any species that don't have Pol III?
  • You could still have a lot more wikilinks. For example, transcription (genetics), promoter region, translation (biology)
  • I can see that your citations have improved dramatically, but a couple of sections still lack any citations whatsoever: "Global control and epigentic regulation", and "Gene-specific activation", at a glance. Please cite this material before the end of the class -- it's very important, otherwise the material is subject to being removed.

• Lead:
  • "The greater complexity of the eukaryotic genome" -- greater than what? You haven't introduced what you are comparing against (presumably, prokaryotes).
• RNA Polymerase
• Initiation
  • "many of the initiated syntheses are aborted before the transcripts reach a significant length" -- I don't see a citation for this.

Again, good job! Klortho (talk) 22:47, 8 December 2013 (UTC)

Thank you, Klortho. These are great suggestions. I will address flattening and references in the next few days, including the Wiki links.

Birdy0124 (talk) 17:24, 10 December 2013 (UTC)