Talk:Terminator (genetics)

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"The terminator gene" refered to technology produced by Monsanto which would render their patented plants incapable of producing viable seeds. The pollen from such plants would also produce non-viable seeds. Monsanto has vowed to never commercialize the technology. 
http://news.bbc.co.uk/1/hi/sci/tech/465222.stm
: OK, created Terminator gene needs some work though. Onco_p53 05:30, 14 November 2005 (UTC)
replies: text:  Made Dab link to Terminator Technology. --137.120.145.117 16:19, 11 May 2006 (UTC)
thread_title:  Terminator gene 

message: Hi guys, here are my comments on what you've done so far. Please ask if you have any questions!
* Don't bold terms at the beginning of sections (rho-independent and dependent terminators), just the beginning of the article as a whole.
* Obviously, the eukaryotes section needs a lot of expansion & some citations. I'm looking forward to seeing what you come up with!
* The two sources you have are good, but you definitely need more than two for such a big topic. I would start with textbooks and specialist encyclopedias and work from there.
* The language in both sections you have worked on is very jargon-heavy. Think of your audience as a smart 15-year-old with basic science knowledge. You don't have to explain what a cell is or what RNA is, but you do need to explain the hairpin motifs and such.
Keep working! All the best, Keilana|Parlez ici 21:14, 3 November 2013 (UTC)
thread_title:  Comments from Keilana 

message: Overall – You’ve definitely expanded on the original work by a great deal.  It’s a good start, but a lot more detail and references are out there to be added.
Lead section – The lead looks good.  It provides the general background and indicates why the topic is important.  It is able to stand alone and leads into the rest of the material naturally.
In prokaryotes – This section looks like it’s really off to a good start.  You could go more into the machinery and its function, especially about Rho itself.  As well, any evolutionary explanation tends to put most concepts into a broad and more understandable framework.  The referenced articles are good and should lead you to more material in their cited works and work that cites them.  Be careful about attributing all material in a review article or introduction to just the review and not to the original sources as cited in the review. 
In eukaryotes – Obviously there is a lot more that can be added here.  It’s a complex but decently well understood system.  And even where things aren’t understood so well, like how exactly polyadenylation is linked to termination, current hypotheses can be stated as such.  There is a lot of good information out there.  A simple PubMed search on “eukaryotic transcription termination” leads to quite a few review articles to get you started.
Images – I know it can be hard to find relevant commercial use images for topics like these, but they really can be helpful and make the article more aesthetically pleasing.  
I second everything Keilana said.  I was told our page was too technically jargon laden as well.  While not dumbing it down, try to break up the sentences a little into material digestible by someone not working on a master’s degree.   
You did a good job with the intra-wiki links.  Just a few additional suggestions -
*mRNA
*genome
*allosteric
*RNA polymerase
*prokaryotes
*eukaryotes
Hope this all was helpful.  Good luck.  Seanmcaruthers (talk) 00:16, 5 November 2013 (UTC)
replies: text: Thanks for the constructive comments, I will try to address them as best I can. I have created an image for the terminating hairpin if you care to comment on that. Also do you know if one intralink should be sufficient or should all instances be linked?Oalnafo1 (talk) 02:39, 10 November 2013 (UTC)
replies: text: Good question.  Just from looking around at a few featured articles, it looks like you only need to do it for the first instance.Seanmcaruthers (talk) 18:35, 10 November 2013 (UTC)

text: thanks for commenting. We're adding eukaryote part. We will try to use less jargonsChandler.c.ho (talk) 20:54, 10 November 2013 (UTC)
replies: text: You guys have done a lot of great improvement.  The new graphics are great. I'm impressed and jealous.  I think it would be great if you could include some things on eukaryotic termination with RNA polymerase I and III.  There’s a nice review at PMC 2763537, doi:  10.1101/gad.1792809 - Transcription termination by nuclear RNA polymerases.  There are a lot of interesting details on antitermination that might be worth including in the Santangelo, TJ.; Artsimovitch, I. (May 2011) article you cited.   As Rebecca said, try to add the PubMed numbers to everything (which you mostly did) and I believe if possible we should put a link to the paper at the publisher’s website. Again, good work.  It’s coming along nicely. Seanmcaruthers (talk) 01:13, 20 November 2013 (UTC)
thread_title:  Comments from Seanmcaruthers 

message: I thought I'd add my 0.02NZD too. 
*I second the image request. I made this one for intrinsic terminators a long time ago:
*I don't know of any good Rho-dependent terminator figures. It should be possible to create a cartoon version or perhaps a Sequence logo. 
*The eukaryotes (and archaea) section definitely need expanding. I suggest splitting into the different polymerases. E.g. RNA_polymerase_III#Termination
Keep up the good work folks. --Paul (talk) 01:23, 5 November 2013 (UTC)
replies: text: I agree on the images, I actually made a simple schematic if you care to comment on it. I am working on the Rho-dependent termination. Thanks for the input! Oalnafo1 (talk) 02:43, 10 November 2013 (UTC)
replies: text: It doesn't look too bad. I was under the impression that the hairpin was somehow within/near the complex. Involved in causing pol to pause (via nusA). I could be horribly wrong, although I think Fig. 6 in Gusarov & Nudler supports this. Are there any more recent reviews? E.g. Fig. 2, Santangelo & Artsimovitch.--Paul (talk) 22:59, 11 November 2013 (UTC)
replies: text: You are completely right, I have attempted to address your point. Please let me know what you think!Oalnafo1 (talk) 05:12, 13 November 2013 (UTC)
thread_title:  Comments from Paul 

message: hey oalnafo
I added torpedo section. do you want me to add the allosteric model too? Please add more information to torpedo if needed. Thanks Chandler.c.ho (talk) 20:55, 10 November 2013 (UTC)
replies: text: yes it would be good if you could add more to the eukaryotic section allosteric model or other information.64.183.84.198 (talk) 04:31, 13 November 2013 (UTC)
thread_title: Comments from Chandler

message: The article is looking great so far! I only have a few suggestions / comments:
* I think the layout should be altered slightly in regard to the images.  They are great images (clear / simple enough to follow) but right now they look like they belong both in the prokaryotes and eukaryote section of the article.  Maybe move the graphics to underneath the corresponding section? Just a thought!   
*The headings of "In Prokaryotes" and "In Eukaryotes" could be a little stronger to make them their own section. Maybe "Terminators found in Prokaryotes"? They read more like subheadings than full section headings as they are now.  
* In the final section, some more clarification might be needed.  The sentence "After transcription is completed, processed mRNA with 5’ CAP and 3’ poly A is cleaved with the help of CPSF and CstF." I think it would be helpful to write out what those two acronyms mean (CPSF and CstF) to have the section be more complete.  
* You also have a lot of great opportunities for some links to other Wiki articles in that last section such as RNase and RNA Polymerase II. 
*The external links section is a great addition! I need to add one of those to my article...
*The format of the references look good.  I would add a PMID number to the last article just for consistency in the references (it's PMID: 15620350 just after a quick NCBI search).  
It looks great! Rebeccachappel (talk) 21:03, 19 November 2013 (UTC)
replies: text: I agree with the image placement; unfortunately, there I cannot finely control the position so I think I will end up combining them into 1 side-by-side image. I have changed the subsection titles to clarify. Thanks for the PMID. Yes I agree that the eukaryotic section needs more clarification. Thanks for the PMID and thank you for all of your comments! Oalnafo1 (talk) 03:56, 27 November 2013 (UTC)
replies: text: The changes look great! I had the same difficulty trying to get an image to do what I wanted...your change looks great.  Rebeccachappel (talk) 20:12, 7 December 2013 (UTC)
thread_title:  Comments from R. Chappel 

message: Hi,
The article seems to be really moving away from a stub and towards being a Good Article!  I like the figures in the article too.
I think that a title “In Prokaryotes” is a slightly awkward, maybe you should name it “Termination in Prokaryotes.”  Can you also add “And/or” between end and transcription in the paragraph under your “In Pprokaryotes”?
I think that there will be a better flow of an article if you switched the order two sections: Rho-independent terminators and Rho-Dependent Terminators, because I first would like to know what Rho function is and how termination occurs when it depends on Rho, and then It’s easier to follow Rho independent termination description.
Under Rho independent Terminators, can you clarify this part of a sentence: “hairpin formation causes RNA polymerase stalling indirectly promoting dissociation of the complex” .  Also, maybe expanding on the basis of NusA interactions with RNA polymerase will help expand on this topic.  I also noticed that Tau can be one other transcription factor, so that can also be expanded into a potential new paragraph, especially when your article is not very long yet.
Let me know if these comments help,
rokas (talk) 03:06, 20 November 2013 (UTC)
replies: text: I have made corrections to the subsection titles, I have reordered the order of Rho dependence which makes much more sense. I have tried to reword the competitive kinetics according to my understanding. I will expand further on the other factors involved in the process. Thank you for the comments, they were helpful and offered an alternative view. Oalnafo1 (talk) 04:17, 27 November 2013 (UTC)
thread_title: Comments from Rokas 

message: * Lead
** Could use some more wikilinks (mRNA, for example)
** I would drop the phrase "which varies depending upon the specific gene and organism."  It has pronoun confusion and verb-number mismatch, anyway, and seems unnecessary.
* "In prokaryotes" section
** "to end discontinue transcription upon complete transcription of the ..." -- this is just sloppy
** In the introduction here, before the subsections, you should name the two.  That provides a real introduction to the forthcoming subsections.
** I'm confused by the word "early".  To me, that connotes something abnormal is going on.  Is that what you mean?
* General:
** The text is written at a level that is way too difficult.  I see that Keilana mentioned this in her review from two weeks ago.  Did you attempt to address this at all?  Just please read this sentence yourself, and see if you dont' agree, "Intrinsic transcription terminators or Rho-independent terminators require the formation of a self-annealing hairpin structure on the nascent elongating transcript which results in the disruption of the mRNA-DNA-RNA polymerase ternary complex.".  This could be written in much simpler language.
** Needs more content.  Especially, in eukaryotes.  In general, the article is too short for such an important topic.
Klortho (talk) 06:18, 20 November 2013 (UTC)
replies: text: Addressed: wikilinks, confusing phrase, sloppy grammar, naming of two types in section intro, context for early. Will work on increasing the readability and increasing content. Chandler.c.ho will add content to the eukaryotic section. Thanks for the comments, they were helpful. Oalnafo1 (talk) 04:54, 27 November 2013 (UTC)

text: Allosteric model is added for eukaryotes. pending improvement include rewording with less jargons.  Chandler.c.ho (talk) 07:51, 27 November 2013 (UTC)

text: Multiple wikilinks added in Eukaryote section.Chandler.c.ho (talk) 17:26, 2 December 2013 (UTC)
thread_title:  Comments from Klortho 

message: * In the lead, should it be "the end of a gene or operon on genomic DNA" or "IN genomic DNA"? On seems to indicate to me that something is binding to the DNA.
* Similarly, shouldn't it be processes WHICH release the mRNA? P.s. this sentence is really long, maybe cut it into 2?
* I think these things should also be included in the lead and/or article: Is it a conserved/specific sequence? What is the length of a terminator? Mention that terminators occur in both prokaryotes and eukaryotes. Do they differ between the two? Is there any notable history associated with the study of this topic?
* Good job wikilinking lots of terms, but make another pass and make sure you've got them all. Like processivity, for example.
* The article seems like it should be longer. Is there anything in your sources that has been left out that might be of interest?
* The article reads a little bit too technical to me. If I were a high school or college student reading this for class, I might find it a bit dense. Try to explain some things a little more, like your audience is unfamiliar with the topic.
Sarah Facci (talk) 06:07, 5 December 2013 (UTC)
replies: text: in is a better word; which and sentence split; still working Oalnafo1 (talk) 04:15, 11 December 2013 (UTC)
thread_title: Comments from sefacci (Sarah) 

message: Your article's biggest strength is in its organization. You have done a great job breaking the topic down into bite sized pieces that are easy to digest. You also manage to give a good overview of these topics in their associated sections. Your wikilinking is done quite well, the sources are solid, and the picture does a good job of overviewing prokaryotic termination. So I would say that everything that you have added is well done and necessary.
In terms of what can be improved, I feel like the topics warrant more information. Especially in the eukaryotic section I feel like there is still much to be written and explained. In the last paragraph you talk about conformational change but you do not explain it. I think you should go into more detail there about why polyadenylation is not compatible with RNA polymerase. I feel like more can be added to all of your sections. If you do not feel like expanding, you should at least find more articles to back up your few claims. The more definitive the subject is, the less you have to write but the more you need to cite. I also believe that a picture for eukaryotic termination or some chart comparing it to prokaryotic termination would be a great addition.
Also for a small edit, clean up your see also section. Make sure those are bullet points.
Dmille96 (talk) 03:22, 8 December 2013 (UTC)
replies: text: bullet points added thanks!Chandler.c.ho (talk) 17:40, 15 December 2013 (UTC)
thread_title:  Comments from Dmille96 

message: Hi everybody! I'm so happy to see a lot of improvement from last time. Here's a few more comments as we reach the end of the semester.
=== General comments ===
* In the "See also" section, your links aren't listing properly. Try putting a line break between the terms, that should fix your problem.
* The image you've chosen is really illustrative and the caption is pretty good. I would simply the language a bit, though.
=== Lead ===
* Your second lead sentence ("This sequence mediates transcriptional termination by providing signals in the newly synthesized mRNA that trigger processes to release the mRNA from the transcriptional complex which can be mediated by the direct activity of the mRNA secondary structure and/or by the indirect activities of recruited termination factors.") is quite a mouthful and should be broken down into a couple sentences.
* In the lead, you should link RNA polymerase.
=== Terminators in prokaryotes ===
* This section needs at least one citation.
* Can you give one sentence explaining what Rho-independent and Rho-dependent terminators are to preview the next two sections?
* This phrase is unclear, I think it's a grammar issue but I'm not sure: "and to ensuring the termination of runaway transcriptional complexes".
* The second sentence in this section (beginning "These widely distributed sequences") is way too long/wordy.
=== Rho-dependent terminators ===
* Link and/or gloss bacteriophage and cytosine.
* The citation at the end needs to come after the period.
* Explain allosteric effects for a less-technical reader.
=== Rho-independent terminators ===
* I read through the papers you cite here and they don't discuss everything you have written about in this section. I suggest you find a few more papers or perhaps an advanced genetics textbook to explicitly cite everything.
* This section is still really jargon-heavy.
=== Terminators in eukaryotes ===
* This section needs to be expanded - just give a brief overview of what's coming in the next couple sections.
* This section also needs at least one citation.
=== Torpedo model ===
* Unless it's a proper noun, don't capitalize "model".
* What is the torpedo model? You never address it explicitly.
* You need to explain what the 5' cap and 3' poly(A) tail are.
* Check over the grammar in this section - I saw a couple of errors, mostly in agreement.
* Don't abbreviate terms, spell the whole thing out every time ("RNA polymerase II" instead of "RNA pol II").
* "Similar to rho-dependent termination, XRN2 could either push polymerase out of the DNA template or pull the template out of the RNA polymerase." - This is unclear. Are you trying to say that the mechanism of action is unknown?
:hi kailena thanks for the valuable input. model has been lowercased. I added explanation to 5' cap and 3' poly (A) and wikilinked them. Terms like XRN2 are spelled out for clarification.  Yes, the mechanism is still unclear.Chandler.c.ho (talk) 17:38, 15 December 2013 (UTC)
replies: text: processivity wikilinked Chandler.c.ho (talk) 17:41, 15 December 2013 (UTC)
thread_title:  More comments from Keilana 

message: * Unless it's a proper noun, don't capitalize "model".
* What is the torpedo model? You never address it explicitly.
* You need to explain what the 5' cap and 3' poly(A) tail are.
* Check over the grammar in this section - I saw a couple of errors, mostly in agreement.
* Don't abbreviate terms, spell the whole thing out every time ("RNA polymerase II" instead of "RNA pol II").
* "Similar to rho-dependent termination, XRN2 could either push polymerase out of the DNA template or pull the template out of the RNA polymerase." - This is unclear. Are you trying to say that the mechanism of action is unknown?
:hi kailena thanks for the valuable input. model has been lowercased. I added explanation to 5' cap and 3' poly (A) and wikilinked them. Terms like XRN2 are spelled out for clarification.  Yes, the mechanism is still unclear.Chandler.c.ho (talk) 17:38, 15 December 2013 (UTC)
thread_title:  Torpedo model 

message: * Check your grammar throughout the section.
* Explain what processivity is. 
* This sentence is confusing: "In this case, termination is not completed but degradation of mRNA but through limiting RNA polymerase's capabilities."
Good luck with the end of the semester, and feel free to ask me any questions! Best, Keilana|Parlez ici 00:16, 9 December 2013 (UTC)
replies: text: processivity wikilinked Chandler.c.ho (talk) 17:41, 15 December 2013 (UTC)
thread_title:  Allosteric model 

message: Substituted at 07:49, 30 April 2016 (UTC)
thread_title: Assessment comment