Talk:Eukaryotic DNA replication

Really bad
This article is really pretty bad looking, it may need to essentially be totally re-written, definitely it at least needs expansion and re-structuringPstanton 07:22, 10 December 2008 (UTC) —Preceding unsigned comment added by Pstanton (talk • contribs)

Parallel with Prokaryotic_DNA_replication
I suggest to make a parallel with Prokaryotic_DNA_replication when this stub is completed. The structure initiation/elongation/termination is the one used in most learning materials and it will allow easy comparison between the two. Cghislai (talk) 13:42, 1 June 2009 (UTC)

Article Improvement Ideas from Ambassadors
In looking for ways to improve this article it appears that there needs to be some serious restructuring. We propose to begin with a lead section to include an overview on location of replication in the cell and in the cell cycle and the importance of complete and precise replication of all DNA only once as errors can lead to incorrect links between daughter chromosomes, chromosome breaks or loss, or DNA lesions. This should then lead in to the need for and challenges faced by multiple origins of replication. At this point the article can then branch into a more detailed discussion regarding the mechanisms of DNA replication. Here we intend to begin a new section entitled Mechanisms of Replication with subsections labeled: Origins and Initiation, Replication Fork, Regulation and Termination. Topics to be covered in the origins section would include pre-RC assembly to entail ORC, protein requirements (Cdc6 and Cdt1), DNA helicase and Mcm2-7 complex. This section will also discuss the need for kinases and polymerases α, δ, and ε for the formation of the replication fork. The replication fork section will encompass leading and lagging strand information and other important components such as DNA gyrase, SSBs, and sliding clamp/loaders. The regulation section will go into a bit more detail regarding the location in the cell cycle and the various checkpoints and progression through these checkpoints. And finally termination will detail telomere regions and telomerase. This would provide better development of this topic and would flow better. We also intend to include images for the cell cycle, pre-RC formation and replication fork in the appropriate areas to facilitate understanding.Er1cah0p3 (talk) 11:29, 13 March 2013 (UTC) Autumn Zack-Taylor (talk) 15:27, 13 March 2013 (UTC)

Comments from Sharkeyr
The lead setion is clearly written and follows the style guidelines. You can get a good amount of information in this section if you just needed a basic idea of eukaryotic replication. There are no citations for the termination and replication sections of the article, as well as the last part of the paragraphs for the Pre-replicative complex and Cdc6p along with the entire Transition to replication paragraph. The second citation does not seem to match with the information it is citing. In general, the citations are for well written information that does not plagiarize the original source. As a whole the sections are divided up well and the content makes sense where it is ordered. The article maintains a neutral tone and the basic points are easy for anyone to understand, with the more scientific information buried deeper in the article for those who need more detail. Sharkeyr (talk) 18:52, 7 April 2013 (UTC)
 * I think we have greatly improved our lead section now, and we have added references for the termination and replication sections. Autumn Zack-Taylor (talk) 18:59, 7 May 2013 (UTC)

Typo / broken link
Subheading: Minichromosome maintenance (Mcm 2-7) protein complex

First sentence: ... inichromosome maintenance ...

Comment: missing letter "m" in quoted words and link broken.

I am not an accomplished editor so I am leaving a comment so someone else can fix this. Edsilha (talk) 13:53, 13 April 2013 (UTC)
 * The link to the Wikipedia article "minichromosome maintenance" has been fixed. Autumn Zack-Taylor (talk) 14:25, 15 April 2013 (UTC)

Comments from Klortho

 * Very good so far!
 * Link "G1 stage"
 * I think this article should include some discussion of how this process differs from Prokaryotic DNA replication
 * Perhaps "initiation", "elongation", and "termination" should all be grouped together as subsections of a new top-level section called "Process" or "Mechanism".
 * You should introduce terms, e.g. protein names, before you use them. For example, "the ORC".
 * Also, spell out "pre-RC" the first time you use it, and link it: Pre-replication complex.  I see that you do that in the section below, but it needs to be done the first time you use it.
 * Link all these proteins and/or complexes, if possible: pre-RC  ORC, cdc6p, cdt1p
 * Under "The Pre-replicative complex", put a "Main article: xxxx" link to the aforementioned page.
 * Same goes for other sections, wherever there is a more detailed article specifically on that topic, add a "main article" link right under the header.

Klortho (talk) 15:39, 21 April 2013 (UTC)
 * Hello Klortho, Thanks so much for the feedback! I believe I have updated many of the improvements that you mention regarding introducing full terms before using abbreviated versions. Comparing to prokaryotic DNA replication has been mentioned a couple of times, however, I feel that with the link to DNA replication this topic is already covered fairly thoroughly. I am not sure that it would contribute much to the eukaryotic article to include prokaryotic information. Please let me know if you see anything else. Thanks!Er1cah0p3 (talk) 17:17, 24 April 2013 (UTC)
 * I agree with Er1cah0p3 with regards to adding comparisons with prokayotic DNA replication. Eukaryotic DNA replication is such a large topic in itself and to add information comparing prokayotic DNA replication might be too much in my opinion. Maybe we could add a section briefly describing the differences between the two but not going into great detail. Let us know what you think. Thanks! Autumn Zack-Taylor (talk) 18:56, 24 April 2013 (UTC)

Lead Section

 * The lead section served as a decent introduction to the subject of eukaryotic DNA replication.
 * Unlike most articles, the first sentence serves to show the topic's importance rather than explain what it is. Perhaps the first two sentences can be switched.
 * The content is concise and accessible, and follows Style Guidelines.
 * I switched the first two sentences and this does help the flow of the lead article.Autumn Zack-Taylor (talk) 18:57, 24 April 2013 (UTC)

Content and Organization

 * Authors provided ample sources and cited correctly. Most current article cited is over 2 years old. This makes the molecular biology article somewhat dated. Try to include more recent sources.
 * Organization (subheadings of "Initiation", "Elongation", "Termination" and "Regulation) is perfectly fitting and should not be changed.
 * We have added more relevant journal articles but some of the references will be dated, mainly because these papers talk about fundamental facts about eukaryotic DNA replication that haven't changed much since written. Thanks for the comment!! — Preceding unsigned comment added by Azackta1 (talk • contribs) 19:02, 7 May 2013 (UTC)

Gaps in Content

 * As Klortho mentioned, a comparison to prokaryotic DNA replication is necessary. A sentence contrasting the two should show up early in the lead. A separate section, perhaps after Eukaryotic DNA Replication Proteins, might be useful.
 * I added a sentence or two to the lead paragraph briefly comparing prokaryotic DNA replication to eukaryotic. Let me know what you think and we may be adding a paragraph to the end of the article again briefly comparing the two. Thanks! Autumn Zack-Taylor (talk) 19:29, 24 April 2013 (UTC)

Typographical Errors Corrected
MonopterusAlbus (talk) 21:13, 21 April 2013 (UTC)
 * All instances of S. cerevisiae --> S. cerevisiae
 * Thanks so much for helping to improve the article by italicizing S. cerevisiae. We will continue to search for newer articles for reference. Please also see my comments under Klortho's assessments regarding adding prokaryotic replication information into the eukaryotic replication article as I am not sure that there would be much improvement in the article by adding this in. Let me know what you think. Thanks!!Er1cah0p3 (talk) 17:22, 24 April 2013 (UTC)

Too many links, now
Oh, noooooo! I know I said to add more links, but now there are too many, I'm afraid. Please take a look at WP:Link, especially the bits about "Care should be taken to avoid both underlinking and overlinking, as described below." Well, I can see that somebody spent a great deal of time to add all those links, and so I feel very guilty. The main problem here is that you should only link something, in general, the first time you use it, not every time. To quote the style guide page: "A term should be linked, generally, at most once in an article's lead, perhaps once again in the main article body, and perhaps once at first occurrence in each infobox, table, caption, and footnote." Well, at this point, I hate to say that you should go through and remove all those links -- maybe concentrate on adding and improving the content, and then we can come back and clean up the excessive links after the class is over. Make a note on your final project report that I said this would be okay. Klortho (talk) 00:49, 26 April 2013 (UTC)


 * It's ok, this can be easily fixed and relatively fast. The only question I have is should we keep the links for every abbreviation? Like for pre-replicative complex, we use pre-RC in the rest of the paragraphs, should we keep all of these links or just keep the ones the first time we used the abbreviation? Thanks for your help! Autumn Zack-Taylor (talk) 14:11, 26 April 2013 (UTC)


 * I've taken out many links from the article. Let me know what you think and if this is enough. Thanks! Autumn Zack-Taylor (talk) 16:13, 26 April 2013 (UTC)

Comments(Unit13)from DougCovert
Hi there, I'm one of your next commentors. This article is put together nicely. The lead section is well set up and follows style guidelines. The content is very accurate and the writing is clear with no jargon. There still may be too many links, and a bit more information on prokaryotic replication might be a worthy addition. The only minor need for structure is a section at the beginning to provide the reader a general overview of eukaryotic DNA replication. In there you may add the basics for initiation, elongation, and termination briefly mentioning the major proteins involved. Throughout the article you do give brief intros, but for the non-science reader it may be too detailed as they read further, and they may get lost without a small “intro section”. There are a few concepts that may need to be added. You describe topoisomerase in the “Termination of Replication” section, but did not mention its use removing supercoils at the replication fork. Including a general description of the mechanism of DNA polymerase detailing it’s catalytic and exonuclease activity would be good. Also, processivity may be warranted as a topic, and mention of SSBs. You may want to list primase, topoisomerase, ligase, SSBs and telomeres in the listing of proteins. The article is expressing a neutral point of view with no observance of plagiarism. With these slight additions this will be a great article. DougCovert (talk) 18:17, 27 April 2013 (UTC)
 * Thank you for your comments! I do agree that some of the information given can be a little detailed, we will go through the article and revise some parts to become less detailed once all the components of this topic are in place. Thanks for the additional proteins to add to the list. Thanks again for the helpful suggestions. Autumn Zack-Taylor (talk) 13:15, 1 May 2013 (UTC)
 * Great work, nicely done. You guys went back in and cleaned up the links and added short summary sentences to provide a simple explanation before getting into the details of the topic. Also you did a good job in the comparison to prokayotic DNA replication. Thanks for implementing any of my suggestionsDougCovert (talk) 02:28, 10 May 2013 (UTC)

Comments from WeberOwl
Hey guys, article is looking good. Here are some suggestions:

Introduction
I'm not sure the first sentence is the best way to start off the article. Maybe focus more on what the mechanism is then a somewhat random (if important) fact about it (that it is limited to once per cycle). Also, in this sentence "the completion of eukaryotic DNA replication is more difficult" the use of the word difficult is somewhat vague. Maybe replace it with "complex?"
 * I do agree that the lead section could have a little more information other than being so vague about the replication process. Once all other components about this topic are in place, we will revise the lead section. Autumn Zack-Taylor (talk) 13:17, 1 May 2013 (UTC)

Initiation of Replication
It's awesome how thorough this is, though I wonder if it's almost too much so. The introduction to the section might want to explain in slightly more detail, and the subsections can become an optional, not required, read for somebody who is interested in this aspect of replication.
 * I agree, there is so much information on this topic its hard to decide whats most important. Having introduction sections that briefly describe the topic and then having subsections with more detail is a great suggestion. Autumn Zack-Taylor (talk) 13:19, 1 May 2013 (UTC)

Elongation
Similar to the prior section, try to avoid details where they aren't really needed. For example with the sentences " Cdc45 is an essential component of the replication fork.[17][56] It has been shown that antibodies against Cdc45 block DNA unwinding during replication in Xenopus egg extracts" is it really worthwhile mentioning that such antibodies exist? It doesn't add much to the reader's knowledge of eukaryotic replication, which is what this article should focus on.
 * Do you think it is important to describe where some of this information came from in terms of experiments? Autumn Zack-Taylor (talk) 13:20, 1 May 2013 (UTC)

Termination of Replication
The first two paragraphs don't have any citations (and the third only 1). We need more info on where these facts came from.

Regulation of Replication
This is a great section: concise, focused, and well cited. If all of the sections copied this format I think that the article would be better as a complete item.
 * Thank you! We will strive to have all sections be formatted in this way. Autumn Zack-Taylor (talk) 13:23, 1 May 2013 (UTC)

Some feedback on the article as a whole is that a section detailing the specific differences between eukaryotic and prokaryotic replication would add a lot. I have a feeling that a majority of the traffic coming through this page will be in search of such differences. Also, while the detail of the article is well researched and explained accurately, it might detract from the main focus of this topic. WeberOwl (talk) 20:43, 30 April 2013 (UTC)
 * This is a good point. Some the components of eukaryotic DNA replication still need to be added to the article. Once they are all there, then I think it would be useful to have a comparison. In my opinion it would be hard to compare when all of the aspects of eukaryotic DNA replication aren't there. But this is on the "to do" list! Autumn Zack-Taylor (talk) 13:22, 1 May 2013 (UTC)
 * You could always keep the comparison more general, just highlighting the key differences and not going into detail about each aspect of replicationWeberOwl (talk) 00:38, 2 May 2013 (UTC)
 * Checking in as the semester ends. The article is really thorough, and will be of great use to anyone looking for more information on the topic. I'm not sure that the table at the end adds much, but overall, great job.WeberOwl (talk) 21:06, 9 May 2013 (UTC)

Contradiction/omission
These sentences in the replication fork section,

"Each Okazaki fragment is preceded by an RNA primer, which is displaced by the procession of the next Okazaki fragment during synthesis. RNAse H recognizes the DNA:RNA hybrids that are created by the use of RNA primers and is responsible for removing these from the replicated strand, leaving behind a primer:template junction. DNA polymerase α, recognizes these sites and elongates the breaks left by primer removal."

are if not contradicted in the lagging strand section a few paragraphs down, at least aren't a full or even basic explanation of okazaki fragment maturation. I understand this may not be a settled matter, since the literature implicates RNAse H, FEN1, Dna2, and others, with either contradictory or complementary models. But it's confusing to read one thing and then a few paragraphs later find no mention of it. I don't know where the front of the field currently is on the issue.

173.25.54.191 (talk) 21:14, 28 July 2013 (UTC)

Simplification
Very detailed, but not very readable for the novice. It seems to me the article could have started with a simple version describing the purpose (replication of the DNA of the cell). Then describe the high level steps; orc, primase, polymerase, exonase replicating the leading strand, okazaki fragments, (primase, polymerase, exonase, ligase) repeated on the trailing strand. Once you have a simple explanation described in one section, you can then expand giving your detailed explanation in sub sections.

Thepigdog (talk) 14:13, 23 June 2014 (UTC)

Citation requests
Three diagrams are very similar to the figures published in Genes (Basel) 4(1): 1-32. Leman AR, Noguchi E. (Reference #1) These diagrams include: 1) Diagram of the formation of pre-replication complex transforming into an active replisome. 2) Eukaryotic replisome complex and associated proteins. 3) Depiction of replication through histones. Although the article is cited throughout the text and the figures are modified, I feel that it is appropriate to cite the original article in the diagram.Enognog (talk) 16:22, 24 September 2014 (UTC)

Bidirectional replication in prokaryotes, not unidirectional
In comparing prokaryotic and eukaryotic replication, several times the article states that prokaryotic replication is unidirectional, clockwise from the origin. In Escherichia coli, the replication has been shown multiple times to be bidirectional. Several papers showing this are: "Evidence for the Bildirectional Replication of the E. coli Chromosome, M. Masters, P. Broda, Nature New Biology 232, 137-140 (1971); Bidirectional Replication of the Chromosome in Escherichia coli, D. Prescott, P. Keumpel, Proc. Nat. Acad. Sci. USA 69, 2842-45 (1974).  A careful analysis of the grain densities on some of Cairns' published EM's of autoradiographs also show the replication to be bidirectional, even though Cairns himself interpreted the pictures as showing unidirectional replication.

Clarifications needed
Hi. this article is very informative, but a few bits are really hard to understand, sometimes because of wording, and sometimes because it seems that assumptions are not explained. I freely admit my ignorance of this subject, I realise this article is over 12 years old, and this Talk forum may no longer be being monitored, so sorry for this intrusion, but here goes: Consider this paragraph, currently second in the section entitled "Comparisons between prokaryotic and eukaryotic DNA replication": ====Eukaryotic DNA is bidirectional. Here the meaning of the word bidirectional is different. Eukaryotic linear DNA has many origins (called O) and termini (called T). "T" is present to the right of "O". One "O" and one "T" together form one replicon. After the formation of pre-initiation complex, when one replicon starts elongation, initiation starts in second replicon. Now, if the first replicon moves in clockwise direction, the second replicon moves in anticlockwise direction, until "T" of first replicon is reached. At "T", both the replicons merge to complete the process of replication. Meanwhile, the seco[ no]nd replicon is moving in forward direction also, to meet with the third replicon. This clockwise and counter-clockwise movement of two replicons is termed as bidirectional replication.==== These are my problems with this - the text says "T" is present to the right of "O" - what does "to the right" mean ? Further in the 5'-to-3' direction along the coding strand ? - references to "replicons" here seem consistent with the next article paragraph and other linked Wiki articles, since all imply that DNA replication of a eukaryotic (linear) chromosome can start independently at, and run concurrently from multiple replication origins, and this reduces the time to replicate the whole chromosome. But the latter part of this paragraph is very puzzling. - initiation of the "second replicon" is said to start after the first has started elongation. Is this just saying that when the two initial complexes are assembled at a replication origin, so as to move in both physical directions along the DNA molecule, replication in the second direction is not started until RNA priming has completed and elongation has started in the first direction ? - the sentence "Now if the first replicon moves in clockwise direction…" refers to clockwise and anti-clockwise, which suggests we have just switched from discussing eukaryotes to circular DNA. (Or does this refer to mitochondrial DNA?) - again the idea of replication completing when opposed replications meet belongs to circular DNA. But suddenly a "third replicon" is mentioned. Is this just a misprint for "first"? Otherwise this third replicon is presumably further along In one direction or the other, maybe following the first. If so, it isn’t clear here, nor in any other Wiki replication discussion I've found, just what happens if replication from different origins can indeed start independently. Surely when replication in one direction for any stretch reaches its "T-point", the next section might be complete, still being built, or maybe not even started. How are these different cases covered ? AconUK (talk) 18:31, 10 April 2019 (UTC)