Talk:Histone octamer

Improving the Article

Hello,

I'm currently involved in a project through Johns Hopkins University that will attempt to improve this article. I am working with another user Rokasj1 and our target goal is to get the article somewhere between B and GA. Currently there is very little information for this article so we see this as starting from ground zero. Comments have been made considering combining this article with histone but we would like to try and build up this article separately. We will try to avoid overlap but as of right now we will cover: the history of research on the topic, molecular structure of the topic, its role in DNA regulation, and the clinical relevance of associated mutations. If anyone has any feelings about the above, feel free to let me know.

Dmille96 (talk) 03:24, 23 October 2013 (UTC)

Hi, I am going to be working with Dmille96 on this article, and I am also from JHU. I hope that this will be a well structured and informative article before the mid December where readers can also find a good list of references on the topic. I agree that this article should not be combined with histone.

rokas (talk) 03:43, 23 October 2013 (UTC)

let us know if you have any comments on the article so far

rokas (talk) 02:52, 30 October 2013 (UTC)

Comments from LutyeusMaximus

Hi Rokas1 & Demille96, So far your article has a good start. Here are a few things I noticed that I think you could do easily to help move your article along:

• the very first sentence which defines octamer with the word octamer is a little redundant and some of the grammar in the sentence needs improvement.
• add citations in first paragraph
• I know the article isn't big yet but I would add a contents box at the top of the page, this seems to be general wikipedia format and as your article expands I think it will help you keep things organized

The contents box is created automatically, by the mediawiki software, when the article has enough headings to warrant it. Klortho (talk) 05:16, 3 November 2013 (UTC)

Ooooh Ok, my bad, so you can ignore that comment!! Thanks for the clarification Klortho LutyeusMaximus (talk) 21:37, 13 November 2013 (UTC)

• I would remove top banner about citations since you guys are starting to add them now
• In the first paragraph you jump right into the structure of histone octamers. I think this could be a sub-section. I think in the first paragraph readers are just looking for some information on general function and maybe location of histone octamers
• the sentence in the first paragraph about histone formation in vivo, is a little confusing. It took me a couple reads to figure out what is trying to be said.
• I think the second section about histone octamer research really has more information on the history of histone ocatmers and their structure.
• the first sentence of the second section about post-translational modifications is the start to an entirely separate section I think for later in the article.
• I updated one of your sources which had a few spaces missing between words

I hope you don't think I was too nit-picky but I think you have a good start to your article! LutyeusMaximus (talk) 23:43, 30 October 2013 (UTC)

Thanks for the input. It is difficult finding the right balance of basic and new in the first paragraph so it is good to hear your opinion; I'll definitely give that a rewrite as the article develops.

Dmille96 (talk) 23:23, 12 November 2013 (UTC)

No Problem, I hope what I said helped. Let me know if you have any questions. LutyeusMaximus (talk) 21:37, 13 November 2013 (UTC)

Comments from Klortho

• General:
  • I think you should have more content than this by now, and/or at least an outline, so that one can get a sense of what is to come.
  • This article could definitely use some figures to help the reader understand the geometry of this thing, and how the eight peices all fit together, for example.
  • You could borrow a lot of ideas from the histone article, which is much more developed. But take care not to just repeat the stuff there -- be clear about how your article will be different (by focussing more on the "octomer" feature than that article, and how and why that is important)
  • When you link to something like "nucleosome core particle", note how it gets redirected to "Nucleosome". So you should use a piped link, like this: nucleosome core particle
• Lead:
  • "2" should be spelled out as "two".
  • Why are these notable? Give some introduction about how histone octamers fit into the larger scheme of things. See the histone article lead to see what I mean.
• Histone octamer research
  • This section might better be titled "History"
  • The sentence beginning, "Each peptide of a histone has an element of helix-loop helix and therefore named histone fold", seems to switch to talking about structure. If you're trying to describe the naming itself as an historical event, then that needs to be made more clear, I think.
  • It is not clear to me why you are talking about the linker histone H1, because it is not part of the octamer.
  • This section could use some more links. For example, X-ray crystallography, helix loop helix, etc.
• References: You should be using the instructions here for formatting your references. First look up the articles in PubMed and get the PMID. If you did, then your first reference would look like the following. Note the link to PubMed, which makes it much easier for others to get the reference.

Allfrey, VG (1964 May 1). "Structural Modifications of Histones and their Possible Role in the Regulation of RNA Synthesis". Science (New York, N.Y.). 144 (3618): 559. PMID 17836360. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

Klortho (talk) 05:36, 3 November 2013 (UTC)

I didn't realize we were supposed to put our outline out front. We have one in Rokas' sandbox that we are using. I suppose I can add it here to use it for direction. We have also been looking at the histone and nucleosome pages as influence but we are finding it difficult to relate the information without repeating the same information. There is a considerable amount of overlap. Either way, we'll fix up those references and links as something seems to have gone wrong there.

Dmille96 (talk) 23:32, 12 November 2013 (UTC)

Comments from donbinincom

Like the other reviewers, I think the lead is a bit confusing and could use some cleanup. One small thing is that the "octamer" link in the first sentence links to "oligomer", so it can take a while for someone unfamiliar to even decipher the subject. My suggestion would be to first explain that an octamer is an 8-membered collection of molecules and then go more specifically into what a histone octamer is and why it's important. I would also suggest citing a very basic reference for the lead that would allow a neophyte to quickly get the big picture. I would also suggest not dropping directly into histone research in the next section but rather easing the reader into the subject. Don Brown (talk) 06:10, 3 November 2013 (UTC)

Thanks for the bit about the octamer. I must have overlooked that when I was writing. I'll definitely try to rewrite that bit to make it simpler.

Dmille96 (talk) 23:28, 12 November 2013 (UTC)

It's much clearer now. I realize it's a balancing act, but I think it's best that the reader not have to click on a link in every other word in order to understand the topic. Your revised version does a much better job of communicating the big picture without having to drill down via links. Don Brown (talk) 23:03, 18 November 2013 (UTC)

Second Review

You guys have come a long way! This is a big improvement from where you were at the time of my first review. I really like have you've broadened the lead to make it more of a high-level overview. One suggestion I'd make is to follow the lead with the paragraph about "The Histone Octamer in the Nucleosome". I think it's easier on readers to take them through incrementally more detailed levels. Talking about the role of the histone octamer in the nucleosome would seem to me to be the next logical step. Second, I'm sure you know this already, but this subject cries out for some good illustrations. I'm thinking of something like the two-sided disc illustrations in our text. If you can't find anything good in the public domain, let me know and I have some good graphics art contacts (my son) who could whip up something for free. Third suggestion, it would be great to cite a very general reference the reader could use to get more "big picture" information. One I found is -

Alan P. Wolffe, Dmitry Guschin, Review: Chromatin Structural Features and Targets That Regulate Transcription, Journal of Structural Biology, Volume 129, Issues 2–3, April 2000, Pages 102-122, ISSN 1047-8477, http://dx.doi.org/10.1006/jsbi.2000.4217. (http://www.sciencedirect.com/science/article/pii/S1047847700942175)

In the "History of Research" section, it strikes me as strange to talk immediately about post-translational modifications of histones when the subject is the histone octamer itself. How did scientists come to realize an octamer was involved? Also, you may plan to cover it later, but how does the octamer form? How long does it last? What happens to it during replication? These are some other good questions to consider answering.

Finally, there are still several awkward sentences. For example, in the lead you say "either in vivo...". I would expect that to be followed by "in vitro" later. The only "or" to follow the "either" is "without DNA". There are several other sentences with minor grammatical errors.

Hope that all helps. Don Brown (talk) 22:55, 18 November 2013 (UTC)

Thank you for a review, Don, I really appreciate, and I will defintely take it into account editing the "history" section. I will also address the additional questions about the histone octamer in respective sections.

rokas (talk) 01:54, 20 November 2013 (UTC)

I would still recommend a more conceptual illustration of the histone octamer - the type we have in our text that shows the octamer as a two-sided disk. I think an illustration of this sort would help the reader get the big picture more quickly. Don Brown (talk) 19:34, 2 December 2013 (UTC)

Comments from Igenes

In addition to the feedback from other reviewers I have some listed out from my side. I think more content needs to be added in each section of your article, I believe you must be working on it.

• You mentioned about types of histone proteins in the first paragraph and again under ‘The Histone Octamer in Molecular Detail’ I think one of these duplications can be left out.
• The frist paragraph does not have citation, which was identified among other reviewers too.
• In your history section you can mention who first discovered the histone octomer. I think there should be a link to ‘Richmond et al's article as this would help to navigate the reader to further understanding or exploring the topic.
• You may want to consider history section at the bottom of your article.
• Consider adding more pictures and tables. Igenes (talk) 16:35, 18 November 2013 (UTC)

I agree with most of Harshil's comments, although I personally don't find a little repetition that harmful. So long as you're not just restating the same thing verbatim but rather adding some level of detail, I don't think it's bad. It seems to me that you're introducing the four subcomponents of the octamer in the lead and then elaborating on that in the paragraph on structure. Don Brown (talk) 23:08, 18 November 2013 (UTC)

We're going to leave the repetition for now but the first paragraph is definitely going to be changing as the article nears completion. A lot of people have added good comments about it, and I'll keep them in mind when rewriting. Pictures and tables are going to be out last focus once we get everything covered in the writing.

Dmille96 (talk) 00:41, 27 November 2013 (UTC)

If you decide to create a table, you may want to consider having your table sortable. This option is usually in the header, let me know if you have trouble creating table(s).Igenes (talk) 16:16, 27 November 2013 (UTC)

Thanks we'll keep that in mind.

Dmille96 (talk) 03:24, 8 December 2013 (UTC)

Comments from Keilana

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

• The lead needs to be expanded and many of the terms need to be glossed so it is comprehensible to the lay reader. (The audience I think of when writing a lead is a smart 15 year old high school student, if that helps.)
• Lots of terms in the lead need linking, but you have a pretty good start.
• Do you have a secondary source for the 1964 discovery? That would be a good addition.
• The article really needs to be copy-edited for grammar and clarity. I'm happy to do this if you would like, just drop me a note on my talk page.
• Titles of sections should only have the first word capitalized.
• In general, a good rule of thumb is to not name researchers unless they are very significant, and to not use the "et al" construction. Instead, say "So-and-so and his/her/their research group".
• "Furthermore the details of protein-protein and protein-DNA interactions were fine tuned by X-ray crystallography studies at 2.8 and 1.9 ˚A in the 2000s." - this needs a citation.
• "Histone tails are subject to a wide array of modifications which includes phosphorylation, acetylation, and methylation of serine, lysine and arginine residues." - this also needs a citation.
• You need lots of links throughout - several sections had no links whatsoever.
• Saying that something will be discussed in a later section is unnecessary.
• All of your citations need PMIDs or DOIs so other people can find them easily. PMIDs are preferred.
• "In solution, histone-fold domain of core histones pair tightly to form interlocked crescent shaped quasi symmetric heterodimers, the histone-only intermediates." - this is too closely paraphrased. Please rewrite.
• You do not need to repeat citations one after the other as you did with Luger - as long as you have the citation at the end of the section drawn from that material you are fine.
• "Second, the histones’ N terminal tails can be modified in several ways—most commonly acetylation, phosphorylation, or methylation—to limit or increase their transcription. The interactions between the histone octamer and DNA, however, are not permanent. The two can be separated quite easily and often are during replication and transcription. Specific remodeling proteins are constantly altering the chromatin structure by breaking the bonds of the nucleosome." - this needs a citation.
• There are 3 blank sections, do you intend to fill them in?

All the best, Keilana|^{Parlez ici} 02:49, 21 November 2013 (UTC)

Thanks, we are working on getting our links and citations. Those should be coming very soon. As for the opening, I am planning on rewriting the first paragraph once we have finished the article. That way we can give a good summary of everything that we are going to present; I'll definitely keep your comments in mind. All of the section will be filled in before the next peer review.

Dmille96 (talk) 00:38, 27 November 2013 (UTC)

Thanks, Keilana, in the "history" section I took out the et. al, inserted missing citations in the "history" and the "molecular detail" paragraphs.

rokas (talk) 22:13, 14 December 2013 (UTC)

Comments from Mtee87

1) I went ahead to add place holders as one of the reviewers did for my group about two weeks ago. This is to let others know that it is currently being worked on, and to give others who may be interested a chance to edit.

2) On the whole, I like the progression of the article. The image seems great, although I wish it was more centralized in the image box.

3) With the lead section, I wondered if you wanted to cite any portion of it. I don’t know that any of the information in that section is common knowledge. Therefore I was wondering if you can add at least one inline citation where most of the information in this section can be found.

4) It is also great to see your high quality references ranging from published research articles to books.

5) In developing the rest of the sections, I wanted to suggest being careful with the language. To avoid heavy scientific language so that it does not seem too technical, I think you should do good summary of the facts

6) Also, using the creative commons page, you can find images on histone octamer assembly. I believe this will help buttress your point in “Histone Octamer in Molecular Detail” section, where you touch on the process of assembly Mtee87 (talk) 17:29, 22 November 2013 (UTC)

Thanks so much for that creative commons page. I'd never seen that before, its pretty perfect for this. We'll keep your points in mind as we touch everything up over the next week. We'll try to tone down the technical language.

Dmille96 (talk) 03:29, 8 December 2013 (UTC)

Comments from grabriggs

The article looks very good so far, I can see you've made a lot of progress and have had a lot of suggestions already. The overall article is in good shape in my opinion, but I'll try to give a couple suggestions that can be easily fixed in our last week. First, the lead has two links to "nucleosome core particle" so the second can be removed. The lead reads well, but like all of our articles seems a bit technical for the non-scientist. There is a lot of description about what a histone is made of, what its chemical composition is, etc. I was half way through the article before you told me what a histone does and why they exist. Why is a big question in mind when reading an article. I would consider moving this explanation further forward in the article. The reader is then aware that this is a structure used to compact and regulate DNA and can read on about how that works if interested. One editor mentioned in a review for my article that we needed PMID or DOI for each of our citations. I noticed you are missing a couple as well. It was fairly easy to add them using the "cite" tool. There are some minor grammatical improvements that could be made as well, but overall this is a great improvement over what you started with! Grabriggs (talk) 01:29, 3 December 2013 (UTC)

Hmm yes it seems like we went a little over board with technical language. We'll tone it down for the final edits. I thought I added PMIDs but I must have reverted one of my edits, we'll be sure to clean that up as well. In terms of reformatting the article, I think moving the nucleosome section ahead of the molecular detail section would help solve the issue. As would changing up the opening paragraph, which is my focus as we finish the article.

Dmille96 (talk) 03:33, 8 December 2013 (UTC)

Comments from chandler.c.ho

The lead section follows style guidelines. Content of each section accurately represents the cited sources. wikilink to p300,CBP, and acetyltransferase should be added. The image on octamer structure helps on picturing a quasi symmetry. This article uses clear and comprehensible writing to explain the role histone octamer. When jargons are introduced, most terms are wikilinked for further explanation. What is the role of histone octamer? It would be more clear if you explain the in the beginning of the article. Physical and chemical interactions can be separated into 2 sub topics. The three approaches to nucleosome remodeling and dis-assembly can be separated and expanded. You guys have done a good job expanding this topic overall.Chandler.c.ho (talk) —Preceding undated comment added 16:10, 6 December 2013 (UTC)

Thanks for the input. The why issue seemed to get lost in our fractured writting style. We'll focus on getting everything flowing for the final edit. As for breaking up some sections, I'll give it a try and see how it reads. It was a thought I had initially but I wasn't sure I had enough information. Thanks again.

Dmille96 (talk) 03:36, 8 December 2013 (UTC)

Comments from KevinBrownJHU

Overall this is a good article. The leader section still needs a bit of work like more links to cover terms (like Minor Groove). Grammar does need to be fixed up throughout the article as the sentences in some places are a bit rough. Example: "has been able to elucidate a crystal structure of the histone octamer" instead of "has been able to elucidate a crystal structure of histone octamer". The article could use a few more appropriate images and the caption on the current image could be expanded to be more explanatory of the image. It's too bad that the image has so much wasted whitespace off to the side of it. Makes it harder to increase the size of the image. Maybe consider editing it and upload it in place of the current image without the excess whitespace. Keep up the good work. It is almost there. KevinBrownJHU (talk) 21:06, 7 December 2013 (UTC)

Yeah we had trouble finding a good, free-to-use picture but someone posted a good resource that we will look into. Grammar and sentence structure will be the large focus of our last edits.

Dmille96 (talk) 03:40, 8 December 2013 (UTC)

Some more comments from Klortho

Hi, I see you have made quite a lot of progress on this article. But, I think there is still some room for improvement.

First of all, it seems to me you didn't address all of Keilana's comments above. In particular, the two I noticed were:

• "In general, a good rule of thumb is to not name researchers unless they are very significant, and to not use the 'et al' construction. Instead, say "So-and-so and his/her/their research group"."
• "'Furthermore the details of protein-protein and protein-DNA interactions were fine tuned by X-ray crystallography studies at 2.8 and 1.9 ˚A in the 2000s.' - this needs a citation."

I didn't check thoroughly, so maybe there are others. Did you not get a chance yet? She is a very accomplished WP editor, and her comments are really valuable.

Here are a few other comments. I didn't get a chance to go through the whole article, just the first 60% or so:

• General
  • Headings should only have the first word capitalized.
• Lead:
  • Could use a couple more links, e.g. "C-terminals" (to C-terminus), "expression" (to Gene_expression).
• History of research:
  • Needs to be copy-edited for grammar and sentence structure. For example, this sentence is not good: "Each peptide of a histone has an element of helix-loop helix and therefore named histone fold".
  • Numerals less than ten, used in text, should be spelled out. "7" -> "seven".
  • "α-helix" should be glossed, or, at a minimum, linked.
• "The Histone Octamer in the Nucleosome"
  • You wrote, "The histone core and nucleosomal DNA primarily interact through two methods.", but as far as I can tell, you don't list two methods. You have one method, interacting through the minor groove, but the other "method" seems to be about modification of histone tails. Modifications can change the interactions, but are not interactions themselves, I don't think.

Keep up the good work! I think, with a bit more work this last week, you can improve this article quite a lot. Klortho (talk) 18:53, 8 December 2013 (UTC)

Thanks for the comments. I've added in the citations that were missing and changed up some of my confusing wording. We've taken Wikilinking to the max with this edit so I think we've covered any of those as well.

Dmille96 (talk) 21:49, 14 December 2013 (UTC)

Thank you for reminding about some of the items: I have rephrased confusing sentence in the "history" paragraph, added in more wikilinks, missing citations.

rokas (talk) 01:02, 15 December 2013 (UTC)

Additional Comments from Harshil (Igenes)

• You should consider adding wikilinks under 'Physical & Chemical interactions of nucleosomes' , 'Nucleosome modeling & diassembly' and 'Clinical relevance' sections.
• Under 'Clinical Relevance' you abbreviated 'CBP' without using the full word earlier. Use the full word at least once before you abbreviate that word. Consider wikilink to that word too.
• I noticed there is only one picture added to your article. You may want to consider adding more pictures to make it visually attractive and informative. I posted a picture from wikimedia commons, you can use it in our main article. Igenes (talk) 02:55, 12 December 2013 (UTC)

Igenes (talk) 02:55, 12 December 2013 (UTC)

Thanks for the picture. I've included it in the article. I'll be adding more wikilinking soon.

Dmille96 (talk) 04:44, 14 December 2013 (UTC)

CBP full name added in. Thanks!

rokas (talk) 01:03, 15 December 2013 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Histone octamer/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

Rated "high" for consistency with histone, merge those two pages? - tameeria 03:46, 19 February 2007 (UTC)

Last edited at 03:46, 19 February 2007 (UTC). Substituted at 17:58, 29 April 2016 (UTC)