Talk:Histone

Histone was nominated as a Natural sciences good article, but it did not meet the good article criteria at the time (March 20, 2021). There are suggestions on the review page for improving the article. If you can improve it, please do; it may then be renominated.

Molecular Biology: Genetics / MCB

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Historical omission

Please include the contributions of Marie Maynard Daly; ca. 1955 she determined that a major component of DNA-binding histones is lysine, while the predominant idea at the time was that the major component was arginine (see Albrecht Kossel). There is an article for her on Wikipedia that links out to this article, but this article on histones does not reference her. http://en.wiki.x.io/wiki/Marie_Maynard_Daly — Preceding unsigned comment added by 170.140.104.4 (talk) 22:25, 11 November 2021 (UTC)[reply]

Unclear Sentence

Under the heading 'classes', near the end of the paragraph, it says "During meiosis, through the combination of nucleosome interactions with other proteins, the chromosome is assembled." I can't make sense of this sentence... and don't think it's as clear as it could be. --Seans Potato Business 03:52, 22 April 2007 (UTC)[reply]

Hopefully it's better now. --chodges 19:03, 6 August 2007 (UTC)[reply]

Time to update?

the picture in this article should probably be updated. It doesn't match with the text, and is misleading. The H2A-H2B dimers act as endcaps to the (H3-H4)₂ tetramer... Also we're kind of missing the flexibility and disorder of the H1 histone. I know you can't put everything in a picture, but the model of a nucleosome core particle illustrated here could be a bit better. --74.230.134.53 21:22, 14 May 2007 (UTC)[reply]

In my opinion, this figure is not suitable for use. This image is unsuitable for inclusion into the Histone page for the following reasons:

The DNA shown is not biologically inspired. There is neither major nor minor groove, and its scale in proportion to the histone proteins is much too small.
The DNA is displayed as having a right-handed superhelical twist around the histone octamer, when the the crystal structure (Luger, et al, Nature 389: 251, 1997, PDB entry 1AOI) shows that the DNA's superhelical spiral around the nucleosome is instead left-handed.

These major inaccuracies are probably strong enough to warrant its removal from the page. Can we remove this image from the Histone article? --chodges 18:09, 25 July 2007 (UTC)[reply]

Another unclear sentence

"There are some variant forms in some of the major classes." What are classes, and what are variant forms, and how does this relate to the previous paragraph? -Pgan002 02:09, 15 June 2007 (UTC)[reply]

Not mentioning any history about the issue or who discovered the histone proteins

The article does not mention anything about the work of the Nobel Prize Winner Roger D. Kornberg , he was the one to do the crystal structure of histone and propose the method by which DNA is wrapped around it.

Eukaroya and Prokarya

I'm confused. The article's header references chromatin, a DNA based composite within both Prokaryotic and Eukaryotic cells, for the purpose of defining Histones. To the best of my knowledge, Histone proteins only exist in eukaryotes... Isn't that misleading? perhaps a proper notation should be made at the opening paragraph, to clarify this. cheers Martin fed (talk) 14:22, 4 March 2009 (UTC)[reply]

Ok, it's been 4 years since I talked about the histone interaxions with DNA and still there's a citation needed tag around highly basic nature contributing to water solubility. This is 2+2 stuff here, folks. If you want a pI plot for histones, I'm sure you can find one in about 5 seconds on google. Ionization = water solubility. Q.E.D. —Preceding unsigned comment added by 169.230.107.220 (talk) 08:59, 14 March 2009 (UTC)[reply]

Need infobox

Could someone add {{protein}}? LeadSongDog come howl 15:44, 19 June 2009 (UTC)[reply]

—Preceding unsigned comment added by 129.128.216.243 (talk) 19:47, 24 February 2010 (UTC)[reply]

classes of histones

   * core histones – H2A, H2B, H3 and H4
   * linker histones – H1 and H5

H5? really? kindly provide reference.

Sameerbau (talk) 20:10, 4 March 2011 (UTC)sameer[reply]

I think H5 is in chicken. https://www.uniprot.org/uniprot/P02259

It is, however had, not closely linked to "linker histones", so it should not be grouped into that, IMO:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC325741/

2A02:8388:1604:CA80:3AD5:47FF:FE18:CC7F (talk) 19:22, 14 October 2018 (UTC)[reply]

How many of each type

Couldnt see any mention of how many of each type a cell might have.
Is each section of the genome always wound around the same type of histone ?
What proportion of the cells histones are not wrapped in DNA at the various stages in the mitosis cell cycle ? - Rod57 (talk) 12:18, 15 September 2015 (UTC)[reply]

Assessment comment

The comment(s) below were originally left at Talk:Histone/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.

Changed rating to "high" as this is high school/SAT biology content. - tameeria 21:51, 18 February 2007 (UTC)[reply]

Last edited at 21:51, 18 February 2007 (UTC). Substituted at 17:58, 29 April 2016 (UTC)

This isn't tested yet or we simply missed it, if you find it in the future mention it in the article

It's been proposed that histones and DNA methylation cause:

the homologous recombination during meiotic prophase I not to be random due to the remaining misshape of the DNA (statistics aren't neutral).

This shouldn't normally happen. We all know that. "Shouldn't normally happen" is a dialectic phrase. We need proof in the lab, we cannot simply imagine that all goes statistically well. We should test it on corn and microorganisms.

More History Needed

I agree that history of histones is needed and I suggest adding the period when histones were found to be just a few types and highly conserved across taxonomically diverse organisms. James F. Bonner and his collaborators in the 1960s showed isolated chromatin would not support RNA transcription in vitro but if the histones were extracted, RNA could be transcribed. They went on to develop methods to purify each type of histones, to compare amino acid compositions from peas and calf thymus, and compare sequences to find almost no variation. Before this period, T'so and Bonner had called together a conference, published in Nucleohistones, a volume of conference papers, in which it was clear that the number of kinds of histone was estimated to be very different by different investigators and that no one know how they would compare when isolated from different organisms. I will add a reference to sequence comparisons to this note in about 10 minutes. <ref>Huang RCC and Bonner J "Physical and Biological Properties of soluble nucleohistones." Journal of Molecular Biology 8(1):54-64 (January 1964)<ref>.LLMHoopes (talk) 23:23, 4 August 2018 (UTC)LLMHoopes (talk) 07:56, 20 September 2018 (UTC)Here are references on history and on sequence comparison: Robert DeLange, Douglas Fambrough, Emil Smith, and James F. Bonner (1969) "Calf and Pea Histone IV: III Complete sequence of pea seedling Histone IV: comparison with calf thymus histone." J Biol Chem 244 (20): 5669-5679. James F. Bonner. (1994)"Chapters from my life" Annu Rev Plant Physiol Plant Mol Biol 45:1-23. Campos and Reinberg (2009) "Historic perspective on histones" Annu Rev Genetics 43 (Supplement: Histones, Annotating Chromatin).LLMHoopes (talk) 08:01, 20 September 2018 (UTC)[reply]

Early History of chemistry and biology of histones in the 1960s

=I have added a section of material to the history section describing the analyses of the chemistry and biology of histones in the 1960s by James F Bonner and collaborators and Allfrey and Mirsky. This addition addresses an imbalance in the treatment of structure of nucleosomes versus the histone molecules themselves and their effects on trancription of RNA in general terms. James Bonner was a member of the National Academy of Sciences and a Caltech faculty member who had published 10 books and over 200 articles in plant physiology (see WP article). His contributions are an important part of this history. Allfrey and Mirsky suggested regulation by acetylation of histones very early, a phenomenon well established now as shown later in the Histone article. They showed a general effect but could not show a gene-specific regulation due to lack of the techniques now available such as ChIP. LLMHoopes (talk) 09:21, 24 September 2018 (UTC)[reply]

Role of phosphorylation of Histones

The article presently states:

"It is not clear what structural implications histone phosphorylation has, but histone phosphorylation has clear functions as a post-translational modification, and binding domains such as BRCT have been characterised"

There has been at the least one paper that linked some form of phosphorylation on histones with the condensation of chromatin. I read it in a book for graduates not so long ago - if anyone knows the paper, the article could be extended in this regard. 2A02:8388:1604:CA80:3AD5:47FF:FE18:CC7F (talk) 19:21, 14 October 2018 (UTC)[reply]

make paragraph: Meiosis

Are then all histones and methyl groups removed?

Iff they are, does any slight fold remain even at larger orders of magnitude than a few nucleobases.

During meiosis homologous chromosomes exchange parts.

Is that 100% random or are there biased preferred "junctions" due to chemical differences of the bases or other differentiation.

Watch all HHMI YouTube videos.

If you say something give us official data. Anyone can say lies. — Preceding unsigned comment added by 2A02:587:4123:AB00:899:26D0:B533:907D (talk) 01:30, 20 September 2019 (UTC)[reply]

GA Review

This review is transcluded from Talk:Histone/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Esculenta (talk · contribs) 19:22, 12 March 2021 (UTC)[reply]

I'll take on this review. I think the article is quite a long ways from reaching GA standard. Here are some problems:

the lead is quite short and does not adequately summarize the contents of the article as per WP:LEAD
there is some material in the lead that is not present in the article body, for example, the facts about 90 micrometers of chromatin and 120 micrometers of chromosomes.
The biggest problem: the sourcing in this article is way off balance. There are sometimes multiple citations for what seem to be relatively simple statements of fact ("Five major families of histones exist: H1/H5, H2A, H2B, H3, and H4.[2][4][5][6]"), while in other cases there are unsourced sentences, and many unsourced paragraphs. I would expect a higher diversity of secondary sources for an article like this, there are many out there. The secondary sources that are being used (e.g. Lehninger 2005) does not cite page numbers, making it difficult to verify the material. The high number of primary sources, and the tendency to use multiple citations of primary soueces (e.g. "H3K56 is acetylated by the p300/Rtt109 complex,[91][92][93]") is a problem for an article that should mostly be sourced to textbooks and review articles. All of the unsourced bits would have to be properly cited before we could go any further. I also note that the nominator has not made any edits to this article; I would think some biochemistry background and access to scholarly sources, including/especially textbooks, would be required to undertake this sort of effort. Is the nominator prepared for this? Esculenta (talk) 19:22, 12 March 2021 (UTC)[reply]

@Esculenta and Firestar464: Thanks Esculenta for taking on this GA review and for your comments. I have attempted to provide a better summary of the whole article in the lead in these edits. There is still a lot more work to be done. If Firestar464 take the lead in addressing Esculenta concerns, I would be willing to help. Boghog (talk) 17:26, 14 March 2021 (UTC)[reply]

Well, thanks for the offer of help Boghog, but given there's been no response from the nominator for more than a week (despite the nominator being quite active on Wikipedia during that time), I don't think this review is going anywhere. Closing now. Esculenta (talk) 17:43, 20 March 2021 (UTC)[reply]

(minor) TYPO? in the "Classes and variants" section

As of the "07:47, 24 December 2022‎" version of this article -- (the latest version as of the date of this comment) -- there seems to be a TYPO in the caption of the picture in the "Classes_and_variants" section.

The caption there says:

Histone heterooctamer (H3,H4,H2A,H2B) + DNS fragment, Frog

but the acronym "DNS" there looks (to me) like a TYPO.
It probably should be [spelled] "DNA" ! ... (right?)

Please forgive me if I should have just changed it, instead of asking questions here, first.

By the way, I looked for a possible "mishap" ... by checking to see if that caption had ever contained the spelling "DNA" at some time in the past. Apparently not. I found that: when that caption was introduced -- (along with the picture) -- in a 2-step edit (3 minutes apart) on 24 October 2021 (03:42 and 03:45) ((See: http://en.wiki.x.io/w/index.php?title=Histone&diff=1051576048&oldid=1045209384 )) ... the spelling "DNS" was present right off the bat.

PS: While I was typing this, some well-intentioned robot (a spell checker of some kind? perhaps) "suggested" correcting the word "heterooctamer" (in that same caption) to "heterotetramer" instead. Now in that case, I rhink the original author of the caption was smarter than the robot. (right?)

I also did some checking to see whether the character string "DNS" could be found anywhere else in the latest version of this article. The fact that it could not ... "suggests" that the chance of the spelling "DNS" having been intentional (vs. accidental) is remote.

That "checking" was not 100% conclusive, but ... it was easy to do.
(Also; Note: "S" and "A" are close neighbors on a QWERTY keyboard.)

Any comments? Mike Schwartz (talk) 04:57, 22 January 2023 (UTC)[reply]

Up-to-date and easier-to-understand Histone names nomenclature

The names nomenclatures used in the table about classification of histone families and variants are not the most up-to-date versions. This table shows names for both replication-dependent and -independent histones in two different nomenclatures (Ej.: H1F0 independent, HIST1H1A dependent). This nomenclature is difficult to understand for non-expert people and it has been recently standardized by the HGNC and MGNC (in mice) in 2022.[1] In addition, the table does not show pseudogenes of histones.

I think the article would benefit from adding this information. If nobody disagrees I can update the table.

As a consequence, I also believe that the names of all histones variants articles should be renamed to the newest nomenclature, redirecting old names titles. Is this something better to discuss in Wikipedia talk:WikiProject Molecular Biology? Are there any similar cases of articles names changed because of nomenclature changes? Aarón Mayo (talk) 15:31, 24 September 2023 (UTC)[reply]