Talk:Nucleosome

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Merge Nucleosome core particle with this one?

I propose that we replace the small and redundant information found in the core particle page with a redirect to this page. Any comments? Would anybody oppose if I added a redirect from that page to this one? -RockyRaccoon 03:36, 3 April 2006 (UTC)[reply]

What's a "core nucleosome"? Please define!

"A chain of nucleosomes can be arranged in a 30-nm-fiber, a compacted structure (once thought to be a helical solenoid, but now considered likely to exist as a zig-zag structure in vivo)"

It seems to me that the idea that 30-nm-fiber is not a solenoid but a zig-zag could be very controversial. Study books, such as Genes VIII by Benjamin Lewin, depict the structure as a solenoid as late as 2003. What source is used to make a claim for zig-zag structure? --EnSamulili 16:22, 15 Mar 2005 (UTC)

---

This should serve as a reference. I'll do it myself when I have time, unless someone else beats me to it. -Jenks

"Rydberg B; Holley WR; Mian IS; Chatterjee A. Chromatin conformation in living cells: support for a zig-zag model of the 30 nm chromatin fibre. Journal of Molecular Biology, 1998 Nov 20, 284(1):71-84.

   A new method was used to probe the conformation of chromatin in living
   mammalian cells. The method employs ionizing radiation and is based on the
   concept that such radiation induces correlated breaks in DNA strands that are
   in spatial proximity. Human dermal fibroblasts in G0 phase of the cell cycle
   and Chinese hamster ovary cells in mitosis were irradiated by X-rays or
   accelerated ions. Following lysis of the cells, DNA fragments induced by
   correlated breaks were end-labeled and separated according to size on
   denaturing polyacrylamide gels. A characteristic peak was obtained for a
   fragment size of 78 bases, which is the size that corresponds to one turn of
   DNA around the nucleosome. Additional peaks between 175 and 450 bases reflect
   the relative position of nearest-neighbor nucleosomes. Theoretical
   calculations that simulate the indirect and direct effect of radiation on DNA
   demonstrate that the fragment size distributions are closely related to the
   chromatin structure model used. Comparison of the experimental data with
   theoretical results support a zig-zag model of the chromatin fiber rather
   than a simple helical model. Thus, radiation-induced damage analysis can
   provide information on chromatin structure in the living cell."

some links:

   http://nano.chem.emory.edu/~dlm/chromatin.html
   http://www.lbl.gov/lifesciences/NSCORT/pages/publications/abstracts1.html
   http://www.lorentz.leidenuniv.nl/~schiessel/two_angle.html   (good pictures)
   http://www.biophysj.org/cgi/content/full/82/6/2847
   http://www.mpip-mainz.mpg.de/~heli/langowski.pdf

---

1998 is pretty old for molecular biology. "Molecular Biology" By Weaver (2005), still explains in great detail (more than the other proposed structures) the 30nm fiber taking a solenoid shape. However, he does note that a zig-zag pattern, a superbead pattern, and no special pattern have also been proposed. Unless there is clear evidence (which I haven't seen in any so far) that the solenoid is now generally rejected, the article shouldn't imply it, or that the zig-zag pattern is likely to be it. The only thing that everyone can agree on is that the structure is disputed. --jag123 02:03, 28 Apr 2005 (UTC)

Illustration?

I created an illustration a while back when this was on the now-nonexistent Image Recreation Requests page, and just got around to finishing it up and uploading it. Is it irrelevant now, or should it be added? (Note: The new version is on the commons, I'm working on getting the old one deleted. For now, link)

--The Human Spellchecker 04:41, 3 February 2006 (UTC)[reply]

Thank you for your effort. I'm sorry to say, however, that nucleosome doesn't look quite like that (the old, deleted picture was also in error). -EnSamulili 20:15, 4 February 2006 (UTC)[reply]

I had based it off of the image that was removed because of copyright issues, one similar to this one. It's a simplified view, but it helps get a basic idea of what a nucleosome looks like. --The Human Spellchecker 21:53, 4 February 2006 (UTC)[reply]

I think something like this should be included to give a vague idea of what this thing looks like. I could modify it - i.e. duplicate it and make a chain, make the bubbles little twisty proteins, make it 1.6 revolutions, etc. --The Human Spellchecker 23:03, 17 February 2006 (UTC)[reply]

I agree there should be a cartoon schematic, instead of only crystal structures. Perhaps if there is a way to make it a cartoon model—but still accurate—this would be much better? The major issues I see are the scale and handedness of the DNA relative to the histones. It's important to be accessible to those of differing education levels, but not at the expense of accuracy. Currently, the geometry of the the image is demonstrably wrong, which isn't so great given its prominence in the Nucleosome and Histone articles. I think these should be corrected quickly, or it ought to be removed from the articles, unfortunately. --chodges 22:26, 3 August 2007 (UTC)[reply]

I appreciate your effort in creating the image, Spellcheck, but In my opinion, this figure is not suitable for use 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, giving the immediate impression that much more than 146 bases wrap around the histones.
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.

Can we correct these issues or remove this image from the Nucleosome article? --chodges 18:54, 25 July 2007 (UTC)[reply]

I just wanted to specify in the 2nd illustration of the nucleosome core particle cross section, also for the beginners in molecular biology that the helices in the core are the histones (proteins), with the DNA double helix around it, despite the fact that this is clear from the structure and orientation of the helices. But if this is thought to be superfluous. please revert to the old version. Thanks. Osterluzei (talk) 23:11, 21 March 2011 (UTC)[reply]

Recursive definition

A nucleosome is the fundamental repeating subunit of eukaryotic DNA, and is made up of DNA and...

How can a nucleosume be a subunit of something which it comprises? Do you mean eukaryotic chromatin? 129.7.56.177 05:42, 12 February 2006 (UTC)[reply]

Changed it. -EnSamulili 14:43, 12 February 2006 (UTC)[reply]

Possible image

User:TimVickers produced the following image which I nominated for deletion last week because it wasn't being used anywhere. User:Deryck Chan was nice enough to look through my nominations at my request and thought that this one was worth saving, and might be useful on this article. ~ Bigr Tex 17:10, 5 February 2007 (UTC)[reply]

No chromatin structure should be here

There is an extra page for chromatin. So speculations about the structure like sthe structure by Richmond should presented there, not here. We should delete the section Higher order structure.

Nucleosome a repeating chromatin unit, except in sperm

I removed this exception in the introduction. It is unsourced, and a cursory PubMed search proves that this statement isn't true, or at least not universally true (see: PMID 17303352). This might be an old vandalism that never got replaced? If anyone wants this statement to stay, then please cite a source. --chodges (talk) 22:52, 12 February 2008 (UTC)[reply]

Oops, I didn't read enough. Cited this statement in the article. --chodges (talk) 23:03, 12 February 2008 (UTC)[reply]

sin mutations

the current text is incorrect. Swi/Snf is not essential for yeast viability. It is however normally required for expression of a certain subset of genes which is subsequently overcome in the presence of particular point mutations within histones (sin mutations) Swi/Snf independence mutations Ging3rnut (talk) 23:05, 15 July 2008 (UTC)[reply]

New article

Hi everybody, I rewrote the whole article based on the papers cited - I felt that the original article was in really bad shape and needed a complete work over. I feel that now several points are made clearer and some of the less related stuff like chromatin and SIN has been reduced to what is necessary. What do you think? Greetings --hroest 00:21, 27 July 2008 (UTC)[reply]

layout

hello, i changed the layout, and rewrote several sections with references to the original data in the literature. I I feel that the whole article is still quite shallow and does not reflect the current scientific understanding. I've tried to add more detail, let me know if you think it is too much or not easily understandable. Ging3rnut (talk) 23:27, 17 August 2008 (UTC)[reply]

Hi, thanks a lot for the work you put into the article. I just recently rewrote the whole thing giving it some more structure but I obviously didnt have the background on the topic that you have. That's maybe why you still think that it is a little bit shallow although I feel that a lot of quite advanced stuff is covered. I was unsure about a couple of things: I originally thought that Arginines insert into the minor grooves at all 14 locations? I also thought that in the previous version there is more clarity about the Histones contacting the DNA at the minor groove with the a1a1 and L1L2 folds and how the superhelix bends around the octamer. Then I also thought that free B-DNA had a twist of 10.5 bp / turn and not 10.6 as you write and 10.5 is also the number that is mentioned in a paper by Richmond. It would also be interesting to know what kind of nucleosomes Widom et al used (e.g. euchromatin or heterochromat?) since I guess that makes a difference. I really like your part on remodeling although I feel that the SWI SNF complex could be mentioned at the ATP-dependent remodeling section, what do you think?

Great work, I really like it. What do you say to the points mentioned above? Greetings --hroest 14:01, 19 August 2008 (UTC)[reply]

thanks for the feedback. You're right about the twist of B-form DNA, it is 10.5 and not 10.6...sorry. The arginine-minor groove interaction 10/14 times is mentioned in the luger 1997 nature paper, so i'm pretty sure about that. I was perhaps a bit too abrupt in changing some of the text so it may very well be that the section on DNA binding is less clear now than it was, please feel free to change and improve it. I don't think there is any problem in mentioning Swi/Snf in the remodelling section, but given that there are 17 Swi/Snf homologues in budding yeast, many of which are very poorly understood, perhaps it could reflect some of this complexity.

As for the Widom data, that was performed on mono-nucleosomes assembled onto an artificial sequence "601" selected for its ability to form nucleosomes with high affinity. So in that sense it is neither eu- nor heterochromatic but I think he has a recent paper (which i haven't read) on this also occurring within nucleosomal arrays

Ging3rnut (talk) 21:32, 19 August 2008 (UTC)[reply]

I will look the arginine interactions up, but it seemed to me that there were arginines at all 14 interactions. I will post it here as soon as I get home. Greetings --hroest 12:59, 4 September 2008 (UTC)[reply]

I quote "The structure of DNA in the nucleosome core" by Richmond and Davey in Nature 423, May 2003. They say "Minor groove bending is facilitated [...] by the insertion of an arginine side chain into the minor groove at each of the 14 sites". Greetings --hroest 21:26, 22 September 2008 (UTC)[reply]

at promotors

Some time ago, the following section was added; then this correction was made, which corrects a mistake. It seems to me that the nucleosomes are not just missing in the promotor region but rather organized while some variants seem to be enriched there:

Nucleosomes are highly organized at the 5' end of genes and this organization spreads into the adjacent coding sequence. A short nucleosome-free region (NFR, which varies in size from gene to gene) typically lies upstream of nucleosome +1 (the first nucleosome upstream of the translation start site), and is the predominant site for transcription-factor-binding at promoters. Whitehouse et al

The arrangement of nucleosomes at pol II promoters is now established4, 5, 6, 9 as H2A.Z nucleosomes flanking a nucleosome-free promoter region. Albert et al

I think the way the article states it is too simplified regarding these studies, we probably should include one of the above statements from the paper, what do you think? Greetings --hroest 09:08, 25 February 2009 (UTC)[reply]

Yes, definitely mention H2A.Z nucleosomes - although I'm still not sure what they're doing there (if you delete them in yeast, there's no obvious phenotype, and they're not essential). H2A.Z is also found at other regions too, not just flanking promoters.

I'm probably just rambling here, but I'm not sure why people use the translation start site when making these comparisons - they should focus on the transcriptonal unit (i.e. - use the transcription start site if available). Maybe it should be stated that it's been shown in many examples that nucleosome depletion is critical for promoter function (expand on the heat shock studies that were mentioned) - like the PHO5 promoter (a lot of papers by Horz), and also in large-scale studies across the yeast genome - See Badis et al., 2008 PMID: 19111667. In this paper, they deplete sequence-specific factors that are responsible for maintaining/influencing the nucleosome free region in promoters (NFR), and not only do the promoters fill up with nucleosomes, there's an overall reduction in expression levels from those promoters (genome-wide).

This field is moving very quickly - a lot of the papers in this article are just from the past 2 years. --Ilikenucleosomes (talk) 20:37, 4 March 2009 (UTC)[reply]

Mistake in the nucleosome assembly illustration

Hi everybody, I guess there is a mistake concerning the DNA orientation in the nucleosome assembly illustration: according to histone labels and in correspondence to the crystal structure illustration, the DNA should be coming in and getting out the other way around. Best regards

Benjamin

Other nucleosome positioning signals

I hope nobody minds, I updated the page with info about replication origins being depleted for bulk nucleosomes (the Albert 2007 paper touched on this, as have a number of other genome-wide nucleosome papers) and precisely positioning nucleosomes (shown genome-wide in Eaton 2010). I thought some elements other than TSSs should get some love. Someone might also wanted to include insulators (I think human CTCF has been shown to have a strong nucleosome positioning effect?) Soaring brick (talk) 16:26, 17 August 2010 (UTC)[reply]