Talk:Nucleosome
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[edit] 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)
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)
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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
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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)
[edit] 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)
- 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)
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- 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)
- 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)
- 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)
- 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)
- 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)
- I appreciate your effort in creating the image, Spellcheck, but In my opinion, this figure is not suitable for use for the following reasons:
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- 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.
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- Can we correct these issues or remove this image from the Nucleosome article? --chodges 18:54, 25 July 2007 (UTC)
[edit] 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)
- Changed it. -EnSamulili 14:43, 12 February 2006 (UTC)
[edit] 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. ~ BigrTex 17:10, 5 February 2007 (UTC)
[edit] 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.
[edit] 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)
