Editing Nucleosome (section)

===Structure of the core particle===
[[Image:Nucleosome 1KX5 colour coded.png|left|thumb|300px|The crystal structure of the nucleosome core particle consisting of <span style="color:#AAAA00;"> H2A </span>, <span style="color:red;"> H2B </span>, <span style="color:blue;"> H3 </span> and <span style="color:green;"> H4 </span> core histones, and DNA. The view is from the top through the superhelical axis.]]

====Overview====
Pioneering structural studies in the 1980s by Aaron Klug's group provided the first evidence that an octamer of histone proteins wraps DNA around itself in about 1.7 turns of a left-handed superhelix.<ref name="pmid6482966">{{cite journal | vauthors = Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A | title = Structure of the nucleosome core particle at 7 A resolution | journal = Nature | volume = 311 | issue = 5986 | pages = 532–7 | date = 1984 | pmid = 6482966 | doi = 10.1038/311532a0 | bibcode = 1984Natur.311..532R | s2cid = 4355982 }}</ref> In 1997 the first near atomic resolution [[crystal structure]] of the nucleosome was solved by the Richmond group at the [[ETH Zurich]], showing the most important details of the particle. The human [[Centromere#Sequence|alpha satellite]] [[Palindromic sequence|palindromic DNA]] critical to achieving the 1997 nucleosome crystal structure was developed by the Bunick group at Oak Ridge National Laboratory in Tennessee.<ref>{{cite journal | vauthors = Harp JM, Palmer EL, York MH, Gewiess A, Davis M, Bunick GJ | title = Preparative separation of nucleosome core particles containing defined-sequence DNA in multiple translational phases | journal = Electrophoresis | volume = 16 | issue = 10 | pages = 1861–1864 | date = October 1995 | pmid = 8586054 | doi = 10.1002/elps.11501601305 | s2cid = 20178479 }}</ref><ref name="pmid8678288">{{cite journal | vauthors = Palmer EL, Gewiess A, Harp JM, York MH, Bunick GJ | title = Large-scale production of palindrome DNA fragments | journal = Analytical Biochemistry | volume = 231 | issue = 1 | pages = 109–114 | date = October 1995 | pmid = 8678288 | doi = 10.1006/abio.1995.1509 }}</ref><ref name="pmid15299701">{{cite journal | vauthors = Harp JM, Uberbacher EC, Roberson AE, Palmer EL, Gewiess A, Bunick GJ | title = X-ray diffraction analysis of crystals containing twofold symmetric nucleosome core particles | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 52 | issue = Pt 2 | pages = 283–288 | date = March 1996 | pmid = 15299701 | doi = 10.1107/S0907444995009139 | doi-access = free | bibcode = 1996AcCrD..52..283H }}</ref><ref name="pmid11092917">{{cite journal | vauthors = Harp JM, Hanson BL, Timm DE, Bunick GJ | title = Asymmetries in the nucleosome core particle at 2.5 A resolution | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 56 | issue = Pt 12 | pages = 1513–1534 | date = December 2000 | pmid = 11092917 | doi = 10.1107/s0907444900011847 }}</ref><ref name="pmid14870658">{{cite book | vauthors = Hanson BL, Alexander C, Harp JM, Bunick GJ | title = Chromatin and Chromatin Remodeling Enzymes, Part A | chapter = Preparation and crystallization of nucleosome core particle | series = Methods in Enzymology | volume = 375 | pages = 44–62 | year = 2004 | pmid = 14870658 | doi = 10.1016/s0076-6879(03)75003-4 | isbn = 9780121827793 }}</ref> The structures of over 20 different nucleosome core particles have been solved to date,<ref name=pmid15680970>{{cite journal | vauthors = Chakravarthy S, Park YJ, Chodaparambil J, Edayathumangalam RS, Luger K | title = Structure and dynamic properties of nucleosome core particles | journal = FEBS Letters | volume = 579 | issue = 4 | pages = 895–898 | date = February 2005 | pmid = 15680970 | doi = 10.1016/j.febslet.2004.11.030 | s2cid = 41706403 | doi-access = free | bibcode = 2005FEBSL.579..895C }}</ref> including those containing histone variants and histones from different species. The structure of the nucleosome core particle is remarkably conserved, and even a change of over 100 residues between frog and yeast histones results in electron density maps with an overall [[root mean square deviation]] of only 1.6Å.<ref name="pmid11566884">{{cite journal | vauthors = White CL, Suto RK, Luger K | title = Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions | journal = The EMBO Journal | volume = 20 | issue = 18 | pages = 5207–5218 | date = September 2001 | pmid = 11566884 | pmc = 125637 | doi = 10.1093/emboj/20.18.5207 }}</ref>

====The nucleosome core particle (NCP)====
The nucleosome core particle (shown in the figure) consists of about 146 [[base pair]] of DNA<ref name="diffbp"/> wrapped in 1.67 left-handed [[Supercoil|superhelical turns]] around the [[histone octamer]], consisting of 2 copies each of the core histones [[Histone H2A|H2A]], [[Histone H2B|H2B]], [[Histone H3|H3]], and [[Histone H4|H4]]. Adjacent nucleosomes are joined by a stretch of free DNA termed [[linker DNA]] (which varies from 10 - 80 bp in length depending on species and tissue type<ref name="pmid12540921"/>).The whole structure generates a cylinder of diameter 11&nbsp;nm and a height of 5.5&nbsp;nm.

[[File:Apoptotic DNA Laddering.png|right|thumb|[[Apoptotic DNA fragmentation|Apoptotic DNA laddering]]. Digested chromatin is in the first lane; the second contains DNA standard to compare lengths.]]
[[File:Nucleosome organization.png|right|thumb|220px|Scheme of nucleosome organization<ref name="Stryer95" />]]
[[File:Nucleosome core particle 1EQZ v.2.gif|thumb|220px|The crystal structure of the nucleosome core particle ({{Pdb|1EQZ}}<ref name="Harp00">{{cite journal | vauthors = Harp JM, Hanson BL, Timm DE, Bunick GJ | title = Asymmetries in the nucleosome core particle at 2.5 A resolution | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 56 | issue = Pt 12 | pages = 1513–1534 | date = December 2000 | pmid = 11092917 | doi = 10.1107/S0907444900011847 | id = PDB ID: 1EQZ }}</ref>)]]

Nucleosome core particles are observed when chromatin in interphase is treated to cause the chromatin to unfold partially. The resulting image, via an electron microscope, is "beads on a string". The string is the DNA, while each bead in the nucleosome is a core particle. The nucleosome core particle is composed of DNA and histone proteins.<ref>{{cite book | vauthors = Alberts B | title = Essential Cell Biology | edition = 2nd | location = New York | publisher = Garland Science | date = 2009 }}</ref>

Partial [[DNAse]] digestion of [[chromatin]] reveals its nucleosome structure. Because DNA portions of nucleosome core particles are less accessible for DNAse than linking sections, DNA gets digested into fragments of lengths equal to multiplicity of distance between nucleosomes (180, 360, 540 base pairs etc.). Hence a very characteristic [[DNA laddering|pattern similar to a ladder]] is visible during [[gel electrophoresis]] of that DNA.<ref name=Stryer95>{{cite book | vauthors = Stryer L |year=1995 |title=Biochemistry |publisher=W. H. Freeman and Company |location=New York - Basingstoke |edition=fourth |isbn=978-0716720096 }}</ref> Such digestion can occur also under natural conditions during [[apoptosis]] ("cell suicide" or programmed cell death), because [[Apoptotic DNA fragmentation|autodestruction of DNA]] typically is its role.<ref>{{Cite journal |last1=Allen |first1=Paul D. |last2=Newland |first2=Adrian C. |date=1998-06-01 |title=Electrophoretic DNA analysis for the detection of apoptosis |url=https://doi.org/10.1007/BF02915798 |journal=Molecular Biotechnology |language=en |volume=9 |issue=3 |pages=247–251 |doi=10.1007/BF02915798 |pmid=9718585 |issn=1559-0305|url-access=subscription }}</ref>

=====Protein interactions within the nucleosome=====
The core histone proteins contains a characteristic structural motif termed the "histone fold", which consists of three alpha-helices (α1-3) separated by two loops (L1-2). In solution, the histones form H2A-H2B heterodimers and H3-H4 heterotetramers. Histones dimerise about their long α2 helices in an anti-parallel orientation, and, in the case of H3 and H4, two such dimers form a 4-helix bundle stabilised by extensive H3-H3' interaction. The H2A/H2B dimer binds onto the H3/H4 tetramer due to interactions between H4 and H2B, which include the formation of a hydrophobic cluster.<ref name="autogenerated1"/>
The histone octamer is formed by a central H3/H4 tetramer sandwiched between two H2A/H2B dimers. Due to the highly basic charge of all four core histones, the histone octamer is stable only in the presence of DNA or very high salt concentrations.

=====Histone - DNA interactions=====
The nucleosome contains over 120 direct protein-DNA interactions and several hundred water-mediated ones.<ref name="pmid12079350">{{cite journal | vauthors = Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ | title = Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution | journal = Journal of Molecular Biology | volume = 319 | issue = 5 | pages = 1097–1113 | date = June 2002 | pmid = 12079350 | doi = 10.1016/S0022-2836(02)00386-8 }}</ref> Direct protein - DNA interactions are not spread evenly about the octamer surface but rather located at discrete sites. These are due to the formation of two types of DNA binding sites within the octamer; the α1α1 site, which uses the α1 helix from two adjacent histones, and the L1L2 site formed by the L1 and L2 loops. Salt links and [[hydrogen bonding]] between both side-chain basic and hydroxyl groups and main-chain amides with the DNA backbone phosphates form the bulk of interactions with the DNA. This is important, given that the ubiquitous distribution of nucleosomes along genomes requires it to be a non-sequence-specific DNA-binding factor. Although nucleosomes tend to prefer some DNA sequences over others,<ref>{{cite journal | vauthors = Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, Wang JP, Widom J | display-authors = 6 | title = A genomic code for nucleosome positioning | journal = Nature | volume = 442 | issue = 7104 | pages = 772–778 | date = August 2006 | pmid = 16862119 | pmc = 2623244 | doi = 10.1038/nature04979 | bibcode = 2006Natur.442..772S }}</ref> they are capable of binding practically to any sequence, which is thought to be due to the flexibility in the formation of these water-mediated interactions. In addition, non-polar interactions are made between protein side-chains and the deoxyribose groups, and an arginine side-chain intercalates into the DNA minor groove at all 14 sites where it faces the octamer surface.
The distribution and strength of DNA-binding sites about the octamer surface distorts the DNA within the nucleosome core. The DNA is non-uniformly bent and also contains twist defects. The twist of free B-form DNA in solution is 10.5 bp per turn.  However, the overall twist of nucleosomal DNA is only 10.2 bp per turn, varying from a value of 9.4 to 10.9 bp per turn.

====Histone tail domains====
The histone tail extensions constitute up to 30% by mass of histones, but are not visible in the crystal structures of nucleosomes due to their high intrinsic flexibility, and have been thought to be largely unstructured.<ref name="pmid12666178">{{cite journal | vauthors = Zheng C, Hayes JJ | title = Structures and interactions of the core histone tail domains | journal = Biopolymers | volume = 68 | issue = 4 | pages = 539–546 | date = April 2003 | pmid = 12666178 | doi = 10.1002/bip.10303 }}</ref> The N-terminal tails of histones H3 and H2B pass through a channel formed by the minor grooves of the two DNA strands, protruding from the DNA every 20 bp. The [[N terminus|N-terminal]] tail of histone H4, on the other hand, has a region of highly basic amino acids (16–25), which, in the crystal structure, forms an interaction with the highly acidic surface region of a H2A-H2B dimer of another nucleosome, being potentially relevant for the higher-order structure of nucleosomes. This interaction is thought to occur under physiological conditions also, and suggests that [[acetylation]] of the H4 tail distorts the higher-order structure of chromatin.{{citation needed|date=February 2024}}