Editing Nucleosome

{{Short description|Basic structural unit of DNA packaging in eukaryotes}}
[[File:Basic units of chromatin structure.svg|thumb|Basic units of [[chromatin]] structure]]

A '''nucleosome''' is the basic structural unit of [[DNA]] packaging in [[eukaryotes]]. The structure of a nucleosome consists of a segment of DNA wound around eight [[histone|histone proteins]]<ref name="Campbell">{{cite book | vauthors = Reece J, Campbell N | title = Biology | publisher = Benjamin Cummings | location = San Francisco | year = 2006 | isbn = 978-0-8053-6624-2 | url-access = registration | url = https://archive.org/details/biologyc00camp }}</ref> and resembles thread wrapped around a [[bobbin|spool]]. The nucleosome is the fundamental subunit of [[chromatin]]. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a [[histone octamer]]. Each histone octamer is composed of two copies each of the histone proteins [[Histone H2A|H2A]], [[Histone H2B|H2B]], [[Histone H3|H3]], and [[Histone H4|H4]].

DNA must be compacted into nucleosomes to fit within the [[cell nucleus]].<ref name="AlbertMBOCp207">{{cite book | vauthors = Alberts B |title=Molecular biology of the cell |chapter=Chromosomal DNA and Its Packaging in the Chromatin Fiber |publisher=Garland Science |location=New York |year=2002 |page=207 |isbn=978-0-8153-4072-0 |edition=4th |url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=Nucleosome&rid=mboc4.section.608#630}}</ref> In addition to nucleosome wrapping, eukaryotic [[chromatin]] is further compacted by being folded into a series of more complex structures, eventually forming a [[chromosome]]. Each human cell contains about 30 million nucleosomes.<ref name="howmany">{{cite book |title=Chromosomal DNA and Its Packaging in the Chromatin Fiber |year = 2002 |url= https://www.ncbi.nlm.nih.gov/books/NBK26834/#:~:text=On%20average%2C%20therefore%2C%20nucleosomes%20repeat,contains%20approximately%2030%20million%20nucleosomes | vauthors = lberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P  |publisher = Garland Science }}</ref>

Nucleosomes are thought to carry [[Epigenetics|epigenetically]] inherited information in the form of [[covalent modification]]s of their core [[histones]]. Nucleosome positions in the genome are not random, and it is important to know where each nucleosome is located because this determines the accessibility of the DNA to [[regulatory protein]]s.<ref>{{cite journal | vauthors = Teif VB, Clarkson CT | title = Nucleosome Positioning | journal = Encyclopedia of Bioinformatics and Computational Biology | volume = 2| pages = 308–317 | date = 2019 | doi = 10.1016/B978-0-12-809633-8.20242-2 | isbn = 9780128114322 | s2cid = 43929234 }}</ref>

Nucleosomes were first observed as particles in the electron microscope by Don and Ada Olins in 1974,<ref>{{cite journal | vauthors = Olins AL, Olins DE | title = Spheroid chromatin units (v bodies) | journal = Science | volume = 183 | issue = 4122 | pages = 330–332 | date = January 1974 | pmid = 4128918 | doi = 10.1126/science.183.4122.330 | s2cid = 83480762 | bibcode = 1974Sci...183..330O }}</ref> and their existence and structure (as histone octamers surrounded by approximately 200 base pairs of DNA) were proposed by [[Roger Kornberg]].<ref>{{cite journal | vauthors = McDonald D | title = Milestone 9, (1973-1974) The nucleosome hypothesis: An alternative string theory | journal = Nature Milestones: Gene Expression. | date = December 2005 | url = http://www.nature.com/milestones/geneexpression/milestones/articles/milegene09.html | doi=10.1038/nrm1798| url-access = subscription }}</ref><ref>{{cite journal | vauthors = Kornberg RD | title = Chromatin structure: a repeating unit of histones and DNA | journal = Science | volume = 184 | issue = 4139 | pages = 868–871 | date = May 1974 | pmid = 4825889 | doi = 10.1126/science.184.4139.868 | bibcode = 1974Sci...184..868K }}</ref> The role of the nucleosome as a regulator of transcription was demonstrated by Lorch et al. in vitro<ref>{{cite journal | vauthors = Lorch Y, LaPointe JW, Kornberg RD | title = Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones | journal = Cell | volume = 49 | issue = 2 | pages = 203–210 | date = April 1987 | pmid = 3568125 | doi = 10.1016/0092-8674(87)90561-7 | s2cid = 21270171 | doi-access = free }}</ref> in 1987 and by Han and Grunstein<ref>{{cite journal | vauthors = Han M, Grunstein M | title = Nucleosome loss activates yeast downstream promoters in vivo | journal = Cell | volume = 55 | issue = 6 | pages = 1137–1145 | date = December 1988 | pmid = 2849508 | doi = 10.1016/0092-8674(88)90258-9 | s2cid = 41520634 }}</ref> and Clark-Adams et al.<ref>{{cite journal | vauthors = Clark-Adams CD, Norris D, Osley MA, Fassler JS, Winston F | title = Changes in histone gene dosage alter transcription in yeast | journal = Genes & Development | volume = 2 | issue = 2 | pages = 150–159 | date = February 1988 | pmid = 2834270 | doi = 10.1101/gad.2.2.150 | doi-access = free }}</ref> in vivo in 1988.

The nucleosome core particle consists of approximately 146 [[base pair]]s (bp) of [[DNA]]<ref name="diffbp">In different crystals, values of 146 and 147 basepairs were observed</ref> wrapped in 1.67 left-handed [[Supercoil|superhelical turns]] around a [[histone]] octamer, consisting of 2 copies each of the core histones [[Histone H2A|H2A]], [[Histone H2B|H2B]], [[Histone H3|H3]], and [[Histone H4|H4]].<ref name="autogenerated1">{{cite journal | vauthors = Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ | title = Crystal structure of the nucleosome core particle at 2.8 A resolution | journal = Nature | volume = 389 | issue = 6648 | pages = 251–260 | date = September 1997 | pmid = 9305837 | doi = 10.1038/38444 | s2cid = 4328827 | bibcode = 1997Natur.389..251L }}</ref> Core particles are connected by stretches of [[linker DNA]], which can be up to about 80 bp long. Technically, a nucleosome is defined as the core particle plus one of these linker regions; however the word is often synonymous with the core particle.<ref name="Alberts5edp211">{{cite book | vauthors = Alberts B |title=Molecular Biology of the Cell |publisher=Garland Science |location=New York |year=2007 |page=211 |isbn=978-0-8153-4106-2 |edition=5th}}</ref> Genome-wide nucleosome positioning maps are now available for many model organisms and human cells.<ref>{{cite journal | vauthors = Shtumpf M, Piroeva KV, Agrawal SP, Jacob DR, Teif VB | title = NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA | journal = Chromosoma | volume = 131 | issue = 1–2 | pages = 19–28 | date = June 2022 | pmid = 35061087 | pmc = 8776978 | doi = 10.1007/s00412-021-00766-9 }}</ref>

Linker histones such as [[Histone H1|H1]] and its isoforms are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA.<ref>{{cite journal | vauthors = Zhou YB, Gerchman SE, Ramakrishnan V, Travers A, Muyldermans S | title = Position and orientation of the globular domain of linker histone H5 on the nucleosome | journal = Nature | volume = 395 | issue = 6700 | pages = 402–405 | date = September 1998 | pmid = 9759733 | doi = 10.1038/26521 | s2cid = 204997317 | bibcode = 1998Natur.395..402Z | doi-access = free }}</ref> Non-condensed nucleosomes without the linker histone resemble "beads on a string of DNA" under an [[electron microscope]].<ref>{{cite journal | vauthors = Thoma F, Koller T, Klug A | title = Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin | journal = The Journal of Cell Biology | volume = 83 | issue = 2 Pt 1 | pages = 403–427 | date = November 1979 | pmid = 387806 | pmc = 2111545 | doi = 10.1083/jcb.83.2.403 }}</ref>

In contrast to most eukaryotic cells, mature sperm cells largely use [[protamines]] to package their genomic DNA, most likely to achieve an even higher packaging ratio.<ref name="pmid1297351">{{cite journal | vauthors = Clarke HJ | title = Nuclear and chromatin composition of mammalian gametes and early embryos | journal = Biochemistry and Cell Biology | volume = 70 | issue = 10–11 | pages = 856–866 | year = 1992 | pmid = 1297351 | doi = 10.1139/o92-134 }}</ref> Histone equivalents and a simplified chromatin structure have also been found in [[Archaea]],<ref name="pmid12540921">{{cite journal | vauthors = Felsenfeld G, Groudine M | title = Controlling the double helix | journal = Nature | volume = 421 | issue = 6921 | pages = 448–453 | date = January 2003 | pmid = 12540921 | doi = 10.1038/nature01411 | doi-access = free | bibcode = 2003Natur.421..448F }}</ref> suggesting that eukaryotes are not the only organisms that use nucleosomes.

== Structure ==
===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}}

===Higher order structure===
[[Image:Chromatin Structures.png|right|thumb|600px|The current chromatin compaction model]]
The organization of the DNA that is achieved by the nucleosome cannot fully explain the packaging of DNA observed in the cell nucleus. Further compaction of [[chromatin]] into the cell nucleus is necessary, but it is not yet well understood.  The current understanding<ref name=pmid15680970/> is that repeating nucleosomes with intervening "linker" DNA form a ''10-nm-fiber'', described as "beads on a string", and have a packing ratio of about five to ten.<ref name="pmid12540921"/> A chain of nucleosomes can be arranged in a ''30&nbsp;nm fiber'', a compacted structure with a packing ratio of ~50<ref name="pmid12540921"/> and whose formation is dependent on the presence of the [[Histone H1|H1 histone]].

A crystal structure of a tetranucleosome has been presented and used to build up a proposed structure of the 30&nbsp;nm fiber as a two-start helix.<ref>{{cite journal | vauthors = Schalch T, Duda S, Sargent DF, Richmond TJ | title = X-ray structure of a tetranucleosome and its implications for the chromatin fibre | journal = Nature | volume = 436 | issue = 7047 | pages = 138–141 | date = July 2005 | pmid = 16001076 | doi = 10.1038/nature03686 | s2cid = 4387396 | bibcode = 2005Natur.436..138S }}</ref>
There is still a certain amount of contention regarding this model, as it is incompatible with recent [[electron microscopy]] data.<ref name="pmid16617109">{{cite journal | vauthors = Robinson PJ, Fairall L, Huynh VA, Rhodes D | title = EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 17 | pages = 6506–6511 | date = April 2006 | pmid = 16617109 | pmc = 1436021 | doi = 10.1073/pnas.0601212103 | doi-access = free | bibcode = 2006PNAS..103.6506R }}</ref>  Beyond this, the structure of chromatin is poorly understood, but it is classically suggested that the 30&nbsp;nm fiber is arranged into loops along a central protein scaffold to form transcriptionally active [[euchromatin]]. Further compaction leads to transcriptionally inactive [[heterochromatin]].

==Dynamics==
Although the nucleosome is a very stable protein-DNA complex, it is not static and has been shown to undergo a number of different structural re-arrangements including nucleosome sliding and DNA site exposure. Depending on the context, nucleosomes can inhibit or facilitate transcription factor binding. Nucleosome positions are controlled by three major contributions: First, the intrinsic binding affinity of the histone octamer depends on the DNA sequence. Second, the nucleosome can be displaced or recruited by the competitive or [[cooperative binding]] of other protein factors. Third, the nucleosome may be actively translocated by ATP-dependent remodeling complexes.<ref>{{cite journal | vauthors = Teif VB, Rippe K | title = Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities | journal = Nucleic Acids Research | volume = 37 | issue = 17 | pages = 5641–5655 | date = September 2009 | pmid = 19625488 | pmc = 2761276 | doi = 10.1093/nar/gkp610 }}</ref>

===Nucleosome sliding===
When incubated thermally, nucleosomes reconstituted onto the 5S DNA positioning sequence were able to reposition themselves translationally onto adjacent sequences.<ref name="pmid2738923">{{cite journal | vauthors = Pennings S, Muyldermans S, Meersseman G, Wyns L | title = Formation, stability and core histone positioning of nucleosomes reassembled on bent and other nucleosome-derived DNA | journal = Journal of Molecular Biology | volume = 207 | issue = 1 | pages = 183–192 | date = May 1989 | pmid = 2738923 | doi = 10.1016/0022-2836(89)90449-X }}</ref> This repositioning does not require disruption of the histone octamer but is consistent with nucleosomes being able to "slide" along the DNA ''in cis''. [[CTCF]] binding sites act as nucleosome positioning anchors so that, when used to align various genomic signals, multiple flanking nucleosomes can be readily identified.<ref name="pmid18654629">{{cite journal | vauthors = Fu Y, Sinha M, Peterson CL, Weng Z | title = The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome | journal = PLOS Genetics | volume = 4 | issue = 7 | pages = e1000138 | date = July 2008 | pmid = 18654629 | pmc = 2453330 | doi = 10.1371/journal.pgen.1000138 | veditors = Van Steensel B | doi-access = free }}</ref> Although nucleosomes are intrinsically mobile, eukaryotes have evolved a large family of ATP-dependent chromatin remodelling enzymes to alter chromatin structure, many of which do so via nucleosome sliding. Nucleosome sliding is one of the possible mechanism for large scale tissue specific expression of genes. The transcription start site for genes expressed in a particular tissue, are nucleosome depleted while, the same set of genes in other tissue where they are not expressed, are nucleosome bound.<ref name="pmid22821566">{{cite journal |display-authors=6 |vauthors=Bargaje R, Alam MP, Patowary A, Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S, Brahmachari V, Pillai B |date=October 2012 |title=Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain |journal=Nucleic Acids Research |volume=40 |issue=18 |pages=8965–8978 |doi=10.1093/nar/gks665 |pmc=3467062 |pmid=22821566}}</ref>

===DNA site exposure===
Nucleosomal DNA is in equilibrium between a wrapped and unwrapped state. DNA within the nucleosome remains fully wrapped for only 250 ms before it is unwrapped for 10-50 ms and then rapidly rewrapped, as measured using time-resolved [[Förster resonance energy transfer|FRET]].<ref name="pmid15580276">{{cite journal | vauthors = Li G, Levitus M, Bustamante C, Widom J | title = Rapid spontaneous accessibility of nucleosomal DNA | journal = Nature Structural & Molecular Biology | volume = 12 | issue = 1 | pages = 46–53 | date = January 2005 | pmid = 15580276 | doi = 10.1038/nsmb869 | s2cid = 14540078 }}</ref> This implies that DNA does not need to be actively dissociated from the nucleosome but that there is a significant fraction of time during which it is fully accessible. Introducing a DNA-binding sequence within the nucleosome increases the accessibility of adjacent regions of DNA when bound.<ref name="pmid15258568">{{cite journal | vauthors = Li G, Widom J | title = Nucleosomes facilitate their own invasion | journal = Nature Structural & Molecular Biology | volume = 11 | issue = 8 | pages = 763–769 | date = August 2004 | pmid = 15258568 | doi = 10.1038/nsmb801 | s2cid = 11299024 }}</ref> 

This propensity for DNA within the nucleosome to "breathe" has important functional consequences for all DNA-binding proteins that operate in a chromatin environment.<ref name="pmid15580276"/> In particular, the dynamic breathing of nucleosomes plays an important role in restricting the advancement of [[RNA polymerase II]] during transcription elongation.<ref>{{cite journal | vauthors = Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C | title = Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II | journal = Science | volume = 325 | issue = 5940 | pages = 626–628 | date = July 2009 | pmid = 19644123 | pmc = 2775800 | doi = 10.1126/science.1172926 | bibcode = 2009Sci...325..626H }}</ref>

=== Nucleosome free region ===
Promoters of active genes have nucleosome free regions (NFR). This allows for promoter DNA accessibility to various proteins, such as transcription factors. Nucleosome free region typically spans for 200 nucleotides in ''S. cerevisiae''<ref>{{cite journal | vauthors = Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ | title = Genome-scale identification of nucleosome positions in S. cerevisiae | journal = Science | volume = 309 | issue = 5734 | pages = 626–630 | date = July 2005 | pmid = 15961632 | doi = 10.1126/science.1112178 | s2cid = 43625066 | bibcode = 2005Sci...309..626Y | doi-access = free }}</ref> Well-positioned nucleosomes form boundaries of NFR. These nucleosomes are called +1-nucleosome and −1-nucleosome and are located at canonical distances downstream and upstream, respectively, from transcription start site.<ref name="Understanding nucleosome dynamics">{{cite journal | vauthors = Lai WK, Pugh BF | title = Understanding nucleosome dynamics and their links to gene expression and DNA replication | journal = Nature Reviews. Molecular Cell Biology | volume = 18 | issue = 9 | pages = 548–562 | date = September 2017 | pmid = 28537572 | pmc = 5831138 | doi = 10.1038/nrm.2017.47 }}</ref> +1-nucleosome and several downstream nucleosomes also tend to incorporate H2A.Z histone variant.<ref name="Understanding nucleosome dynamics"/>

==Modulating nucleosome structure==
Eukaryotic genomes are ubiquitously associated into chromatin; however, cells must spatially and temporally regulate specific loci independently of bulk chromatin. In order to achieve the high level of control required to co-ordinate nuclear processes such as DNA replication, repair, and transcription, cells have developed a variety of means to locally and specifically modulate chromatin structure and function. This can involve covalent modification of histones, the incorporation of histone variants, and non-covalent remodelling by ATP-dependent remodeling enzymes.

===Histone post-translational modifications===
[[File:Histone tails and their function in chromatin formation.svg|thumb|Histone tails and their function in chromatin formation]]

Since they were discovered in the mid-1960s, histone modifications have been predicted to affect transcription.<ref name="pmid14172992">{{cite journal | vauthors = Allfrey VG, Faulkner R, Mirsky AE | title = Acetylation and Methylation of Histones and Their Possible Role in the Regulation of RNA Synthesis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 51 | issue = 5 | pages = 786–794 | date = May 1964 | pmid = 14172992 | pmc = 300163 | doi = 10.1073/pnas.51.5.786 | doi-access = free | bibcode = 1964PNAS...51..786A }}</ref> The fact that most of the early post-translational modifications found were concentrated within the tail extensions that protrude from the nucleosome core lead to two main theories regarding the mechanism of histone modification. The first of the theories suggested that they may affect electrostatic interactions between the histone tails and DNA to "loosen" chromatin structure. Later it was proposed that combinations of these modifications may create binding epitopes with which to recruit other proteins.<ref name="pmid10638745">{{cite journal | vauthors = Strahl BD, Allis CD | title = The language of covalent histone modifications | journal = Nature | volume = 403 | issue = 6765 | pages = 41–45 | date = January 2000 | pmid = 10638745 | doi = 10.1038/47412 | s2cid = 4418993 | bibcode = 2000Natur.403...41S }}</ref> Recently, given that more modifications have been found in the structured regions of histones, it has been put forward that these modifications may affect histone-DNA<ref name="pmid15523479">{{cite journal | vauthors = Cosgrove MS, Boeke JD, Wolberger C | title = Regulated nucleosome mobility and the histone code | journal = Nature Structural & Molecular Biology | volume = 11 | issue = 11 | pages = 1037–1043 | date = November 2004 | pmid = 15523479 | doi = 10.1038/nsmb851 | s2cid = 34704745 }}</ref> and histone-histone<ref name="pmid15808514">{{cite journal | vauthors = Ye J, Ai X, Eugeni EE, Zhang L, Carpenter LR, Jelinek MA, Freitas MA, Parthun MR | display-authors = 6 | title = Histone H4 lysine 91 acetylation a core domain modification associated with chromatin assembly | journal = Molecular Cell | volume = 18 | issue = 1 | pages = 123–130 | date = April 2005 | pmid = 15808514 | pmc = 2855496 | doi = 10.1016/j.molcel.2005.02.031 }}</ref> interactions within the nucleosome core. Modifications (such as acetylation or phosphorylation) that lower the charge of the globular histone core are predicted to "loosen" core-DNA association; the strength of the effect depends on location of the modification within the core.<ref name="pmid20816070">{{cite journal | vauthors = Fenley AT, Adams DA, Onufriev AV | title = Charge state of the globular histone core controls stability of the nucleosome | journal = Biophysical Journal | volume = 99 | issue = 5 | pages = 1577–1585 | date = September 2010 | pmid = 20816070 | pmc = 2931741 | doi = 10.1016/j.bpj.2010.06.046 | bibcode = 2010BpJ....99.1577F }}</ref>
Some modifications have been shown to be correlated with gene silencing; others seem to be correlated with gene activation. Common modifications include [[acetylation]], [[methylation]], or [[ubiquitination]] of [[lysine]]; [[methylation]] of [[arginine]]; and [[phosphorylation]] of [[serine]]. The information stored in this way is considered [[epigenetic]], since it is not encoded in the DNA but is still inherited to daughter cells. The maintenance of a repressed or activated status of a gene is often necessary for [[cellular differentiation]].<ref name="pmid12540921"/>

===Histone variants===
Although histones are remarkably conserved throughout evolution, several variant forms have been identified. This diversification of histone function is restricted to H2A and H3, with H2B and H4 being mostly invariant. H2A can be replaced by [[H2AZ]] (which leads to reduced nucleosome stability) or [[H2AX]] (which is associated with DNA repair and [[T cell]] differentiation), whereas the [[X-inactivation|inactive X chromosomes]] in mammals are enriched in macroH2A. H3 can be replaced by H3.3 (which correlates with activate genes and regulatory elements) and in [[centromere]]s H3 is replaced by [[CENPA]].<ref name="pmid12540921"/>

===ATP-dependent nucleosome remodeling===
A number of distinct reactions are associated with the term [[ATP-dependent chromatin remodeling]]. Remodeling enzymes have been shown to slide nucleosomes along DNA,<ref name="pmid10466730">{{cite journal | vauthors = Whitehouse I, Flaus A, Cairns BR, White MF, Workman JL, Owen-Hughes T | title = Nucleosome mobilization catalysed by the yeast SWI/SNF complex | journal = Nature | volume = 400 | issue = 6746 | pages = 784–787 | date = August 1999 | pmid = 10466730 | doi = 10.1038/23506 | s2cid = 2841873 | bibcode = 1999Natur.400..784W }}</ref> disrupt histone-DNA contacts to the extent of destabilizing the H2A/H2B dimer<ref name="pmid12620227">{{cite journal | vauthors = Kassabov SR, Zhang B, Persinger J, Bartholomew B | title = SWI/SNF unwraps, slides, and rewraps the nucleosome | journal = Molecular Cell | volume = 11 | issue = 2 | pages = 391–403 | date = February 2003 | pmid = 12620227 | doi = 10.1016/S1097-2765(03)00039-X | doi-access = free }}</ref><ref name="pmid14690611">{{cite journal | vauthors = Bruno M, Flaus A, Stockdale C, Rencurel C, Ferreira H, Owen-Hughes T | title = Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities | journal = Molecular Cell | volume = 12 | issue = 6 | pages = 1599–1606 | date = December 2003 | pmid = 14690611 | pmc = 3428624 | doi = 10.1016/S1097-2765(03)00499-4 }}</ref> and to generate negative superhelical torsion in DNA and chromatin.<ref name="pmid11163188">{{cite journal | vauthors = Havas K, Flaus A, Phelan M, Kingston R, Wade PA, Lilley DM, Owen-Hughes T | title = Generation of superhelical torsion by ATP-dependent chromatin remodeling activities | journal = Cell | volume = 103 | issue = 7 | pages = 1133–1142 | date = December 2000 | pmid = 11163188 | doi = 10.1016/S0092-8674(00)00215-4 | s2cid = 7911590 | doi-access = free }}</ref> Recently, the Swr1 remodeling enzyme has been shown to introduce the variant histone H2A.Z into nucleosomes.<ref name="pmid14645854">{{cite journal | vauthors = Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C | title = ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex | journal = Science | volume = 303 | issue = 5656 | pages = 343–348 | date = January 2004 | pmid = 14645854 | doi = 10.1126/science.1090701 | s2cid = 9881829 | bibcode = 2004Sci...303..343M | url = https://zenodo.org/record/1230842 | doi-access = free }}</ref> At present, it is not clear if all of these represent distinct reactions or merely alternative outcomes of a common mechanism. What is shared between all, and indeed the hallmark of ATP-dependent chromatin remodeling, is that they all result in altered DNA accessibility.

Studies looking at gene activation ''in vivo''<ref name="pmid14675539">{{cite journal | vauthors = Métivier R, Penot G, Hübner MR, Reid G, Brand H, Kos M, Gannon F | title = Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter | journal = Cell | volume = 115 | issue = 6 | pages = 751–763 | date = December 2003 | pmid = 14675539 | doi = 10.1016/S0092-8674(03)00934-6 | s2cid = 145525 | doi-access = free }}</ref> and, more astonishingly, remodeling ''in vitro''<ref name="pmid15099516">{{cite journal | vauthors = Nagaich AK, Walker DA, Wolford R, Hager GL | title = Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling | journal = Molecular Cell | volume = 14 | issue = 2 | pages = 163–174 | date = April 2004 | pmid = 15099516 | doi = 10.1016/S1097-2765(04)00178-9 | doi-access = free }}</ref> have revealed that chromatin remodeling events and transcription-factor binding are cyclical and periodic in nature. While the consequences of this for the reaction mechanism of chromatin remodeling are not known, the dynamic nature of the system may allow it to respond faster to external stimuli. A recent study indicates that nucleosome positions change significantly during mouse embryonic stem cell development, and these changes are related to binding of developmental transcription factors.<ref>{{cite journal | vauthors = Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T, Rippe K | title = Genome-wide nucleosome positioning during embryonic stem cell development | journal = Nature Structural & Molecular Biology | volume = 19 | issue = 11 | pages = 1185–1192 | date = November 2012 | pmid = 23085715 | doi = 10.1038/nsmb.2419 | s2cid = 34509771 }}</ref>

===Dynamic nucleosome remodelling across the Yeast genome===
Studies in 2007 have catalogued nucleosome positions in yeast and shown that nucleosomes are depleted in [[Promoter (biology)|promoter]] regions and [[Origin of replication|origins of replication]].<ref name="pmid17392789">{{cite journal | vauthors = Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF | title = Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome | journal = Nature | volume = 446 | issue = 7135 | pages = 572–576 | date = March 2007 | pmid = 17392789 | doi = 10.1038/nature05632 | s2cid = 4416890 | bibcode = 2007Natur.446..572A }}</ref><ref name="pmid17320508">{{cite journal | vauthors = Li B, Carey M, Workman JL | title = The role of chromatin during transcription | journal = Cell | volume = 128 | issue = 4 | pages = 707–719 | date = February 2007 | pmid = 17320508 | doi = 10.1016/j.cell.2007.01.015 | s2cid = 1773333 | doi-access = free }}</ref><ref name="pmid18075583">{{cite journal | vauthors = Whitehouse I, Rando OJ, Delrow J, Tsukiyama T | title = Chromatin remodelling at promoters suppresses antisense transcription | journal = Nature | volume = 450 | issue = 7172 | pages = 1031–1035 | date = December 2007 | pmid = 18075583 | doi = 10.1038/nature06391 | s2cid = 4305576 | bibcode = 2007Natur.450.1031W }}</ref>
About 80% of the yeast genome appears to be covered by nucleosomes<ref name="pmid17873876">{{cite journal | vauthors = Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C | title = A high-resolution atlas of nucleosome occupancy in yeast | journal = Nature Genetics | volume = 39 | issue = 10 | pages = 1235–1244 | date = October 2007 | pmid = 17873876 | doi = 10.1038/ng2117 | s2cid = 12816925 }}</ref> and the pattern of nucleosome positioning clearly relates to DNA regions that regulate [[Transcription (genetics)|transcription]], regions that are transcribed and regions that initiate DNA replication.<ref name="pmid20351051">{{cite journal | vauthors = Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM | title = Conserved nucleosome positioning defines replication origins | journal = Genes & Development | volume = 24 | issue = 8 | pages = 748–753 | date = April 2010 | pmid = 20351051 | pmc = 2854390 | doi = 10.1101/gad.1913210 }}</ref> Most recently, a new study examined ''dynamic changes'' in nucleosome repositioning during a global transcriptional reprogramming event to elucidate the effects on nucleosome displacement during genome-wide transcriptional changes in yeast (''[[Saccharomyces cerevisiae]]'').<ref name="pmid18351804">{{cite journal | vauthors = Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR | title = Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation | journal = PLOS Biology | volume = 6 | issue = 3 | pages = e65 | date = March 2008 | pmid = 18351804 | pmc = 2267817 | doi = 10.1371/journal.pbio.0060065 | doi-access = free }}</ref> The results suggested that nucleosomes that were localized to promoter regions are displaced in response to stress (like [[heat shock]]). In addition, the removal of nucleosomes usually corresponded to transcriptional activation and the replacement of nucleosomes usually corresponded to transcriptional repression, presumably because [[transcription factor]] binding sites became more or less accessible, respectively. In general, only one or two nucleosomes were repositioned at the promoter to effect these transcriptional changes. However, even in chromosomal regions that were not associated with transcriptional changes, nucleosome repositioning was observed, suggesting that the covering and uncovering of transcriptional DNA does not necessarily produce a transcriptional event. After transcription, the rDNA region has to protected from any damage, it suggested HMGB proteins play a major role in protecting the nucleosome free region.<ref>{{cite journal | vauthors = Murugesapillai D, McCauley MJ, Huo R, Nelson Holte MH, Stepanyants A, Maher LJ, Israeloff NE, Williams MC | display-authors = 6 | title = DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin | journal = Nucleic Acids Research | volume = 42 | issue = 14 | pages = 8996–9004 | date = August 2014 | pmid = 25063301 | pmc = 4132745 | doi = 10.1093/nar/gku635 }}</ref><ref>{{cite journal | vauthors = Murugesapillai D, McCauley MJ, Maher LJ, Williams MC | title = Single-molecule studies of high-mobility group B architectural DNA bending proteins | journal = Biophysical Reviews | volume = 9 | issue = 1 | pages = 17–40 | date = February 2017 | pmid = 28303166 | pmc = 5331113 | doi = 10.1007/s12551-016-0236-4 }}</ref>

=== DNA Twist Defects ===
DNA twist defects are when the addition of one or a few base pairs from one DNA segment are transferred to the next segment resulting in a change of the DNA twist. This will not only change the twist of the DNA but it will also change the length.<ref>{{cite journal | vauthors = Winger J, Nodelman IM, Levendosky RF, Bowman GD | title = A twist defect mechanism for ATP-dependent translocation of nucleosomal DNA | journal = eLife | volume = 7 | pages = e34100 | date = May 2018 | pmid = 29809147 | pmc = 6031429 | doi = 10.7554/eLife.34100 | doi-access = free }}</ref> This twist defect eventually moves around the nucleosome through the transferring of the base pair, this means DNA twists can cause nucleosome sliding.<ref>{{cite journal | vauthors = Bowman GD | title = Uncovering a New Step in Sliding Nucleosomes | journal = Trends in Biochemical Sciences | volume = 44 | issue = 8 | pages = 643–645 | date = August 2019 | pmid = 31171402 | pmc = 7092708 | doi = 10.1016/j.tibs.2019.05.001 }}</ref> Nucleosome crystal structures have shown that superhelix location 2 and 5 on the nucleosome are commonly found to be where DNA twist defects occur as these are common remodeler binding sites.<ref name=":0">{{cite journal | vauthors = Nodelman IM, Bowman GD | title = Biophysics of Chromatin Remodeling | journal = Annual Review of Biophysics | volume = 50 | issue = 1 | pages = 73–93 | date = May 2021 | pmid = 33395550 | pmc = 8428145 | doi = 10.1146/annurev-biophys-082520-080201 }}</ref> There are a variety of chromatin remodelers but all share the existence of an ATPase motor which facilitates chromatin sliding on DNA through the binding and hydrolysis of ATP.<ref name=":1">{{cite journal | vauthors = Brandani GB, Takada S | title = Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA | journal = PLOS Computational Biology | volume = 14 | issue = 11 | pages = e1006512 | date = November 2018 | pmid = 30395604 | pmc = 6237416 | doi = 10.1371/journal.pcbi.1006512 | bibcode = 2018PLSCB..14E6512B | veditors = Onufriev A | doi-access = free }}</ref> ATPase has an open and closed state. When the ATPase motor is changing from open and closed states, the DNA duplex changes geometry and exhibits base pair tilting.<ref name=":0" /> The initiation of the twist defects via the ATPase motor causes tension to accumulate around the remodeler site. The tension is released when the sliding of DNA has been completed throughout the nucleosome via the spread of two twist defects (one on each strand) in opposite directions.<ref name=":1" />

==Nucleosome assembly ''in vitro''==
[[Image:Nucleosome structure.png|right|thumb|Diagram of nucleosome assembly]]
Nucleosomes can be assembled ''[[in vitro]]'' by either using purified native or recombinant histones.<ref>{{cite journal | vauthors = Hayes JJ, Lee KM | title = In vitro reconstitution and analysis of mononucleosomes containing defined DNAs and proteins | journal = Methods | volume = 12 | issue = 1 | pages = 2–9 | date = May 1997 | pmid = 9169189 | doi = 10.1006/meth.1997.0441 | doi-access = free }}</ref><ref>{{cite book | vauthors = Dyer PN, Edayathumangalam RS, White CL, Bao Y, Chakravarthy S, Muthurajan UM, Luger K | title = Chromatin and Chromatin Remodeling Enzymes, Part A | chapter = Reconstitution of nucleosome core particles from recombinant histones and DNA | series = Methods in Enzymology | volume = 375 | pages = 23–44 | year = 2004 | pmid = 14870657 | doi = 10.1016/s0076-6879(03)75002-2 | isbn = 9780121827793 }}</ref> One standard technique of loading the DNA around the histones involves the use of salt [[Kidney dialysis|dialysis]]. A reaction consisting of the histone octamers and a naked DNA template can be incubated together at a salt concentration of 2 M. By steadily decreasing the salt concentration, the DNA will equilibrate to a position where it is wrapped around the histone octamers, forming nucleosomes.  In appropriate conditions, this reconstitution process allows for the nucleosome positioning affinity of a given sequence to be mapped experimentally.<ref>{{cite journal | vauthors = Yenidunya A, Davey C, Clark D, Felsenfeld G, Allan J | title = Nucleosome positioning on chicken and human globin gene promoters in vitro. Novel mapping techniques | journal = Journal of Molecular Biology | volume = 237 | issue = 4 | pages = 401–414 | date = April 1994 | pmid = 8151701 | doi = 10.1006/jmbi.1994.1243 }}</ref>

=== Disulfide crosslinked nucleosome core particles ===
A recent advance in the production of nucleosome core particles with enhanced stability involves site-specific [[disulfide]] crosslinks.<ref>{{cite journal | vauthors = Frouws TD, Barth PD, Richmond TJ | title = Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability | journal = Journal of Molecular Biology | volume = 430 | issue = 1 | pages = 45–57 | date = January 2018 | pmid = 29113904 | pmc = 5757783 | doi = 10.1016/j.jmb.2017.10.029 }}</ref> Two different crosslinks can be introduced into the nucleosome core particle. A first one crosslinks the two copies of [[Histone H2A|H2A]] via an introduced cysteine (N38C) resulting in [[histone octamer]] which is stable against H2A/H2B dimer loss during nucleosome reconstitution. A second crosslink can be introduced between the H3 N-terminal histone tail and the nucleosome DNA ends via an incorporated convertible nucleotide.<ref>{{cite book | vauthors = Ferentz AE, Verdine GL |chapter=The Convertible Nucleoside Approach: Structural Engineering of Nucleic Acids by Disulfide Cross-Linking |pages=14–40 |doi=10.1007/978-3-642-78666-2_2 | veditors = Eckstein F, Lilley DM |title=Nucleic Acids and Molecular Biology |volume=8 |year=1994 |isbn=978-3-642-78668-6 }}</ref> The DNA-histone octamer crosslink stabilizes the nucleosome core particle against DNA dissociation at very low particle concentrations and at elevated salt concentrations.

== Nucleosome assembly '' in vivo '' ==
[[File:Steps in nucleosome assembly.svg|thumb|Steps in nucleosome assembly]]

Nucleosomes are the basic packing unit of genomic DNA built from histone proteins around which DNA is coiled. They serve as a scaffold for formation of higher order chromatin structure as well as for a layer of regulatory control of gene expression. Nucleosomes are quickly assembled onto newly synthesized DNA behind the replication fork.

=== H3 and H4 ===
Histones [[Histone H3|H3]] and [[Histone H4|H4]] from disassembled old nucleosomes are kept in the vicinity and randomly distributed on the newly synthesized DNA.<ref>{{cite journal | vauthors = Yamasu K, Senshu T | title = Conservative segregation of tetrameric units of H3 and H4 histones during nucleosome replication | journal = Journal of Biochemistry | volume = 107 | issue = 1 | pages = 15–20 | date = January 1990 | pmid = 2332416 | doi = 10.1093/oxfordjournals.jbchem.a122999 }}</ref> They are assembled by the [[chromatin assembly factor 1]] (CAF-1) complex, which consists of three subunits (p150, p60, and p48).<ref>{{cite journal | vauthors = Kaufman PD, Kobayashi R, Kessler N, Stillman B | title = The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication | journal = Cell | volume = 81 | issue = 7 | pages = 1105–1114 | date = June 1995 | pmid = 7600578 | doi = 10.1016/S0092-8674(05)80015-7 | s2cid = 13502921 | doi-access = free }}</ref> Newly synthesized H3 and H4 are assembled by the replication coupling assembly factor (RCAF). RCAF contains the subunit Asf1, which binds to newly synthesized H3 and H4 proteins.<ref>{{cite journal | vauthors = Tyler JK, Adams CR, Chen SR, Kobayashi R, Kamakaka RT, Kadonaga JT | title = The RCAF complex mediates chromatin assembly during DNA replication and repair | journal = Nature | volume = 402 | issue = 6761 | pages = 555–560 | date = December 1999 | pmid = 10591219 | doi = 10.1038/990147 | s2cid = 205097512 | bibcode = 1999Natur.402..555T }}</ref>  The old H3 and H4 proteins retain their chemical modifications which contributes to the passing down of the epigenetic signature. The newly synthesized H3 and H4 proteins are gradually acetylated at different lysine residues as part of the chromatin maturation process.<ref>{{cite journal | vauthors = Benson LJ, Gu Y, Yakovleva T, Tong K, Barrows C, Strack CL, Cook RG, Mizzen CA, Annunziato AT | display-authors = 6 | title = Modifications of H3 and H4 during chromatin replication, nucleosome assembly, and histone exchange | journal = The Journal of Biological Chemistry | volume = 281 | issue = 14 | pages = 9287–9296 | date = April 2006 | pmid = 16464854 | doi = 10.1074/jbc.M512956200 | doi-access = free }}</ref> It is also thought that the old H3 and H4 proteins in the new nucleosomes recruit histone modifying enzymes that mark the new histones, contributing to epigenetic memory.

=== H2A and H2B ===
In contrast to old H3 and H4, the old [[Histone H2A|H2A]] and [[Histone H2B|H2B]] histone proteins are released and degraded; therefore, newly assembled H2A and H2B proteins are incorporated into new nucleosomes.<ref>{{cite journal | vauthors = Louters L, Chalkley R | title = Exchange of histones H1, H2A, and H2B in vivo | journal = Biochemistry | volume = 24 | issue = 13 | pages = 3080–3085 | date = June 1985 | pmid = 4027229 | doi = 10.1021/bi00334a002 }}</ref> H2A and H2B are assembled into dimers which are then loaded onto nucleosomes by the nucleosome assembly protein-1 (NAP-1) which also assists with nucleosome sliding.<ref>{{cite journal | vauthors = Park YJ, Chodaparambil JV, Bao Y, McBryant SJ, Luger K | title = Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding | journal = The Journal of Biological Chemistry | volume = 280 | issue = 3 | pages = 1817–1825 | date = January 2005 | pmid = 15516689 | doi = 10.1074/jbc.M411347200 | doi-access = free }}</ref> The nucleosomes are also spaced by ATP-dependent nucleosome-remodeling complexes containing enzymes such as Isw1 Ino80, and Chd1, and subsequently assembled into higher order structure.<ref>{{cite journal | vauthors = Vincent JA, Kwong TJ, Tsukiyama T | title = ATP-dependent chromatin remodeling shapes the DNA replication landscape | journal = Nature Structural & Molecular Biology | volume = 15 | issue = 5 | pages = 477–484 | date = May 2008 | pmid = 18408730 | pmc = 2678716 | doi = 10.1038/nsmb.1419 }}</ref><ref>{{cite journal | vauthors = Yadav T, Whitehouse I | title = Replication-Coupled Nucleosome Assembly and Positioning by ATP-Dependent Chromatin-Remodeling Enzymes | journal = Cell Reports | volume = 15 | issue = 4 | pages = 715–723 | date = April 2016 | pmid = 27149855 | pmc = 5063657 | doi = 10.1016/J.CELREP.2016.03.059 }}</ref>

==Gallery==
<gallery>
File:Nucleosome core particle 1EQZ v.3.jpg
File:Nucleosome core particle 1EQZ v.4.jpg
File:Nucleosome core particle 1EQZ v.5.jpg
</gallery>
The crystal structure of the nucleosome core particle ({{Pdb|1EQZ}}<ref name="Harp00"/>) - different views showing details of histone folding and organization. Histones {{color|#AAAA00|H2A}}, {{color|red|H2B}}, {{color|blue|H3}}, {{color|green|H4}} and {{color|purple|DNA}} are coloured.

== See also ==
* [[Chromomere]]

== References ==
{{Reflist}}

== External links ==
* [http://www.mechanobio.info/topics/synthesis/go-0006323#01_go-0006323 MBInfo - What are nucleosomes]
* [https://www.ethz.ch/content/specialinterest/biol/institute-molecular-biology-biophysics/richmond-group/en.html Nucleosomes on the Richmond Lab website]
* {{Proteopedia|Nucleosomes}}
* [https://web.archive.org/web/20090111044350/http://pdb.rcsb.org/pdb/static.do?p=education_discussion%2Fmolecule_of_the_month%2Fpdb7_1.html Nucleosome at the PDB]
* [https://web.archive.org/web/20090803083240/http://www.scivee.tv/node/5532 Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation]
* [https://generegulation.org/nucleosome-positioning-data-and-prediction-tools/ Nucleosome positioning data and tools online (annotated list, constantly updated)]
* [https://www.mun.ca/biology/scarr/Histone_Protein_Structure.html Histone protein structure]
* [https://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0 HistoneDB 2.0 - Database of histones and variants]  at [[National Center for Biotechnology Information|NCBI]]
{{Chromo}}
{{Use dmy dates|date=April 2017}}

[[Category:Molecular biology]]
[[Category:Epigenetics]]
[[Category:Nuclear organization]]