Editing Histone octamer (section)

===Histone/DNA interactions===

Histones are composed of mostly positively charged amino acid residues such as [[lysine]] and [[arginine]]. The positive charges allow them to closely associate with the negatively charged DNA through electrostatic interactions. Neutralizing the charges in the DNA allows it to become more tightly packed.<ref name=watson />

====Interactions with the minor groove====

The histone-fold domains’ interaction with the minor groove accounts for the majority of the interactions in the nucleosome.<ref name=luger>{{cite journal|last=Richmond|first=Timothy J.|author2=Luger, Karolin |author3=Mäder, Armin W. |author4=Richmond, Robin K. |author5= Sargent, David F. |journal=Nature|date=18 September 1997|volume=389|issue=6648|pages=251–260|doi=10.1038/38444|pmid=9305837 |title=Crystal structure of the nucleosome core particle at 2.8 A resolution|bibcode=1997Natur.389..251L|s2cid=4328827}}</ref> As the DNA wraps around the histone octamer, it exposes its minor groove to the histone octamer at 14 distinct locations. At these sites, the two interact through a series of weak, non-covalent bonds. The main source of bonds comes from hydrogen bonds, both direct and water-mediated.<ref name=andrews /> The histone-fold hydrogen bonds  with both phosphodiester backbone and the A:T rich bases. In these interactions, the histone fold binds to the oxygen atoms and [[hydroxyl]] side chains, respectively.<ref name=luger /> Together these sites have a total of about 40 hydrogen bonds, most of which are from the backbone interactions.<ref name=watson /> Additionally, 10 out of the 14 times that the minor groove faces the histone fold, an arginine side chain from the histone fold is inserted into the minor groove. The other four times, the arginine comes from a tail region of the histone.<ref name=luger />

====Tail interactions and modifications====
{{Further|Histone}}
As mentioned above the histone tails have been shown to directly interact with the DNA of the nucleosome. Each histone in the octamer has an N-terminal tail that protrudes from the histone core. The tails play roles both in inter and intra nucleosomal interactions that ultimately influence gene access.<ref name=biswas>{{cite journal|last=Biswas|first=Mithun|author2=Voltz, Karine |author3=Smith, Jeremy C. |author4= Langowski, Jörg |title=Role of Histone Tails in Structural Stability of the Nucleosome|journal=PLOS Computational Biology|date=15 December 2011|volume=7|issue=12|pages=e1002279|doi=10.1371/journal.pcbi.1002279|pmid=22207822|pmc=3240580|bibcode=2011PLSCB...7E2279B |doi-access=free }}</ref> Histones are positively charged molecules which allow a tighter bonding to the negatively charged DNA molecule. Reducing the positive charge of histone proteins reduces the strength of binding between the histone and DNA, making it more open to gene transcription (expression).<ref name="biswas"/> Moreover, these flexible units direct DNA wrapping in a left-handed manner around the histone octamer during nucleosome formation.<ref name=watson /> Once the DNA is bound the tails continue to interact with the DNA. The parts of the tail closest to the DNA hydrogen bond and strengthen the DNA's association with the octamer; the parts of the tail furthest away from the DNA, however, work in a very different manner. Cellular enzymes modify the amino acids in the distal sections of the tail to influence the accessibility of the DNA. The tails have also been implicated in the stabilization of 30-nm fibers. Research has shown removing certain tails prevents the nucleosomes from forming properly and a general failure to produce chromatin fiber.<ref name=biswas /> In all, these associations protect the nucleosomal DNA from the external environment but also lower their accessibility to cellular replication and transcriptional machinery.