CHD4 Sandbox: Difference between revisions

==The Nucleosome==

The nucleosome is comprised of <scene name='88/880268/147-mer/2'>146-147 DNA base pairs</scene> wrapped around an <scene name='88/880268/147-mer_octamer/1'>octamer</scene> of four different proteins called histones.  

The four histone proteins: <scene name='88/880268/H4_in_complex/1'>H4</scene>, <scene name='88/880268/H3_histone/1'> H3</scene>, <scene name='88/880268/H2a_histone/1'> H2A</scene>, and <scene name='88/880268/H2b_histone/1'> H2B</scene> make up the nucleosome with two sets of two heterodimers<ref name=num2/>. Heterodimers consisting of H3 and H4 as well as H2A and H2B<ref name=num2>DOI 10.1080/21553769.2012.702667</ref>. These heterodimers form an octamer through the presence of hydrophobic interaction between dimers<ref name=num2/>.

==The Dyad Axis==

The formation of the histones via hydrophobic interactions forms the octamer<ref name=num2/>. This octamer has dyad symmetry between the H3 and H3 histones, forming the dyad axis and referred to as super helical location 0 (SHL 0) <ref name=num2/>.   

The state of the minor groove directionality is referred to as SHL (Super Helical Location) <ref name=num2/>. With the DNA wrapping 1.65 turns around the nucleosome, the status of the minor groove conformation with respect to the orientation of the nucleosome with SHL 0 (the Dyad axis) <ref name=num2/>. It is to be noted that SHL positions can be both + and – but the position remains similar, as they reflect over the dyad axis at SHL 0<ref name=num2/>. The sign of the SHL is referring to which pole of the nucleosome the protein domain binds to on the DNA<ref name=num2/>. The directionality of the DNA bound to the nucleosome changes with the ± sign of the SHL as there is an enter and exit direction of the DNA on the nucleosome<ref name=num2/>.  

==Scaffolding of Histones for DNA==