Ch4 Nucleosomes

• The canonical nucleosome core particle consists of 147 base pairs of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer.
• Histones are very basic proteins (20% Lys, Arg) and 2x4 Histone proteins bind/bend DNA to form the nucleosome.
• Histone core primarily interacts with the sugar-phosphate backbone.
• Electrostatic interactions between phosphates and basic amino acid side chains (Arg, Lys) and hydrogen bonds between phosphates and histone backbone amide N and amino acid hydroxyl side chains are the main interactions in the nucleosome.
• Non-polar interactions with deoxyribose are also present in the nucleosome.
• The nucleosome has a two-fold rotational symmetry along a feature called the dyad axis.
• By making the DNA semi-opaque, the thirteen histone-DNA contacts can be visualized to form a positively-charged staircase along the surface of the octamer, upon which the negatively-charged DNA is wrapped.
• By unwrapping the DNA, the canonical octamer is revealed, and subsequently disassembled into the central H3-H4 tetramer (light green proteins) capped on each end by an H2A-H2B dimer (darker green proteins).
• Following octamer reassembly, the staircase of histone-DNA contacts is again revisited, and the DNA re-wrapped along that staircase to form the nucleosome.
• This type of structural dynamics could be an initial step for nucleosome disassembly and H2A/H2B exchange and may be accelerated by PTMs at histone-histone interfaces.
• Histone tails, which refer to the disordered N-termini, extend out from the nucleosome core and help stabilize higher-order chromatin structure.
• A significant number of the post-translational modifications (PTMs) within nucleosome interfaces are acetylation and phosphorylation.
• The primary level of discussion in this review is the nucleosome core particle, as most studies of histone PTMs in structured regions of the nucleosome to date have been investigated by use of mononucleosomes.
• In the region around the dyad symmetry axis, which coordinates the most internal segment of DNA, contains the strongest DNA-histone interactions.
• DNA unwrapping transiently exposes protein-binding sites that are buried within the fully wrapped nucleosome.
• Lysine acetylation removes a positive charge, phosphorylation introduces negative charge, and both add steric bulk.
• A single PTM can increase the probability of altered structural states by over a factor of 25.
• With unmodified histones, these structural changes require histone chaperones and chromatin remodeling complexes.
• Dyad modifications can enhance both sliding and disassembly.
• We describe select PTMs between H3/H4 and H2A/H2B that appear positioned to weaken the histone-histone interface.
• Nucleosomes can unwrap with the H2A/H2B heterodimer attached to DNA.
• DNA entry/exit regions coordinate the outermost segments of DNA, which are the first to detach from the histones during nucleosome sliding or unwrapping.
• Nucleosome stability also depends on protein-protein interfaces between the histone dimers.
• The introduction of a single PTM can reduce the free energy of nucleosome formation by at least 2 kcal/mol.
• The DNA can slide relative to the histone octamer and nucleosomes can be disassembled to expose DNA-binding sites.
• The PTM location impacts the type of structural fluctuation on the nucleosome.
• In vitro reconstituted purified nucleosomes and DNA in low salt form “beads-on-a-string” structures, 2.5-nm DNA threads decorated with discrete 11-nm nucleosome particles (12, 13).
• Nucleosomes are composed of 12 base pairs of DNA and a protein core.
• These lobes sequentially bind and release DNA, enabling an 'inchworming' mechanism of unidirectional movement in the 3' to 5' direction along the tracking strand.
• The DNA then appears to be pumped by the enzyme, and undergoes rotation during translocation.
• We now depict the RecA-like lobes as mittens that reciprocally move, grip and release from the DNA backbone.
• In order to perceive how this property is applied to the nucleosome, we change perspective and hold the translocating enzyme in a fixed position.
• Monomeric DNA helicases and chromatin remodellers share a common mode of translocation, involving a protein motor core formed by two RecA-like lobes which bind the same strand of DNA with one lobe slightly ahead of the other.
• Chromatin remodellers can conduct nucleosome sliding via monotonous DNA translocation, where the DNA at the entry site moves in concert with DNA at the exit site, one base pair at a time.
• A more sophisticated depiction involving sequential movement, first on the distal size and then on the proximal side, is shown in the next animation.
• Chromatin remodellers can conduct nucleosome sliding via sequential (or discontinuous) DNA translocation, where the two orange RecA-like lobes bind to nucleosomal DNA at a fixed position, two helical turns from the dyad axis and perform directional DNA translocation by pulling in DNA from the proximal side of the nucleosome and pumping it toward the distal side.
• Translocation creates DNA torsion and translational tension on both sides of the mittens, which in this animation, is resolved in 3 base pair increments, in two sequential steps.
• Imitation switch (ISWI), chromodomain helicase DNA-binding (CHD), switch/sucrose non-fermentable (SWI/SNF) and INO80 are families involved in nucleosome regulation.
• Each family usually is involved in one function.
• The physical step size of 1 base pair per ATP hydrolysis depicted here is based on crystal structures and biophysical measurements of translocation (which are 1 to 2 bp) by chromatin remodelling ATPases and related helicases and translocases.