Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
Simulations of Core Histone Modifications on Human Mono Nucleosomes Reveal Alterations in Stability
The organization of chromatin within the eukaryotic cell nucleus is critical to its gene regulation pattern. The efficient packing of the metre long DNA within the nuclear confines follows a structural hierarchy, the fundamental unit of which is a nucleosome. Subtle but powerful mechanisms like histone modifications effect local or global structural alterations at the nucleosomal level or at the level of linker histones and orchestrate the accessibility to the DNA sequestered in chromatin. This work reports our investigations on the structural role of histone modifications in tuning the stability of the chromatin fiber at the mononucleosome level. The high degree of sequence conservation of core histones with the available high resolution crystal structure of a nucleosome was utilized to derive homology models of a human mono nucleosome. Local perturbations to a human mono nucleosome, which modulate the energy of the nucleosome complex, have also been analyzed. The variations in energies of the modified nucleosome with the wild type nucleosome were used as a probe to estimate nucleosome stability. The observations revealed that mutations around the DNA interacting regions of the core histones H3 and H4 induce local structural changes causing substantial changes in the nucleosomal energy and hence stability. The overall structure of the nucleosome remained unaltered as evidenced by the rms deviation, which compared well with those observed experimentally for the crystal structures of 11 mutants in Xenopus laevis. Experimentally established DNA binding estimates perceived as a probable relaxation of the DNA octamer contact and causing instability in the nucleosome were found to correlate well with the energies obtained by modeling.
At the level of epigenetic modifications, our work demonstrates that the nucleosomal stability is affected by the alterations of certain critical lysine residues like K14 on the H3 tail. The observed destabilizing effects of tail acetylation may be due to elimination of certain key DNA ? tail interactions in the nucleosome. The incorporation of variants H2A.Z or H3.3 lower nucleosome stability as evidenced by changes in energy between nucleosome models derived from canonical and variant histones. It is found that the enhancement of the acidic patch in the nucleosome on replacement of canonical H2A with H2A.Z alters interactions of the H2A-H2B dimer with histone H4. The variation in stability caused by the H3.3 variant is attributed to the changes in electrostatic potential caused by the difference in four amino acids between the H3.3 and the canonical H3. Our work hypothesizes that variant nucleosomes may function by modulating the stability of the nucleosome or chromatin fiber, or through changes in the surface residues at interacting regions. Further, ortholog substitution did not alter the structural stability of the nucleosome implying that the formation of the histone octamer is probably conserved despite species specific expansion.
Structural consequences of amino acid substitutions on H3 tails on Lysines at positions 14.The left panel (a) shows the wild type structure and the right panel (b) shows the structural changes in the mutant nucleosome.
1National Centre for Biological Sciences