Nucleosome Dynamics. III. Histone Tail-dependent Fluctuation of Nucleosomes Between Open and Closed DNA Conformations. Implications for Chromatin Dynamics and the Linking Number Paradox. A Relaxation Study of Mononucleosomes on DNA Minicircles

Abstract

The mean linking number (〈 Lk〉) of the topoisomer equilibrium distribution obtained upon relaxation of DNA minicircles with topoisomerase I did not increase linearly, but rather in a step wise fashion, with DNA size between 351 and 366 bp. As a consequence, the corresponding linking number difference (〈Δ Lk〉) did not remain equal to 0, but rather oscillated between ±0.3 with the periodicity of the double helix. This oscillation, not observed with plasmid-size DNA, is an expected consequence of the stiffness of short DNA. When minicircles were reconstituted with a nucleosome, the associated 〈Δ Lk n 〉 oscillated between ∼−1.4 ±0.2. This oscillation appears to result from the combined effects of DNA stiffness, and nucleosome ability to thermally fluctuate between three distinct DNA conformational states. Two of these states, a closed ∼1.75-turn DNA conformation with negatively crossed entering and exiting DNAs, and an open ∼1.4-turn conformation with uncrossed DNAs, are well known, whereas the third state, with a closed DNA conformation and DNAs tending to cross positively rather than negatively, is less familiar. Access to both closed “negative” and “positive” states appears to be mediated by histone N-terminal tails, as shown by specific alterations to the 〈Δ Lk n 〉 oscillation caused by histone acetylation and phosphate ions, a potent tail destabilizator. These results extend previous observations of ethidium bromide fluorescence titration in the accompanying article, which have pointed to an histone tail-dependent flexibility of entering and exiting DNAs to positive crossing. They also show that DNA wrapping around the histones occurred without twist alteration compared to the DNA free in solution, and reveal an intriguing new facet of the “linking-number-paradox” problem: the possibility for linkers in chromatin to adopt different crossing status within an overall dynamic equilibrium which may be regulated by histone acetylation.