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 mononucleosomeson DNA minicircles

The mean linking number ((LK)) of the topoisomer equilibrium distribution o btained upon relaxation of DNA minicircles with topoisomerase I did not inc rease Linearly, but rather in a step wise fashion, with DNA size between 35 1 and 366 bp. As a consequence, the corresponding linking number difference ((Delta 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 shor t DNA. When minicircles were reconstituted with a nucleosome, the associate d (Delta Lk(n)) oscillated between similar to - 1.4 +/-0.2. This oscillatio n appears to result from the combined effects of DNA stiffness, and nucleos ome ability to thermally fluctuate between three distinct DNA conformationa l states. Two of these states, a closed similar to 1.75-turn DNA conformati on with negatively crossed entering and exiting DNAs, and an open similar t o 1.4-turn conformation with uncrossed DNAs, are well known, whereas the th ird state, with a closed DNA conformation and DNAs tending to cross positiv ely rather than negatively, is less familiar. Access to both closed "negati ve" and "positive" states appears to be mediated by histone N-terminal tail s, as shown by specific alterations to the (Delta LKn,) oscillation caused by histone acetylation and phosphate ions, a potent tail destabilizator. Th ese results extend previous observations of ethidium bromide fluorescence t itration in the accompanying article, which have pointed to an histone tail -dependent flexibility of entering and exiting DNAs to positive crossing. T hey also show that DNA wrapping around the histones occurred without twist alteration compared to the DNA free in solution, and reveal an intriguing n ew facet of the "Linking-nunber-paradox" problem: the possibility for linke rs in chromatin to adopt different crossing status within an overall dynami c equilibrium which may be regulated by histone acetylation. (C) 1999 Acade mic Press.