Nucleosome dynamics. VI. histone tail regulation of tetrasome chiral transition. A relaxation study of tetrasomes on DNA minicircles

Abstract

We have recently described the relaxation of mononucleosomes on an homologous series of 351-366 bp DNA minicircles, as a tool to study nucleosome structure and dynamics in vitro. Nucleosomes were found to have a tail-regulated access to three distinct DNA conformations, depending on the crossing between the entering and exiting DNAs, and its polarity. This approach was now used to explore tetrasome chiral transition, and the influence of the histone tails. The data confirmed the existence of two states, with linking number differences Δ Lk t=−0.74(±0.01) and +0.51(±0.06). As expected, the particle free energy is higher in the right-handed state (Δ G t=1.9(±0.I) kT), but it decreased (to 1.3(±0.1) kT) upon histone acetylation and the addition of phosphate, a potent tail destabilizer. Removal of the tails with trypsin further decreased Δ G t (to 0.6 kT), and also induced a loss of supercoiling in both states, to Δ Lk t=−0.64(±0.03) and +0.35(±0.05). The loop end-conditions, and hence the parameters of the DNA superhelix, were then calculated for both states using the explicit solutions to the equations of the mechanical equilibrium in the theory of elastic rod model for DNA. Whereas the pitch of the DNA superhelix may be approximately equal and opposite in the two conformations, its radius ( r) was 20 % larger in the right-handed conformation, confirming previous observations by electron microscopy of a tetrasome lateral opening in that conformation. The above supercoiling losses were found to reflect a further 3 % increase in r (to 23 %) upon removal of the tails in the right-handed conformation, and a 14 % increase in the left-handed conformation. The use of composite tetramers with one histone tail intact and the other removed showed these effects to be essentially due to the H3 tails. Altogether, these results show that the H3 tails oppose the tetrasome opening which is expected to be required to relieve the clash between the entering and exiting DNAs in the course of the transition, but which also appears to be intrinsic to the protein reorientation mechanism. We propose that the block against opening results from the H3 tails intercalating into the small groove of the double helix at ±10 bp from the dyad, and acting as wedges against local DNA straightening. The tails (especially H3) may therefore regulate tetrasome chiral transition in vivo.