Sequence dependence of translational positioning of core nucleosomes

The basis for the choice of translational position of a histone octamer on DNA is poorly understood. To gain further insights into this question we ha ve studied the translational and rotational settings of core particles asse mbled on a simple repeating 20 bp positioning sequence. We show that the tr anslational positions of the core particles assembled on this sequence are invariant with respect to the DNA sequence and occur at 20 by intervals. Ce rtain modifications of the original sequence reduce the spacing of possible dyads to 10 bp. At least one of these alters both the translational and ro tational settings. We conclude that the translational position of a core pa rticle is specified by sequence determinants additional to those specifying rotational positioning. The rotational settings on either side of the dyad s of core particles assembled on the wild-type and a mutant sequence differ by +2 bp, corresponding to an overall helical periodicity of similar to 10 .15 bp. The average helical periodicity of the central two to four turns is 10.5-11 bp whilst that of the flanking DNA is closer to 10 bp. The DNA imm ediately flanking the dyad is also characterised by a more extensive suscep tibility to cleavage by hydroxyl radical. (C) 2001 Academic Press.