Structural features of a phased nucleosome core particle.

Abstract

Chicken erythrocyte inner histones associate with a cloned 260-base-pair (bp) segment of Lytechinus variegatus DNA in a unique location. The fragment contains a 120-bp segment encoding 5S rRNA, a 90-bp flanking sequence to the 5'' side of the transcribed segment, and a 50-bp downstream flanking sequence. Association of DNA, uniquely labeled at one end or the other and at either the 3'' or the 5'' terminus of a given strand, with histones at 0.1 M ionic strength leads to formation of a compact complex which sediments at .apprx. 13 S. Analysis of cutting of the complex by DNase I shows that protection from the nuclease is confined to a region beginning 20 bp from the left end of the segment and extending to .apprx. 165 bp from left end. Within the protected region, the 2 DNA strands differ in their susceptibilities to the nuclease, the precise location of nuclease cutting sites and the spacing between these sites, and the relative susceptibilities of specific cutting locations. Information present in DNA and the histone octomer seems sufficient to create a precisely phased nucleosome in which interactions of the 2 DNA strands with histones are not the same. The structure of this unique nucleosome is not predicted by the intellectual model based on studies of mixed populations of nucleosome core particles.