Relation of Nucleosomes to DNA Sequences

This paper addresses the question of whether a linear array of nucleosomes occurs at a unique loca-tion along the sequence of nucleotides in DNA (Fig. 1). Such a unique location would be found if the formation of the array ofnucleosomes were initiated at a unique point in the DNA sequence, and further-more if the DNA content were the same from one nucleosome to the next so that a unique location, once established, would be maintained for a consid-erable distance along the DNA. The alternative is that the location of nucleosomes varies from one cell, or one copy of the genome, to another, as would be the case if nucleosomes were assembled at ran-dom on the DNA. The results described here indicate that the location ofnucleosomes is random for virtu-ally all single-copy DNA sequences in rat-liver and Drosophila embryo cells. We have studied the location of nucleosomes be-cause it is crucial for many conceivable roles of nu-cleosomes in the control of gene expression; for ex-ample, for a role based on the distinction between core and linker DNA. Core DNA, the central 140 base pairs (bp) in the nucleosome, is inaccessible to certain nucleases, whereas linker DNA, a region of typically about 60 bp which joins one core to the next, is completely degraded. A similar pattern of accessibility of the DNA may apply in the binding of activator or repressor molecules and the like; that is, the function of a DNA sequence may depend on whether it resides in the core or linker. A unique location of nucleosomes would then be required to UNIQUE LOCATION RANDOM LOCATION cell I nucleosomes cell 2 cel l I ce l l