The arrangement of nucleosomes in nucleoprotein complexes from polyoma virus and SV40

Abstract

Abstract We have examined the arrangement of the nucleosomes in relation to DNA base sequence in nucleoprotein complexes from polyoma and SV40. Digestion of polyoma nucleoprotein complex with Hpa II restriction endonuclease showed that each of the nine cleavage sites for this enzyme in the DNA was equally available in the nucleoprotein complex. We conclude that the nucleosomes do not occupy unique positions. The alternatives are that the arrangement of the nucleosomes is completely random, or that each nucleosome can, within the whole population of nucleoprotein complexes, occupy one of a limited number of positions. To investigate this, we have isolated the 140 base pair protected DNA fragments from a micrococcal nuclease digestion of nucleoprotein complex. We have used these fragments to indicate the positions, in relation to the DNA base sequence, of the nucleosomes from which they are derived. The restriction endonucleases Bam I and Eco RI each cut polyoma and SV40 DNA at one site. Digestion of the 140 base pair DNA with these enzymes yielded a reproducible series of about 10 smaller fragments. We conclude that the nucleosomes occupy a small number of distinct alternative positions; the arrangement is not completely random. This interpretation is consistent with a number of other findings, which together suggest that the nucleoprotein complex contains a repeating element of structure extending across both nucleosomes and bridge regions. We have also found that there are preferred cleavage sites in DNA for micrococcal nuclease. Although this is of some interest, we do not believe that it provides the explanation for the generation of the discrete fragments from monomer DNA.