In vitro nucleosome mapping with chicken, frog and a variety of yeast core histones

We have mapped sequence-directed nucleosome positioning in vitro on a variety of genomic DNA molecules using high-throughput sequencing. Chromatins were prepared by reconstitution using chicken, frog or yeast core histones allowing us to compare nucleosome positioning for each type of histone octamer. In one preparation of chromatin formed with a yeast histone octamer, histone H3 was replaced by the centromere-specific histone variant, Cse4. The locations and relative affinities of the nucleosome positioning sites for each type of histone on each DNA were identified and the results were compared using a variety of criteria. Although, in general, all the types of histones tested identified similar patterns of binding sites on the various DNAs, both in terms of position and relative affinity, there were significant differences between the populations of nucleosomal DNA sequences recovered from the different reconstitutes. A number of factors that may contribute to this variation are discussed.