The contribution of histone-DNA interactions to nucleosome positioning in vivo is currently a matter of debate. We argue here that certain nucleosome positions, often in promoter regions, in yeast may be, at least in part, specified by the DNA sequence. In contrast other positions may be poorly specified. Positioning thus has both statistical and DNA-determined components. We further argue that the relative affinity of the octamer for different DNA sequences can vary and therefore the interaction of histones with the DNA is a 'tunable' property.Both in vitro and in vivo the histone octamer can form nucleosomes on a wide spectrum of DNA sequences, independent of base composition. It thus lacks the base-specific sequence selectivity typical of transcription factors. Yet both in vitro and in vivo the octamer adopt a rather precise position on a given DNA sequence (1-10). Importantly in vivo histones are essential participants in gene regulation (11, 12). The in vitro data argue strongly that precise positioning is a consequence of selection by histone-DNA interactions but defining the role, if any, of these interactions in vivo has proved elusive.
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