Nucleosome positioning--what do we really know?

The positioning of nucleosomes on the DNA of eukaryotic genomes is a major determinant of gene expression. In particular nucleosomes in close proximity to regulatory regions are often more precisely positioned in vivo than nucleosomes located elsewhere. In this article we compare data obtained from the most recent studies by a variety of techniques. We argue that the disparate conclusions in the literature could be a consequence of procedural differences sampling alternative arrays of nucleosomes on the same DNA sequence. Importantly, the ostensibly least invasive techniques identify differences between nucleosomes in the vicinity of transcription start sites in budding yeast and those positioned distally within the transcribed region.