Chromatin structure is central for the
regulation of gene expression, but its genome-wide organization is only beginning to be understood. Here, we examine the connection between patterns of nucleosome occupancy and the capacity to modulate
gene expression upon changing conditions, i.e.
transcriptional plasticity. By analyzing a genome-wide data of nucleosome positioning in
yeast, we find that the presence of nucleosomes close to the transcription start site is associated with high
transcriptional plasticity, while nucleosomes at more distant upstream positions are negatively
correlated with
transcriptional plasticity. Based on this, we identify two typical
promoter structures associated with low or high plasticity, respectively. The first class is characterized by a relatively large nucleosome free region close to the start site coupled with well-positioned nucleosomes further upstream, whereas the second class displays a more evenly distributed and dynamic nucleosome positioning, with high occupancy close to the start site. The two classes are further distinguished by multiple
promoter features, including
histone turnover,
binding sites location, H2A.Z occupancy, expression
noise and expression diversity. Analysis of nucleosome positioning in human
promoters reproduce the main observations. Our results suggest two distinct strategies for
gene regulation by
chromatin, which are selectively employed by different genes.
