Application of these methods in a wide range of organisms (Mavrich et al. 2008; Shivaswamy et al. 2008; Valouev et al. 2008, 2011; Chodavarapu et al. 2010; Gilchrist et al. 2010; Tsankov et al. 2010) identifies several structural principles. First, active and poised promoters are nucleosome-depleted, as are active enhancers. Second, nucleosomes bordering regulatory elements are well positioned. Nucleosomes are positioned with decaying precision at greater distances, leading to a fuzzier nucleosome template further away (∼1000–2000 bp) from boundary nucleosomes. Curiously, in yeast, nucleosome delocalization is typically maximal at a point ∼2/3 of the way into coding regions, rather than at the midpoint of the gene (Vaillant et al. 2010). Third, highly transcribed genes tend to have lower nucleosome occupancy and less precise positioning, most likely due to action of RNA polymerase II and its associated factors. Finally, the density of the nucleosome template (average distance between two adjacent nucleosomes) can vary, mostly due to trans factors (Hughes et al. 2012).
