Model depicting various contributors to nucleosome organization in the S. cerevisiae genome. Yellow and green mirrored triangles represent increased AA and TT dinucleotide enrichment toward the 5′ and 3′ ends of nucleosomal DNA, respectively. Their 10-bp periodical placement would rotationally phase the DNA on the nucleosomal surface, although rotational phasing may contribute modestly to translational positioning (Tanaka et al. 1992; Lee et al. 2007). The red half-ellipse represents the distribution of poly(dA:dT) tracts that exclude nucleosomes from the promoter. Black vertical bars represent AT and TA dinucleotide enrichment at nucleosome borders, which might contribute to translational positioning. The contributions of all A/T dinucleotides are diminished beyond the +1 nucleosome, in which statistical phasing takes over and decays toward the 3′ end of the gene (represented as fuzzier nucleosome ovals in gray). AA/TT positioning at the 3′ end of genes is depicted as being antagonized by AATAAA-related cleavage and polyadenylation signals. Transcription factors (TF) are shown to contribute to −1 and +1 positioning. TFIIB-linked looping (B) is shown.
