Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals (original) (raw)
Figure 12
Type I and Type II promoters have distinct architectures.
(A) Shown is a schematic illustration of promoter architectures for the two extreme types of promoters from Figure 11A. The schematic illustrates that in the high noise (Type I, left column) promoters, factor binding sites are measurably occupied by both their cognate factors and nucleosomes (in a cell population), suggesting that their high noise results from competition between nucleosomes and factors for DNA access. In contrast, the low noise (Type II, right column) promoters exhibit a characteristic nucleosome-depleted region upstream of the transcription start site in which bound factor sites are highly concentrated. Also shown is the average number of nucleosome reads in our data (cyan), and the distribution of factor sites (brown) and TATA elements (green, only for Type I promoters), around the transcription start site of the genes in each of the two extreme types of promoters from (A) (left column, Type I promoters; right column, Type II promoters). (B) Genes of the high- and low-noise promoter classes exhibit distinct functional enrichments. Shown is a selected list of functional categories that are significantly enriched (P<10−5) in the set of genes associated with each promoter type (see Figure S7 for the full list and details of all enrichments). (C) The distinct nucleosome organizations in high- and low-noise promoters can be predicted from DNA sequence. Shown is the average nucleosome occupancy predicted by the sequence-based model for nucleosome positioning that we developed here, for each of the two promoter types in (A).