Fig. 10

Promoter nucleosome organization: a two-state model. a Our model predicts two different nucleosome organization of gene promoters. Promoters bound by barrier complexes are predicted to contain an NDR flanked by phased nucleosomes, while promoters that are free of barrier complexes are predicted to have disorganized nucleosomes and lack NDRs. b Drosophila promoters sorted by the transcription level (CAGE-seq data from [40]). c Nucleosome dyad organization confirms the model prediction: promoters of active genes contain NDRs that are flanked by phased nucleosomes on both sides, while promoters of inactive genes contain disorganized nucleosomes and no NDR. The promoters of active genes (top ~ 40% of the genes) are accessible to DNaseI (d) (DNase-seq data from modENCODE [41], modENCODE_3324) and Tn5 transposase (e) (ATAC-seq data from [22]) and are bound by barrier complexes, such as the GAGA factor (f) (ChIP-seq data from [42]). g–i Heat maps of the nucleosome occupancy and the two fitted rates k₁ and k₂, indicating g the probability that a site is occupied by a nucleosome, h chromatin accessibility to MNase, as measured by the nucleosome release rate, and i decay rate