Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals (original) (raw)
Figure 9
The level and length of nucleosome depletion around gene start and gene end sites correlate with boundary strength.
(A) Boundaries were classified into five groups by their nucleosome fold depletion (strength) using sequence rules (see Methods), and every gene was annotated by the classification of the strongest boundary that it has in the 200 bp region upstream of its transcription start site. Shown is the average number of nucleosomes per basepair around the transcription start site of genes from each of the four boundary classification groups. (B) Same as (A), but when annotating each gene by the classification of the strongest boundary that it has in the 200 bp region downstream of its translation end site (translation end site was chosen since transcription end sites are poorly annotated). Note that for a given boundary class, the corresponding genes in (A) are distinct from the corresponding genes in (B). (C,D) Same as (A) and (B), but plotting the average nucleosome occupancy predicted by the sequence-based nucleosome positioning model that we developed here. Predictions are generated in a cross validation scheme, such that the predicted nucleosome occupancy across each chromosome is computed by a model that was learned using only the nucleosome data of all the other chromosomes.