The application of deep sequencing to map 5' capped transcripts has confirmed 
the existence of at least two distinct promoter classes in metazoans: "focused" 
promoters with transcription start sites (TSSs) that occur in a narrowly defined 
genomic span and "dispersed" promoters with TSSs that are spread over a larger 
window. Previous studies have explored the presence of genomic features, such as 
CpG islands and sequence motifs, in these promoter classes, but virtually no 
studies have directly investigated the relationship with chromatin features. 
Here, we show that promoter classes are significantly differentiated by 
nucleosome organization and chromatin structure. Dispersed promoters display 
higher associations with well-positioned nucleosomes downstream of the TSS and a 
more clearly defined nucleosome free region upstream, while focused promoters 
have a less organized nucleosome structure, yet higher presence of RNA 
polymerase II. These differences extend to histone variants (H2A.Z) and marks 
(H3K4 methylation), as well as insulator binding (such as CTCF), independent of 
the expression levels of affected genes. Notably, differences are conserved 
across mammals and flies, and they provide for a clearer separation of promoter 
architectures than the presence and absence of CpG islands or the occurrence of 
stalled RNA polymerase. Computational models support the stronger contribution 
of chromatin features to the definition of dispersed promoters compared to 
focused start sites. Our results show that promoter classes defined from 5' 
capped transcripts not only reflect differences in the initiation process at the 
core promoter but also are indicative of divergent transcriptional programs 
established within gene-proximal nucleosome organization.