Abstract
The nature of chromatin as regular succession of nucleosomes has gained iconic status. The average nucleosome repeat length (NRL) determined by classical means serves as index for bulk chromatin of a given specimen. However, this value is dominated by regular heterochromatin since nucleosomal arrays are often not regular at individual single copy sequences.
To obtain a measure for nucleosome regularity in euchromatin we subjected nucleosome profiles of D. melanogaster embryos to autocorrelation and spectral density estimation. These revealed variation in nucleosome regularity and NRL at different types of euchromatin and yielded a comprehensive catalog of regular phased nucleosome arrays (PNA). The absence of the nucleosome sliding factor ACF1 correlated with global loss of regularity and increased NRL in euchromatin and specifically compromised phasing at a novel class of PNA. Our approach is generally applicable to characterize the functional diversification of nucleosome remodelers in euchromatin organization.
