ACF1 regulates nucleosome spacing in Drosophila euchromatin [ChIP-seq]. Drosophila melanogaster

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 dyad profiles to autocorrelation and spectral density analyses. This 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 in euchromatin and increased NRL and compromised phasing at a novel type of PNA. Our approach is generally applicable to characterize hallmarks of euchromatin organization. Overall design: ChIP-Seq in Drosophila melanogaster embryos

染色质以核小体有序串联为核心构成的本质，已成为学界公认的标志性认知。通过经典实验方法测得的平均核小体重复长度（nucleosome repeat length, NRL），可作为特定样本整体染色质的表征指标。然而，该数值受规整异染色质的主导性影响，因为在单个单拷贝序列区域，核小体阵列往往并不规整。为了量化常染色质中的核小体规整性，我们对核小体二分位点谱开展了自相关分析与光谱密度分析。该分析揭示了不同类型常染色质中核小体规整性与NRL的异质性，并构建了规整相位式核小体阵列（regular phased nucleosome arrays, PNA）的综合目录。核小体滑动因子ACF1的缺失，与常染色质的全局规整性丧失、NRL升高，以及新型PNA的相位紊乱显著相关。本研究方法可广泛用于表征常染色质组构的标志性特征。实验整体设计：对黑腹果蝇（Drosophila melanogaster）胚胎开展染色质免疫共沉淀测序（ChIP-Seq）。