Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation because nucleosomes modulate DNA access by their positioning along the genome. A cell-population nucleosome map requires two observables: nucleosome positions along the DNA ("Where?") and nucleosome occupancies across the population ("In how many cells?"). All available genome-wide nucleosome mapping techniques are yield methods because they score either nucleosomal (e.g., MNase-seq, chemical cleavage-seq) or nonnucleosomal (e.g., ATAC-seq) DNA but lose track of the total DNA population for each genomic region. Therefore, they only provide nucleosome positions and maybe compare relative occupancies between positions, but cannot measure absolute nucleosome occupancy, which is the fraction of all DNA molecules occupied at a given position and time by a nucleosome. Here, we established two orthogonal and thereby cross-validating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae genome via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9-bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called by chemical cleavage-seq have a mean absolute occupancy of 90 ± 6% (±SD). Depending on nucleosome position calling procedures, there are 57,000 to 60,000 nucleosomes per yeast cell. The few low absolute occupancy nucleosomes do not correlate with highly transcribed gene bodies, but correlate with increased presence of the nucleosome-evicting chromatin structure remodeling (RSC) complex, and are enriched upstream of highly transcribed or regulated genes. Our work provides a quantitative method and reference frame in absolute terms for future chromatin studies.

中文翻译：

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酿酒酵母基因组的绝对核小体占据图。

核小体的定位是真核生物中的基本DNA包装单位，对于理解基因组调控至关重要，因为核小体通过沿基因组的定位来调节DNA的进入。细胞群体的核小体图需要两个可观察到的信息：沿着DNA的核小体位置（“ Where？”）和整个群体中的核小体占有率（“多少个细胞？”）。所有可用的全基因组核小体定位技术都是产量方法，因为它们对核小体（例如MNase-seq，化学切割-seq）或非核小体（例如ATAC-seq）DNA评分，但无法追踪每个基因组区域的总DNA群体。因此，它们仅提供核小体位置，并且可能会比较位置之间的相对占有率，但无法测量绝对核小体占有率，这是核小体在给定位置和时间占据的所有DNA分子的分数。在这里，我们建立了两个正交的交叉验证方法，以通过限制酶和DNA甲基转移酶测量酿酒酵母基因组中的绝对核小体占有率。生成的高分辨率（9 bp）图显示了统一的绝对占用率。大多数细胞中大多数核小体位置均被占据：被化学裂解序列调用的所有核小体中有97％的平均绝对占有率为90±6％（±SD）。取决于核小体位置调用程序，每个酵母细胞有57,000至60,000个核小体。少数几个绝对占有率低的核小体与高度转录的基因体无关，但与增加核小体的染色质结构重塑（RSC）复合物的存在相关，并且在高度转录或调控的基因上游富集。我们的工作为将来的染色质研究提供了绝对的定量方法和参考框架。