DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast III)

DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and indicating that DNA accessibility is primarily determined by nucleosome spacing. Remarkably, AluI sites in inactive mouse promoters are accessible in some cells. Furthermore, euchromatin and heterochromatin have very similar accessibilities. Cell-to-cell heterogeneity in DNA accessibility has implications for chromatin models of gene regulation: a transcription factor binding site is blocked in some cells, but not in all cells, guaranteeing neither activation nor repression. 44 samples

DNA可及性（DNA accessibility）被认为在基因表达调控中发挥关键作用。本研究采用限制性内切酶作为染色质结构的探针，并以其作为转录因子的替代标志物，对该假说展开验证。我们在出芽酵母与小鼠肝细胞核的所有基因组AluI酶切位点上，测量了酶切速率与可及DNA的占比。结果显示，肝细胞DNA的可及性高于酵母DNA，这与核小体间更长的连接DNA序列相符，同时表明DNA可及性主要由核小体间距决定。值得注意的是，部分细胞中即便位于小鼠非活性启动子内的AluI酶切位点也具有可及性。此外，常染色质与异染色质的可及性极为相近。细胞间的DNA可及性异质性对基因调控的染色质模型具有重要启示：转录因子结合位点仅在部分细胞中被阻断，而非全部细胞，因此既无法确保基因激活，也无法确保基因沉默。本数据集共包含44个样本。