PDF(Pubmed)
Abstract：
Micrococcal nuclease sequencing is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease and the requirement for high sequencing depth. Here, we present the nucleosome-based MNase accessibility (nucMACC) pipeline unveiling the regulatory chromatin landscape by measuring nucleosome accessibility and stability. The nucMACC pipeline represents a systematic and genome-wide approach for detecting unstable (\"fragile\") nucleosomes. We have characterized the regulatory nucleosome landscape in Drosophila melanogaster, Saccharomyces cerevisiae, and mammals. Two functionally distinct sets of promoters were characterized, one associated with an unstable nucleosome and the other being nucleosome depleted. We show that unstable nucleosomes present intermediate states of nucleosome remodeling, preparing inducible genes for transcriptional activation in response to stimuli or stress. The presence of unstable nucleosomes correlates with RNA polymerase II proximal pausing. The nucMACC pipeline offers unparalleled precision and depth in nucleosome research and is a valuable tool for future nucleosome studies.
摘要：
微球菌核酸酶测序是确定染色质结构和核小体定位的最新方法。由于核酸内切酶的AT依赖性序列偏差和对高测序深度的要求,数据分析是复杂的。这里,我们介绍了基于核小体的MNase可及性（nucMACC）管道，通过测量核小体可及性和稳定性来揭示调节性染色质景观。nucMACC管道代表了一种用于检测不稳定（“脆性”）核小体的系统和全基因组方法。我们已经描述了黑腹果蝇的调节核小体景观，酿酒酵母，和哺乳动物。表征了两组功能不同的启动子，一个与不稳定的核小体相关，另一个被核小体耗尽。我们表明，不稳定的核小体呈现核小体重塑的中间状态，制备可诱导基因用于响应刺激或应激的转录激活。不稳定核小体的存在与RNA聚合酶II近端暂停相关。nucMACC管道在核小体研究中提供了无与伦比的精度和深度，是未来核小体研究的宝贵工具。
