Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.
Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.
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通过小分子 DNA 嵌入和纳米孔测序探测染色质可及性。
DOI：
10.1101/2024.03.20.585815
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Brooks,AngelaN
中科院分区：
文献类型：
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作者：
Bai,Gali;Dhillon,Namrita;Felton,Colette;Meissner,Brett;Saint-John,Brandon;Shelansky,Robert;Meyerson,Elliot;Hrabeta-Robinson,Eva;Hodjat,Babak;Boeger,Hinrich;Brooks,AngelaN
染色质组织和结构的全基因组鉴定通常通过测量潜在DNA对核酸酶或甲基转移酶的可及性来探测。这些方法要么只观察单个核小体的定位，要么依赖于大的酶来修饰或切割DNA。我们开发了加合物测序（Add-seq），这是一种通过用小分子当归素处理染色质来探测染色质可及性的方法，当归素优先嵌入不与核心核小体结合的DNA中。我们表明，当归素修饰的DNA的纳米孔测序是可能的，并允许可视化和分析具有不同染色质结构的长单分子。可以使用在未修饰和修饰的无染色质DNA上训练的神经网络模型从纳米孔电流信号数据检测当归素修饰。将Add-seq应用于酿酒酵母细胞核，我们确定了酵母中注释基因位点周围的可访问性的预期模式。我们还鉴定了在特定酵母基因座处显示不同染色质结构的单分子读数的个体簇，这证明了酵母群体的染色质结构的异质性。因此，使用Add-seq，我们能够分析酵母基因组中长分子的DNA可及性。
Genome-wide identification of chromatin organization and structure has been generally probed by measuring accessibility of the underlying DNA to nucleases or methyltransferases. These methods either only observe the positioning of a single nucleosome or rely on large enzymes to modify or cleave the DNA. We developed adduct sequencing (Add-seq), a method to probe chromatin accessibility by treating chromatin with the small molecule angelicin, which preferentially intercalates into DNA not bound to core nucleosomes. We show that Nanopore sequencing of the angelicin-modified DNA is possible and allows visualization and analysis of long single molecules with distinct chromatin structure. The angelicin modification can be detected from the Nanopore current signal data using a neural network model trained on unmodified and modified chromatin-free DNA. Applying Add-seq to Saccharomyces cerevisiae nuclei, we identified expected patterns of accessibility around annotated gene loci in yeast. We also identify individual clusters of single molecule reads displaying different chromatin structure at specific yeast loci, which demonstrates heterogeneity in the chromatin structure of the yeast population. Thus, using Add-seq, we are able to profile DNA accessibility in the yeast genome across long molecules.