斯坦福大学William J. Greenleaf研究团队揭示真核生物中染色质可及性的长距离单分子图谱。相关论文2020年2月10日发表于国际顶尖学术期刊《自然—方法学》。

课题组已经开发了一种用于分析单个染色质纤维可及性的方法，这是一种单分子、长片段的染色质图谱测序测定法（SMAC-seq），可以促进在多碱基程度上同时的、高分辨率的、单分子染色质状态评估。他们的策略是基于结合低序列特异性DNA甲基转移酶的开放染色质区域的优先甲基化（在这种情况下为EcoGII，N6-甲基腺苷（m6A）甲基转移酶）和纳米孔测序技术直接读取DNA修饰。他们证明，聚合的SMAC-seq信号可匹配批量水平的可及性测量，观察单分子核小体和转录因子保护印记，并量化远端基因组元件的染色质状态之间的相关性。

据悉，映射开放染色质区域已经成为鉴定真核生物中活跃调控元件的一种广泛使用工具。但是，受DNA片段化和短片段测序的限制，现有方法无法提供有关大规模染色质状态的信息，也无法揭示远端调控元件状态之间的协调性。

附：英文原文

Title: Long-range single-molecule mapping of chromatin accessibility in eukaryotes

Author: Zohar Shipony, Georgi K. Marinov, Matthew P. Swaffer, Nicholas A. Sinnott-Armstrong, Jan M. Skotheim, Anshul Kundaje, William J. Greenleaf

Issue&Volume: 2020-02-10

Abstract: Mapping open chromatin regions has emerged as a widely used tool for identifying active regulatory elements in eukaryotes. However, existing approaches, limited by reliance on DNA fragmentation and short-read sequencing, cannot provide information about large-scale chromatin states or reveal coordination between the states of distal regulatory elements. We have developed a method for profiling the accessibility of individual chromatin fibers, a single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq), enabling the simultaneous, high-resolution, single-molecule assessment of chromatin states at multikilobase length scales. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases with low sequence specificity, in this case EcoGII, an N6-methyladenosine (m6A) methyltransferase, and the ability of nanopore sequencing to directly read DNA modifications. We demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule nucleosome and transcription factor protection footprints, and quantify the correlation between chromatin states of distal genomic elements.

DOI: 10.1038/s41592-019-0730-2

Source: https://www.nature.com/articles/s41592-019-0730-2