Erwin Graham S, Grieshop Matthew P, Bhimsaria Devesh, Do Truman J, Rodríguez-Martínez José A, Mehta Charu, Khanna Kanika, Swanson Scott A, Stewart Ron, Thomson James A, Ramanathan Parameswaran, Ansari Aseem Z
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, WI 53706.
Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):E7418-E7427. doi: 10.1073/pnas.1604847113. Epub 2016 Nov 8.
Targeting the genome with sequence-specific DNA-binding molecules is a major goal at the interface of chemistry, biology, and precision medicine. Polyamides, composed of N-methylpyrrole and N-methylimidazole monomers, are a class of synthetic molecules that can be rationally designed to "read" specific DNA sequences. However, the impact of different chromatin states on polyamide binding in live cells remains an unresolved question that impedes their deployment in vivo. Here, we use cross-linking of small molecules to isolate chromatin coupled to sequencing to map the binding of two bioactive and structurally distinct polyamides to genomes directly within live H1 human embryonic stem cells. This genome-wide view from live cells reveals that polyamide-based synthetic genome readers bind cognate sites that span a range of binding affinities. Polyamides can access cognate sites within repressive heterochromatin. The occupancy patterns suggest that polyamides could be harnessed to target loci within regions of the genome that are inaccessible to other DNA-targeting molecules.
用序列特异性DNA结合分子靶向基因组是化学、生物学和精准医学交叉领域的一个主要目标。由N-甲基吡咯和N-甲基咪唑单体组成的聚酰胺是一类合成分子，可通过合理设计来“读取”特定的DNA序列。然而，不同染色质状态对活细胞中聚酰胺结合的影响仍是一个未解决的问题，这阻碍了它们在体内的应用。在这里，我们利用小分子交联来分离与测序偶联的染色质，以直接在活的H1人胚胎干细胞内绘制两种生物活性和结构不同的聚酰胺与基因组的结合图谱。来自活细胞的全基因组视图显示，基于聚酰胺的合成基因组读取器结合具有一系列结合亲和力的同源位点。聚酰胺可以进入抑制性异染色质内的同源位点。占据模式表明，聚酰胺可用于靶向基因组中其他DNA靶向分子无法进入的区域内的位点。
