Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary.
PLoS One. 2019 Nov 20;14(11):e0224936. doi: 10.1371/journal.pone.0224936. eCollection 2019.
The restricted access of regulatory factors to their binding sites on DNA wrapped around the nucleosomes is generally interpreted in terms of molecular shielding exerted by nucleosomal structure and internucleosomal interactions. Binding of proteins to DNA often includes intercalation of hydrophobic amino acids into the DNA. To assess the role of constrained superhelicity in limiting these interactions, we studied the binding of small molecule intercalators to chromatin in close to native conditions by laser scanning cytometry. We demonstrate that the nucleosome-constrained superhelical configuration of DNA is the main barrier to intercalation. As a result, intercalating compounds are virtually excluded from the nucleosome-occupied regions of the chromatin. Binding of intercalators to extranucleosomal regions is limited to a smaller degree, in line with the existence of net supercoiling in the regions comprising linker and nucleosome free DNA. Its relaxation by inducing as few as a single nick per ~50 kb increases intercalation in the entire chromatin loop, demonstrating the possibility for long-distance effects of regulatory potential.
通常情况下，人们会从核小体结构和核小体间相互作用产生的分子屏蔽效应方面，来解释调控因子对其结合在核小体上的 DNA 结合位点的限制访问。蛋白质与 DNA 的结合通常包括疏水性氨基酸插入到 DNA 中。为了评估受限超螺旋在限制这些相互作用中的作用，我们通过激光扫描细胞术在接近天然条件下研究了小分子嵌入剂与染色质的结合。我们证明，DNA 的核小体限制超螺旋构象是嵌入的主要障碍。因此，嵌入化合物实际上被排除在染色质的核小体占据区域之外。嵌入剂与核小体外区域的结合受到的限制较小，这与包含连接子和无核小体 DNA 的区域中存在净超螺旋的情况一致。通过在每 50kb 左右诱导一个单链切口来松弛其超螺旋，可增加整个染色质环中的嵌入，证明了调控潜能的长程效应的可能性。
