In eukaryotes, ribosome biogenesis is driven by the synthesis of the ribosomal RNA (rRNA) by RNA polymerase I (Pol-I) and is tightly linked to cell growth and proliferation. The 3D-structure of the rDNA promoter plays an important, yet not fully understood role in regulating rRNA synthesis. We hypothesized that DNA intercalators/groove binders could affect this structure and disrupt rRNA transcription. To test this hypothesis, we investigated the effect of a number of compounds on Pol-I transcription in vitro and in cells. We find that intercalators/groove binders are potent inhibitors of Pol-I specific transcription both in vitro and in cells, regardless of their specificity and the strength of its interaction with DNA. Importantly, the synthetic ability of Pol-I is unaffected, suggesting that these compounds are not targeting post-initiating events. Notably, the tested compounds have limited effect on transcription by Pol-II and III, demonstrating the hypersensitivity of Pol-I transcription. We propose that stability of pre-initiation complex and initiation are affected as result of altered 3D architecture of the rDNA promoter, which is well in line with the recently reported importance of biophysical rDNA promoter properties on initiation complex formation in the yeast system.

中文翻译：

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DNA嵌入剂通过损害转录起始来抑制真核核糖体RNA合成

在真核生物中，核糖体生物发生是由 RNA 聚合酶 I (Pol-I) 合成核糖体 RNA (rRNA) 驱动的，并且与细胞生长和增殖密切相关。rDNA 启动子的 3D 结构在调节 rRNA 合成中起着重要但尚未完全了解的作用。我们假设 DNA 嵌入剂/凹槽结合剂可能会影响这种结构并破坏 rRNA 转录。为了验证这一假设，我们研究了许多化合物在体外和细胞中对 Pol-I 转录的影响。我们发现嵌入剂/凹槽粘合剂在体外和细胞中都是 Pol-I 特异性转录的有效抑制剂，无论它们的特异性和其与 DNA 相互作用的强度如何。重要的是，Pol-I 的合成能力不受影响，表明这些化合物不针对启动后事件。值得注意的是，测试化合物对 Pol-II 和 III 转录的影响有限，证明了 Pol-I 转录的超敏性。我们建议，由于 rDNA 启动子的 3D 结构改变，会影响预起始复合物和起始的稳定性，这与最近报道的生物物理 rDNA 启动子特性对酵母系统中起始复合物形成的重要性非常吻合。