Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that NELF prevents Pol II elongation. Here, we report cryoelectron microscopy structures of Pol II-DSIF-NELF complexes with NELF in two distinct conformations corresponding to paused and poised states. The paused NELF state supports Pol II stalling, whereas the poised NELF state enables transcription elongation as it does not support a tilted RNA-DNA hybrid. Further, the poised NELF state can accommodate TFIIS binding to Pol II, allowing for Pol II reactivation at paused or backtracking sites. Finally, we observe that the NELF-A tentacle interacts with the RPB2 protrusion and is necessary for pausing. Our results define how NELF can support pausing, reactivation, and elongation by Pol II.

中文翻译：

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独特的负延伸因子构象调节RNA聚合酶II启动子近端暂停

后生动物基因表达调控涉及基因启动子近端区域的 RNA 聚合酶 (Pol II) 暂停，并通过 DSIF 和 NELF 稳定。当延伸因子耗尽时，NELF 似乎伴随着 Pol II 延伸经过暂停位点；然而，先前的研究表明 NELF 可以阻止 Pol II 延伸。在这里，我们报告了 Pol II-DSIF-NELF 复合物与 NELF 的冷冻电镜结构，其具有两种不同的构象，分别对应于暂停和平衡状态。暂停的 NELF 状态支持 Pol II 停滞，而平衡的 NELF 状态则支持转录延伸，因为它不支持倾斜的 RNA-DNA 杂交。此外，平衡的 NELF 状态可以适应 TFIIS 与 Pol II 的结合，从而允许 Pol II 在暂停或回溯位点重新激活。最后，我们观察到 NELF-A 触手与 RPB2 突起相互作用，并且是暂停所必需的。我们的结果定义了 NELF 如何支持 Pol II 的暂停、重新激活和延长。