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Gene expression: high resolution visualization of transcription pausing

A Cryo-EM structure of RNA polymerase (grey) paused elongation complex bound to NusA (yellow).

Structural Basis for NusA Stabilized Transcriptional Pausing.

Guo X(1), Myasnikov AG(1), Chen J(2), Crucifix C(1), Papai G(1), Takacs M(1), Schultz P(1), Weixlbaumer A(3).

Mol Cell March 1, 2018

March 1, 2018

A key step in gene expression in all kingdoms of life is transcription of DNA into RNA. Transcription is carried out by an enzyme called RNA polymerase and is highly regulated by protein transcription factors and by the RNA transcript itself. Through structural studies, Albert Weixlbaumer's team in collaboration with Patrick Schultz has obtained a high-resolution reconstruction of a paused RNA polymerase with a structured RNA transcript that stabilizes the paused state. The complex is also bound to the transcription factor NusA, which stimulates both pausing and termination of transcription and plays a central role in this fundamental process. These results are published on March 01, 2018 in the journal Molecular Cell and featured on the cover.

The first step in the process of converting information stored in DNA into protein is the synthesis of an RNA molecule based on a DNA template by RNA polymerase. This step is essential for the expression of genes in all kingdoms of life and is highly regulated by transcription factors. Transcription is divided into initiation, elongation and termination phases. During elongation, RNA polymerase moves along the DNA template copying it into an RNA transcript. However, elongation is frequently interrupted by pauses, which regulate gene expression. Pausing is modulated by the RNA transcript itself and by protein transcription factors, both of which influence the rate of transcription.


Thanks to reconstructions obtained by high-resolution cryo-electron microscopy, a method to visualize individual molecules coupled with image processing and 3D reconstruction, Albert Weixlbaumer's team visualized the interactions between RNA polymerase, a nascent structured RNA transcript, and the bacterial transcription factor NusA for the first time. The structures reveal four interactions between the enzyme and NusA, explain how transcription is halted, how the structured RNA transcript stabilizes this state, and suggest how NusA stimulates pausing and termination of transcription. This work was possible through a collaboration with Patrick Schultz’s team.


Comparison of RNA polymerase at different stages of transcription provides a better understanding of the dynamic nature of this process, which is essential for gene expression, and thus is also a prime drug target. The result is also important because transcription factors play paramount roles in development while misregulation of transcription is the cause of many diseases.


This study was supported by the ERC and LabEx.

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