Single-molecule reconstruction of eukaryotic factor-dependent transcription termination

Ying Xiong, Weijing Han, Chunhua Xu, Jing Shi, Lisha Wang, Taoli Jin, Qi Jia, Ying Lu, Shuxin Hu, Shuo-Xing Dou, Wei Lin (), Terence R. Strick (), Shuang Wang () and Ming Li
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Ying Xiong: Chinese Academy of Sciences
Weijing Han: Songshan Lake Materials Laboratory
Chunhua Xu: Chinese Academy of Sciences
Jing Shi: Nanjing University of Chinese Medicine
Lisha Wang: Songshan Lake Materials Laboratory
Taoli Jin: Songshan Lake Materials Laboratory
Qi Jia: Songshan Lake Materials Laboratory
Ying Lu: Chinese Academy of Sciences
Shuxin Hu: Chinese Academy of Sciences
Shuo-Xing Dou: Chinese Academy of Sciences
Wei Lin: Nanjing University of Chinese Medicine
Terence R. Strick: CNRS
Shuang Wang: Chinese Academy of Sciences
Ming Li: Chinese Academy of Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract Factor-dependent termination uses molecular motors to remodel transcription machineries, but the associated mechanisms, especially in eukaryotes, are poorly understood. Here we use single-molecule fluorescence assays to characterize in real time the composition and the catalytic states of Saccharomyces cerevisiae transcription termination complexes remodeled by Sen1 helicase. We confirm that Sen1 takes the RNA transcript as its substrate and translocates along it by hydrolyzing multiple ATPs to form an intermediate with a stalled RNA polymerase II (Pol II) transcription elongation complex (TEC). We show that this intermediate dissociates upon hydrolysis of a single ATP leading to dissociation of Sen1 and RNA, after which Sen1 remains bound to the RNA. We find that Pol II ends up in a variety of states: dissociating from the DNA substrate, which is facilitated by transcription bubble rewinding, being retained to the DNA substrate, or diffusing along the DNA substrate. Our results provide a complete quantitative framework for understanding the mechanism of Sen1-dependent transcription termination in eukaryotes.

Date: 2024
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DOI: 10.1038/s41467-024-49527-z

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