Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

Doo Nam Kim, Bernhard C. Thiel, Tyler Mrozowich, Scott P. Hennelly, Ivo L. Hofacker, Trushar R. Patel () and Karissa Y. Sanbonmatsu ()
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Doo Nam Kim: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory
Bernhard C. Thiel: Department of Theoretical Chemistry, University of Vienna
Tyler Mrozowich: Alberta RNA Research & Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge
Scott P. Hennelly: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory
Ivo L. Hofacker: Department of Theoretical Chemistry, University of Vienna
Trushar R. Patel: Alberta RNA Research & Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge
Karissa Y. Sanbonmatsu: Theoretical Biology and Biophysics Group, Los Alamos National Laboratory

Nature Communications, 2020, vol. 11, issue 1, 1-13

Abstract: Abstract Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome, playing important roles in development and disease. However, our understanding of structure-function relationships for this emerging class of RNAs has been limited to secondary structures. Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Braveheart (Bvht), and its complex with CNBP (Cellular Nucleic acid Binding Protein). Using small angle X-ray scattering (SAXS), we elucidate the ensemble of Bvht RNA conformations in solution, revealing that Bvht lncRNA has a well-defined, albeit flexible 3-D structure that is remodeled upon CNBP binding. Our study suggests that CNBP binding requires multiple domains of Bvht and the RHT/AGIL RNA motif. We show that RHT/AGIL, previously shown to interact with CNBP, contains a highly flexible loop surrounded by more ordered helices. As one of the largest RNA-only 3-D studies, the work lays the foundation for future structural studies of lncRNA-protein complexes.

Date: 2020
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DOI: 10.1038/s41467-019-13942-4

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