A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites

Sumirtha Balaratnam, Curran Rhodes, Desta Doro Bume, Colleen Connelly, Christopher C. Lai, James A. Kelley, Kamyar Yazdani, Philip J. Homan, Danny Incarnato, Tomoyuki Numata and John S. Schneekloth ()
Additional contact information
Sumirtha Balaratnam: Chemical Biology Laboratory, National Cancer Institute
Curran Rhodes: Chemical Biology Laboratory, National Cancer Institute
Desta Doro Bume: Chemical Biology Laboratory, National Cancer Institute
Colleen Connelly: Chemical Biology Laboratory, National Cancer Institute
Christopher C. Lai: Chemical Biology Laboratory, National Cancer Institute
James A. Kelley: Chemical Biology Laboratory, National Cancer Institute
Kamyar Yazdani: Chemical Biology Laboratory, National Cancer Institute
Philip J. Homan: Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health
Danny Incarnato: Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen
Tomoyuki Numata: Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University
John S. Schneekloth: Chemical Biology Laboratory, National Cancer Institute

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: Abstract The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ1 riboswitch system, assessing sixteen diverse PreQ1-derived probes for their ability to selectively modify the class-I PreQ1 riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ1, X-ray crystallography and gel-based competition assays demonstrated the mode of binding of the ligand to the aptamer, and functional assays demonstrated that the probe retains activity against the full riboswitch. Transcriptome-wide mapping using Chem-CLIP revealed a highly selective interaction between the bacterial aptamer and the probe. In addition, a small number of RNA targets in endogenous human transcripts were found to bind specifically to 11, providing evidence for candidate PreQ1 aptamers in human RNA. This work demonstrates a stark influence of linker chemistry and structure on the ability of molecules to crosslink RNA, reveals that the PreQ1 aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ1, which is similar in structure to guanine, interacts with human RNAs.

Date: 2021
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DOI: 10.1038/s41467-021-25973-x

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