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

Author

Listed:
  • 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
    Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research)

  • Danny Incarnato

    (Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen)

  • Tomoyuki Numata

    (Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University
    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST))

  • John S. Schneekloth Jr

    (Chemical Biology Laboratory, National Cancer Institute)

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.

Suggested Citation

  • Sumirtha Balaratnam & Curran Rhodes & Desta Doro Bume & Colleen Connelly & Christopher C. Lai & James A. Kelley & Kamyar Yazdani & Philip J. Homan & Danny Incarnato & Tomoyuki Numata & John S. Schneek, 2021. "A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25973-x
    DOI: 10.1038/s41467-021-25973-x
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    1. Yoshiko Maida & Mami Yasukawa & Miho Furuuchi & Timo Lassmann & Richard Possemato & Naoko Okamoto & Vivi Kasim & Yoshihide Hayashizaki & William C. Hahn & Kenkichi Masutomi, 2009. "An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA," Nature, Nature, vol. 461(7261), pages 230-235, September.
    2. John A. Howe & Hao Wang & Thierry O. Fischmann & Carl J. Balibar & Li Xiao & Andrew M. Galgoci & Juliana C. Malinverni & Todd Mayhood & Artjohn Villafania & Ali Nahvi & Nicholas Murgolo & Christopher , 2015. "Selective small-molecule inhibition of an RNA structural element," Nature, Nature, vol. 526(7575), pages 672-677, October.
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