Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq

Shivali Patel, Alec N. Sexton, Madison S. Strine, Craig B. Wilen, Matthew D. Simon and Anna Marie Pyle ()
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Shivali Patel: Yale University
Alec N. Sexton: Yale University
Madison S. Strine: Yale School of Medicine
Craig B. Wilen: Yale School of Medicine
Matthew D. Simon: Yale University
Anna Marie Pyle: Howard Hughes Medical Institute

Nature Communications, 2023, vol. 14, issue 1, 1-11

Abstract: Abstract Compact RNA structural motifs control many aspects of gene expression, but we lack methods for finding these structures in the vast expanse of multi-kilobase RNAs. To adopt specific 3-D shapes, many RNA modules must compress their RNA backbones together, bringing negatively charged phosphates into close proximity. This is often accomplished by recruiting multivalent cations (usually Mg2+), which stabilize these sites and neutralize regions of local negative charge. Coordinated lanthanide ions, such as terbium (III) (Tb3+), can also be recruited to these sites, where they induce efficient RNA cleavage, thereby revealing compact RNA 3-D modules. Until now, Tb3+ cleavage sites were monitored via low-throughput biochemical methods only applicable to small RNAs. Here we present Tb-seq, a high-throughput sequencing method for detecting compact tertiary structures in large RNAs. Tb-seq detects sharp backbone turns found in RNA tertiary structures and RNP interfaces, providing a way to scan transcriptomes for stable structural modules and potential riboregulatory motifs.

Date: 2023
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DOI: 10.1038/s41467-023-38623-1

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