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

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 c...

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Bibliographic Details
Published in:Nature communications 2023-06, Vol.14 (1), p.3426-3426, Article 3426
Main Authors: Patel, Shivali, Sexton, Alec N., Strine, Madison S., Wilen, Craig B., Simon, Matthew D., Pyle, Anna Marie
Format: Article
Language:English
Subjects:
13
45/91
631/1647/2163
631/1647/514/1949
631/45/500
631/45/535
631/92/96
Cations
Cleavage
Gene expression
Humanities and Social Sciences
Interfaces
Magnesium
Modules
multidisciplinary
Next-generation sequencing
Nucleic Acid Conformation
Nucleotide Motifs
Phosphates
Ribonucleic acid
RNA
RNA - metabolism
Science
Science (multidisciplinary)
Structural members
Terbium
Terbium - metabolism
Terbium - pharmacology
Transcriptomes
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Summary: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 Mg 2+ ), which stabilize these sites and neutralize regions of local negative charge. Coordinated lanthanide ions, such as terbium (III) (Tb 3+ ), can also be recruited to these sites, where they induce efficient RNA cleavage, thereby revealing compact RNA 3-D modules. Until now, Tb 3+ 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. Compact RNA structural motifs control many aspects of gene expression, but methods for their identification are lacking. Here the authors present a sequencing-based terbium probing approach to detect complex 3D structural elements, which can be used to pinpoint potential riboregulatory elements.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-023-38623-1