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

• Published in: Nature communications Vol. 14; no. 1; pp. 3426 - 11
• Main Authors: Patel, Shivali, Sexton, Alec N., Strine, Madison S., Wilen, Craig B., Simon, Matthew D., Pyle, Anna Marie
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09.06.2023; Nature Publishing Group; Nature Portfolio
• 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; Phosphates; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Structural members; Terbium; Transcriptomes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-38623-1

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.