Mapping higher-order RNA structures and intermolecular RNA–RNA interactions throughout the transcriptome is critical for understanding RNA functions. We developed KARR-seq, a chemical-assisted RNA proximity capture and sequencing technology that enables sensitive and accurate detection of the RNA structurome and functional RNA–RNA interactions.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Mortimer, S. A., Kidwell, M. A. & Doudna, J. A. Insights into RNA structure and function from genome-wide studies. Nat. Rev. Genet. 15, 469–479 (2014). A review that presents the relationship between RNA structures and functions.
Spitale, R. C. & Incarnato, D. Probing the dynamic RNA structurome and its functions. Nat. Rev. Genet. 24, 178–196 (2023). A review that summarizes methods to probe RNA structures and RNA–RNA interactions.
Ganser, L. R., Kelly, M. L., Herschlag, D. & Al-Hashimi, H. M. The roles of structural dynamics in the cellular functions of RNAs. Nat. Rev. Mol. Cell Biol. 20, 474–489 (2019). A review that describes the dynamic nature of RNA structures and explains how structure changes enable RNA functionality.
Weng, X. et al. Keth-seq for transcriptome-wide RNA structure mapping. Nat. Chem. Biol. 16, 489–492 (2020). This article reports N3-kethoxal for RNA labeling.
You, Q. et al. Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution. Nat. Biotechnol. 39, 225–235 (2021). This article reports dendrimer-mediated DNA conformation capture.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
This is a summary of: Wu, T. et al. KARR-seq reveals cellular higher-order RNA structures and RNA–RNA interactions. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-02109-8 (2024)
Rights and permissions
About this article
Cite this article
KARR-seq maps higher-order RNA structures and RNA–RNA interactions across the transcriptome. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-023-02110-1
Published:
DOI: https://doi.org/10.1038/s41587-023-02110-1