Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers
- 1Stanford University Department of Genetics, Stanford, California 94305
- 2Stanford University Department of Applied Physics, Stanford, California 94025
- 3Chan Zuckerberg Biohub, San Francisco, California 94158
- Correspondence: wjg{at}stanford.edu
SUMMARY
High-throughput sequencing methods have revolutionized our ability to catalog the diversity of RNAs and RNA–protein interactions that can exist in our cells. However, the relationship between RNA sequence, structure, and function is enormously complex, demonstrating the need for methods that can provide quantitative thermodynamic and kinetic measurements of macromolecular interaction with RNA, at a scale commensurate with the sequence diversity of RNA. Here, we discuss a class of methods that extend the core functionality of DNA sequencers to enable high-throughput measurements of RNA folding and RNA–protein interactions. Topics discussed include a description of the method and multiple applications to RNA-binding proteins, riboswitch design and engineering, and RNA tertiary structure energetics.
