Exploring RNA’s Diverse Structural Landscape

A molecule’s structure can tell a lot about its purpose. Proteins with pockets might catalyse reactions, while those with cavities might transport ions. Like proteins, strands of ribonucleic acids (RNA) can also gain new functions when folded into complex 3D structures. But how do we figure out which RNA structures enable which processes?

A new paradigm in biomedical research offers a solution: structuromics. At A*STAR’s Genome Institute of Singapore, Associate Director Yue Wan and her lab are developing new genomic tools to support RNA structuromics, shedding new light on how RNAs work in pathogens and mammalian systems.

1. Structuromics is quite a fresh name in the field of omics research. Can you tell us more about it and what it aims to achieve from a public health perspective?

“Structuromics” is a field whereby thousands of molecular structures can be studied together as opposed to individually, granting a large-scale understanding of their structural and functional features. Consider animal breeds: if you study one cat, it is impossible to know if every cat has the same features, but if you extend that study to over thousands of cats, the features of different breeds become apparent. Using high throughput structure mapping, RNA structuromics reveals an RNA’s shape and how a drug might bind to it, inhibiting its function. It also uncovers certain structural features that increase protein production and stability, or regulate RNA life cycles, which can be used when designing RNA for specific therapeutic purposes.

2. What hidden insights can be deduced from studying RNA structure that could contribute to therapeutics and precision medicine?

Over decades, people have grown to appreciate how RNAs can fold into complex structures with various functions, just like proteins. The 1989 Nobel Prize in Chemistry was awarded to Sidney Altman and Thomas Cech for discovering RNAs could catalyse reactions through their structure. While this applied to ribozymes—a special RNA class—we’ve since learned most RNAs can likewise form structures that interact with and regulate other cellular factors.

Importantly, these structures make ideal targets for small molecules, which opens a vast novel therapeutic space where drugs could be designed for RNAs as well as proteins. Also, that structural knowledge means we can create customised RNA vaccines and gene replacement therapies.

3. How did RNA structuromics become your research focus?

I started working on RNA in 2007 as a graduate student in Howard Chang’s lab in Stanford University. Messenger RNAs (mRNAs) had then been extensively studied, but long noncoding RNAs (lncRNAs) were still mysterious. Unlike mRNAs, lncRNAs generally don’t produce proteins, but they do regulate scaffolding and transcription. Their structure seemed key to interactions within themselves and with other protein and nucleic acid regulators. However, traditional biochemical methods to study RNA structure were tedious, limiting our investigations to one RNA at a time.

Coincidentally, high throughput sequencing was taking off around then. We developed a protocol to capture single and double-stranded bases along an RNA, coupling that with deep sequencing. This was the first high throughput method to structurally probe thousands of RNA structures at once.

We first applied it to the yeast transcriptome; added improvements allowed us to see not only static pictures but also structural dynamics at different temperatures, and to apply the method to human transcriptomes. Since then, the field of RNA structuromics has exploded; there are many new chemical compounds to probe RNA’s different structural aspects. My research group remains deeply interested in developing technologies in this space.

With our collaborators, we have developed new strategies to find RNA sensors by mapping RNA-small molecule interactions, and a method to map intra- and inter-molecular RNA-RNA interactions in RNA viruses. More recently, we have ventured into the realm of single cells and molecules to assess RNA structural dynamics, regulation and heterogeneity within each cell.

4. Why should Singapore be excited about research in mRNA therapeutics? What other research is the Wan Lab currently focusing on?

It’s a new field with great potential and a lot of room for discovery and innovation. Nucleic acids can be rapidly engineered to encode transcripts of medical interest. RNA is also considered a safer therapeutic platform than DNA as it doesn’t usually integrate into genomes. Besides studying RNA structure, our lab is also engineering circular RNAs (circRNAs) to be better payloads for vaccines and gene replacement therapies. CircRNAs degrade differently from mRNAs; they are usually more stable and can produce proteins for a long time.

5. What do the usual structuromics research methodologies look like?

In general, there are two strategies to high throughput structure probing. The first tells you the “landscape” of RNA: whether bases are paired or otherwise. This is typically achieved by chemicals or enzymes that recognise double/single-stranded bases and ‘mark’ an RNA. These marks can be read by high throughput sequencing.

The second strategy reveals the ‘handshakes’ (interactions) between RNAs. When many ‘hands’ exist with unknown partners, we can join them together and map each ‘handshake’ to identify the pairs involved. This lets us identify handshakes even over a long distance along the same RNA, or between different RNAs, revealing important intracellular connections and how they can be disrupted in disease.  Beyond standard lab equipment, we rely heavily on deep sequencing. Extending this to a larger, population-level cohort will allow us to identify structural features unique to individuals, highlight RNA structure biomarkers, and eventually target RNA structures for treatment.

6. How might targeted genomics and therapeutics research be successfully translated to clinical applications?

As every person is unique, a one-size-fits-all approach might not work for different diseases. With growing understandings of individual genetics, medicine is becoming personalised as we can treat each patient according to their health needs.

Reliability and accuracy will be key to bringing genomics to the clinic. To this point, PRECISE and the Genome Institute of Singapore have set up an automated lab to process thousands of patient samples for genome sequencing.  Automation allows consistency in our experimental procedure and increased reliability in the data that is collected in the different patients.

7. What is your vision for the Wan Lab from the perspective of Singapore’s National Precision Medicine Programme?

Through studying RNA structures in healthy individuals and those with disease, we aim to uncover a structural basis of disease and find ways to better target RNA with drugs based on their structures, ultimately enabling a healthier Singaporean population.