Research Overview

RNA is far more than a passive messenger between DNA and proteins—it encodes a dynamic regulatory layer that shapes gene expression across all stages of its life cycle. My research focuses on decoding the “RNA language”, integrating RNA sequence and structure to understand how gene regulation adapts to environmental change.

Our group develops cutting-edge experimental and computational technologies to uncover how RNA structure controls transcription, RNA processing, translation, and degradation. We combine in vivo RNA structuromics, single-molecule approaches, and artificial intelligence to reveal fundamental regulatory mechanisms and translate them into applications in crop resilience and RNA therapeutics.

Ultimately, we aim to build an RNA-based molecular design framework that enables precise engineering of gene expression for agriculture and beyond.

Research Themes

1. RNA Structure as a Regulatory Code

We investigate how RNA structure acts as a regulatory layer controlling gene expression across:

• Transcription
• RNA processing (splicing and polyadenylation)
• Translation
• RNA stability and degradation

Our work has shown that subtle structural features in RNA can determine gene expression outcomes, providing a new paradigm for understanding molecular regulation.

2. RNA Structure Dynamics in Living Cells

RNA structures are highly dynamic and responsive to environmental cues.

We develop technologies to:

• Profile RNA structures in vivo
• Resolve RNA conformations at single-molecule resolution
• Understand how structural changes regulate biological processes

These approaches allow us to move beyond population averages and uncover heterogeneous RNA conformations with distinct functions.

3. RNA Structures in Environmental Adaptation

We explore how RNA structure enables plants to respond to environmental stress, particularly temperature.

Our work has demonstrated that:

• RNA G-quadruplex structures regulate translation and stability
• RNA structural changes contribute to plant adaptation to cold environments
• Natural genetic variation can alter RNA structure and influence traits such as flowering time

4. AI for Decoding RNA Language

We are developing RNA AI foundation models to decode the rules governing RNA function.

Our model, PlantRNA-FM, integrates:

• RNA sequence
• RNA structure
• Large-scale transcriptomic data

This enables prediction of:

• Functional RNA motifs
• Effects of mutations on RNA structure
• Regulatory outcomes across the transcriptome

5. RNA-Based Molecular Design for Climate Resilience

A major goal of our research is to translate RNA biology into real-world applications.

We aim to:

• Identify RNA “codes” underlying environmental adaptation
• Predict how sequence variation alters RNA structure and function
• Design optimized RNA sequences to enhance crop tolerance

Using genome editing and computational design, we are developing a predict–validate–optimise pipeline for engineering climate-resilient crops.

Key Achievements

• Developed in vivo RNA structure profiling technologies revealing regulatory roles in RNA processing
• Discovered structural mechanisms underlying microRNA-mediated RNA degradation
• Identified RNA G-quadruplex structures in living plant cells and their role in environmental adaptation
• Pioneered single-molecule RNA structure profiling (smStructure-seq)
• Established one of the first RNA AI foundation models (PlantRNA-FM)
• Translated RNA structural insights into RNA-guided antiviral and gene silencing strategies

Vision

Our long-term vision is to establish a new framework for biology based on RNA codes, integrating sequence, structure, and function.

By combining RNA biology, artificial intelligence, and molecular design, we aim to:

• Transform understanding of gene regulation
• Enable predictive biology
• Deliver innovative solutions for climate-resilient agriculture and RNA therapeutics

Collaboration & Impact

Our work is highly interdisciplinary, spanning:

• Plant biology
• RNA biophysics
• Computational biology
• AI and machine learning

We actively collaborate with international partners to develop next-generation technologies and applications, and we are committed to building open-access datasets and tools for the wider scientific community.