RNA biology has reached an inflection point where understanding individual molecular processes is insufficient – we need integrated views of RNA's full lifecycle. Here, we present the first unified multi-omic platform combining translation dynamics, epitranscriptomic modifications, and degradation rates within the same cellular context, establishing a new paradigm for defining RNA function in vivo.
Our approach integrates innovative in-house technologies: enhanced Translation Complex Profile sequencing (eTCP-seq) coupled with our Stochastic Translation Efficiency (STE) AI algorithm deliver unprecedented accuracy in translation rate quantification. Direct RNA sequencing (DRS) with our CHEUI/SWARM tools map region-specific RNA modifications (m⁶A, m⁵C, Ψ, ac⁴C) at single-molecule resolution, while INDEGRA quantifies transcript-specific decay rates. This multi-dimensional RNA atlas was generated from the same sample material of naïve and glucose-starved yeast, ensuring perfect experimental coherence.
Our findings reveal remarkable coordination: 635 transcripts show synchronised changes in polysome association, with stress-responsive mRNAs exhibiting enhanced translation efficiency despite nutrient depletion – a counterintuitive finding that challenges conventional models. Hierarchical clustering of degradation rates identifies four distinct regulatory modules, each with unique epitranscriptomic signatures. Strikingly, transcripts encoding ribosomal proteins display coordinated m⁵C enrichment in 5'UTRs coupled with accelerated decay, suggesting epitranscriptome-mediated translational buffering. Meanwhile, stress-adaptive transcripts show pseudouridine accumulation correlating with both enhanced stability and translation efficiency.
Our multi-omic RNA integration provides AI systems with comprehensive training data embedding RNA sequence, structure, modifications, and functional outcomes, which is essential for predictive modelling of RNA function. Our RNA platform captures the true complexity of RNA regulation: a four-dimensional landscape where sequence, modifications, translation, and decay intersect dynamically.
Beyond fundamental discovery, our approach has immediate applications: identifying therapeutic RNA targets, optimising mRNA vaccine design through modification patterns that enhance stability and translation, and engineering synthetic RNA circuits with predictable behaviours. By revealing how cells naturally optimise RNA function through coordinated regulatory networks, we provide blueprints for next-generation RNA therapeutics and biotechnology applications.