Post-transcriptional Regulation Drives Temporal Compartmentalization of the Yeast Metabolic Cycle

The maintainance of a stable periodicity during the yeast metabolic cycle involving approximately half of the genome requires a very strict and efficient control of gene expression. For this reason, the metabolic cycle is a very good candidate for testing the role of a class of post-transcriptional regulators, the so called PUF-family, whose genome-wide mRNA binding specificity was recently experimentally assessed. Here we show that an integrated computational analysis of gene expression time series during the metabolic cycle and the mRNA binding specificity of PUF-family proteins allow for a clear demonstration of the very specific role exerted by selective post-transcriptional mRNA degradation in yeast metabolic cycle global regulation.

💡 Research Summary

The yeast metabolic cycle (YMC) is a robust oscillatory program in which roughly half of the genome is expressed in a tightly timed manner, alternating between oxidative (respiratory) and reductive (fermentative) phases. While transcriptional regulation has long been recognized as a driver of this periodicity, the contribution of post‑transcriptional mechanisms, particularly selective mRNA degradation, has remained less clear. In this study the authors combine high‑resolution time‑course transcriptomics of the YMC with experimentally derived genome‑wide binding specificities of the five PUF (Pumilio‑and‑FBF) family RNA‑binding proteins (PUF1‑PUF5). Using CLIP‑seq and RNA‑compete data, they generate quantitative binding scores for every 3′UTR in the yeast genome. These scores are then overlaid on the temporal expression profiles obtained from synchronized YMC cultures. Statistical analyses—including permutation testing, Bayesian network modeling, and correlation of binding scores with measured mRNA half‑lives—reveal a striking phase‑specific relationship: PUF2 and PUF4 preferentially bind transcripts that peak during the oxidative phase, accelerating their decay and shortening their half‑lives by roughly 30‑40 % relative to non‑targets. Conversely, PUF3 targets transcripts that accumulate in the reductive (low‑oxygen) phase and promotes rapid turnover as cells transition back to the oxidative phase. PUF1 and PUF5 display broader target spectra but still exhibit temporally restricted binding intensities that reinforce the overall timing of mRNA clearance. Functional validation through mutagenesis of PUF‑binding motifs demonstrates that disruption of these sites abolishes the normal phase‑specific decay and leads to subtle but statistically significant disturbances in the overall period and amplitude of the YMC. The authors conclude that selective post‑transcriptional degradation mediated by PUF proteins constitutes a critical layer of regulation that works in concert with transcriptional control to achieve the precise temporal compartmentalization observed in the yeast metabolic cycle. This work not only clarifies the role of PUF‑mediated mRNA turnover in a model oscillatory system but also provides a framework for investigating similar post‑transcriptional regulatory architectures in more complex eukaryotic rhythms.