Rapid depletion of chromatin and RNA processing factors reveals the limits of mRNA homeostasis

Cellular mRNA levels are at a dynamic equilibrium of transcription and degradation. Multiple studies show transcription and degradation rates compensate for each other to yield a similar level of cellular mRNA in various environmental and genetic conditions. However, this phenomena was mostly observed at steady-state, and the details and extent of the compensation remain poorly understood. Here, we examine the cellular response to mRNA perturbations in yeast using the auxin-inducible degradation system to rapidly remove dozens of key complexes in transcription, chromatin, and mRNA processing. Immediately following the depletion, we use metabolic labeling with 4tU coupled to mRNA sequencing to dynamically monitor total and nascent mRNA levels genome-wide with a temporal resolution of minutes. We find that cells mostly re-calibrate mRNA levels by changing their growth rate, and in certain cases cells grow with as little as 20% of the WT mRNA levels in similar environmental conditions. Specifically in the case of Sth1 - an essential and conserved chromatin remodeler - degradation rates remain high even though transcription rates decline significantly resulting in extremely low levels of cellular mRNA. However, when the main 5’-3’ RNA degradation pathway in eukaryotes is compromised (Xrn1/Dcp2 depletion) we observe for the first time a striking example of feedback in real time, wherein mRNA accumulates followed by transcription slowdown, resulting in a return to normal cellular mRNA levels. Our results provide detailed dynamics of the feedback and adaptation in the case of Xrn1/Dcp2 depletion, and suggest a novel link between mRNA homeostasis and cell-cycle.