Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.

While transcription and translation have been shown to be coordinated with mRNA decay across various single-gene studies, their global coordination remains poorly defined. Therefore, we utilize rifampicin sequencing experiments in Caulobacter crescentus to measure genome-wide mRNA lifetimes and analyze the impact of transcription and translation. Based on the RNA polymerase elongation speed, we identify that approximately 20% of the transcriptome is cotranscriptionally degraded. To investigate translation's impact on mRNA decay, we find that translation efficiency measured by ribosome profiling correlates with mRNA lifetime. We compare the 5' P cleavage sites to ribosome occupancy and find that cleavage sites occur preferentially in regions of low ribosome occupancy. Using the translation initiation inhibitor retapamulin, which traps ribosomes at the start codon, and chloramphenicol, which arrests elongating ribosomes, we show that ribosomes directly protect the occupied mRNA regions. Taken altogether, mRNA decay is globally interconnected with transcription and translation.