Post-transcriptional Regulation Coordinating Transcription and Translation During Circadian Oscillation and Stress Recovery in Plants

ABSTRACT Circadian rhythms orchestrate gene expression to align plant growth and development with daily environmental cycles. However, the post-transcriptional mechanisms that coordinate transcriptional and translational rhythmicity remain incompletely understood. To address this, we analyzed time-series transcriptome and translatome profiles in Arabidopsis seedlings, identifying 5,185 genes with rhythmicity at both levels. These genes were classified into four distinct groups based on phase and amplitude differences between transcription and translation. Circadian mRNAs with high oscillation amplitudes tended to undergo co-translational RNA decay (CTRD), whereas intronless genes displayed the lowest amplitudes, likely due to their mRNA instability and short half-lives. While CTRD and NAD⁺ capping modulate amplitude differences, intronless and circadian translational efficiency (TE) influence both phase and amplitude variations. Additionally, CTRD, NAD + capping and circadian TE facilitate fast recovery of heat-induced genes to normal hemostasias. Collectively, our findings demonstrate that these post-transcriptional regulation shapes both synchronized and decoupled transcription and translation during plants response to diel and environmental dynamics.