Time-course transcriptomes from shoot apex and leaves of Arabidopsis thaliana

In multicellular organisms, clock-controlled rhythms differ across tissues and organs; however, the molecular mechanisms that regulate this spatial specificity are not fully understood. Here, we compare circadian transcriptomes from the shoot apex and leaves of Arabidopsis thaliana and reveal that, despite sharing a common core clock composition, these two organs exhibit striking differences in their rhythmic gene expression landscapes.

Notably, rhythmic genes in the shoot apex tend to peak earlier than in leaves, mirroring the phase difference observed in core clock gene expression between the two organs. Our findings suggest that while organ-specific rhythmic gene sets are established independently of core clock transcript levels, their peak expression is governed by the phase of core clock transcript oscillations in each organ.