The Circadian Clock in the Ageing Plant
The plant circadian clock is linked to development on every scale, from control of the cell cycle to determination of flowering time. Of particular importance is the photoperiodic pathway, through which changes of day length (photoperiod) are interpreted. Circadian regulation of this pathway is generally studied in seedlings. This allows researchers to test the effect of different environmental conditions, such as extreme photoperiods or temperature, more rapidly than in adult plants.  However, this approach fails to identify links between the photoperiodic pathway and other ageing-related processes, such as senescence. To close this knowledge gap, we collected data from Arabidopsis thaliana at two different timescales: the 'flowering' timescale and the 'daily' timescale. By shifting the photoperiod from short days (SD) to long days (LD), we induced flowering, via the photoperiodic pathway. We then sampled across 24h at 2, 7, and 12 days after this transition. We find that the regulation of senescence-associated genes begins soon after the transition from SD to LD. We explore how downstream targets of the circadian clock have changes in expression across the flowering timescale. Surprisingly, many genes shift from their time of peak expression, suggesting a widespread rewiring of the circadian clock's targets during the flowering transition. Overall design: We first grew Arabidopsis Ws-2 wild-type plants under short-day (8h light; 16h dark) conditions, for a total of 22 days. We then transitioned the plants to long-day (16h light; 8h dark) conditions. We collected samples across three days (the 2nd, 7th, and 12th days after the transition), at seven timepoints across each day (ZT 0, 1, 4, 8, 12, 16, 20). We performed RNA-seq on each sample to produce a 'timeseries of timeseries' of gene expression.