The role of FRUITFULL controlling cell cycle during early flower development revealed by time-series snRNA-seq experiments

Background: Starting from pools of undifferentiated cells, plants generate new organs postembryonically in response to external and endogenous signals. This requires a dynamic coordination of cell division with cellular growth and differentiation regulatory programs. However, little is known about how this coordination is achieved at the molecular level during flower development. Results: We used time-series single-nucleus RNA sequencing (snRNA-seq) experiments of synchronized Arabidopsis thaliana flower developmental stages to characterize the transcriptome dynamics and the connections between cell cycle and developmental regulatory programs during early flower development. The results show a bifurcation between transcriptional trajectories corresponding to cell cycle progression and floral development. We identify the regulation of the cell cycle inhibitor KIP-RELATED PROTEIN 2 (KRP2) by FRUITFULL (FUL) as a key regulatory point on this bifurcation point and validate the importance of this regulation in vivo. Conclusions: Our work illustrates how time-series snRNA-seq experiments can be used to identify bifurcation points between regulatory programs and to identify candidate regulators on these bifurcations. In particular, we identify the regulation of KRP2 by FUL as an important regulatory point to balance cell division and developmental differentiation in plants.