Regulatory networks in plant stem cells: an integrated bioinformatic and developmental biology analysis

SHOOT MERISTEMLESS (STM) encodes a transcription factor in Arabidopsis essential for ensuring correct stem cell fate. STM is known to impinge on a number of key regulatory processes such as cytokinin synthesis and the cell cycle, and interacts with other core regulatory genes such as CUP-SHAPED COTYLEDON1 (CUC1). In this study inducible STM over-expression and RNAi-mediated downregulation over a time course experiment have been used to identify the genes which form STM's gene regulatory network (GRN). These results reveal for the first time how STM overexpression and knockout phenotypes are mediated and identified the temporal order of transcriptomic changes following STM over-expression. A Bayesian network approach further refined the GRN - identifying conditional dependencies among regulated TFs and core signalling components from an independent dataset (>2,000 experiments). Predictions of direct targets from the network have been tested, demonstrating a high degree of accuracy. Interplay between STM and CUC1 is a biologically interesting sub-module of the STM GRN, with unusual dynamics. Via gene expression and microscopy experiments it has been shown that STM positively regulates the CUC1-targetting microRNA miR164c. Mathematical modelling approaches show that this is consistent with a model in which the boundary is the site of highest STM mRNA production via CUC1, and STM movement with miR164c upregulation produces the observed spatial distributions of both proteins. These relationships recast the boundary zone as a particularly dynamic region of the shoot apical meristem (SAM) and significantly develop our understanding of STM developmental context