Highlights 22 23 •Complete inventories of gene expression in stomatal differentiation state are elucidated 24 •MUTE switches stomatal patterning program initiated by its sister bHLH, SPEECHLESS 25 •MUTE directly induces cell-cycle genes and their direct transcriptional repressors 26 •Incoherent feed-forward loop by MUTE ensures the single division of a stomatal 27 precursor 28 29 30 SUMMARY 31 Precise cell division control is critical for developmental patterning. For the differentiation of a 32 functional stoma, a cellular valve for efficient gas exchange, the single symmetric division of an 33 immediate precursor is absolutely essential. Yet, the mechanism governing the single division 34 event remains unclear. Here we report the complete inventories of gene expression by the 35 Arabidopsis bHLH protein MUTE, a potent inducer of stomatal differentiation. MUTE switches 36 the gene expression program initiated by its sister bHLH, SPEECHLESS. MUTE directly 37 induces a suite of cell-cycle genes, including CYCD5;1, and their transcriptional repressors, 38 FAMA and FOUR LIPS. The architecture of the regulatory network initiated by MUTE represents 39 an Incoherent Type 1 Feed-Forward Loop. Our mathematical modeling and experimental 40 perturbations support a notion that MUTE orchestrates a transcriptional cascade leading to the 41 tightly-restricted, robust pulse of cell-cycle gene expression, thereby ensuring the single cell 42 division to create functional stomata.43 44 93 lineage cells and singular GCs, respectively (MacAlister et al., 2007; Ohashi-Ito and Bergmann, 94 2006). We thus hypothesized that MUTE governs the gene regulatory networks to create 95 stomata. To test this, we performed a genome-wide profiling of early MUTE-responsive genes.96 5 Comparison of SPCH and MUTE target genes revealed how MUTE disconnects stomatal-97 lineage cells from extrinsic inhibitory signals, thus 'locks in' the differentiation program. Contrary 98 to the known role of MUTE in terminating the proliferating meristemoids (Pillitteri et al., 2007), 99 our study identified cell cycle and cell division genes as overwhelming majorities of the MUTE 100 targets. MUTE directly binds to the promoters and upregulates novel and previously described 101 cell-cycle regulators of the GMC symmetric division process. At the same time, MUTE directly 102 binds to the promoters and upregulates FAMA and FLP, which in turn repress the cell-cycle 103 regulators. Our mathematical modeling predictions and experimental perturbations of network 104 motif demonstrate that an incoherent feed-forward loop mediated by MUTE, cell cycle regulators,
105and FAMA/FLP is sufficient to articulate the single symmetric division event with high fidelity.
106Our study establishes the role for MUTE in orchestrating a transcriptional cascade leading to 107 stomatal differentiation and defines a core regulatory circuit for the single symmetric division. 108 109 Results 110 111 MUTE induces and represses specific sets of transcriptomes