Genome-wide Identification of APETALA1 Regulated Genes during Early Flower Development in Arabidopsis. Arabidopsis thaliana

Plant inflorescence-to-floral phase transition is an important developmental stage, in which floral cell identities and many traits of reproductive organs are determined. Two MADS-domain transcription factors, APETALA1 (AP1) and CAULIFLOWER (CAL), have been known as master regulators controlling the early stage of the phase transition in Arabidopsis. In plants with loss-of-function alleles of ap1 and cal double mutations, flower development is heavily delayed at the flower initiation stage and accumulate a large number of inflorescence-like meristem cells compared to wild-type plants, resulting in a cauliflower-like phenotype. To facilitate investigation on molecular mechanisms during inflorescence-to-floral phase transition, an inducible system of synchronized floral development has been developed, in which ap1,cal inflorescence-like meristem cells express a fusion protein of AP1 and the hormone-binding domain of the rat glucocorticoid receptor (GR) driven by 35S constitutive promoter. When inflorescences of 35S:AP1-GR ap1,cal plants are treated by steroid hormone dexamethasone as the activator to allow the AP1-GR fusion protein translocate into nucleus, inflorescence-to-floral phase transition is triggered and plants start to produce hundreds of relatively synchronized floral buds. To explore molecular basis at early stage of flower development in Arabidopsis, we used the inducible system of synchronized floral development (35S:AP1-GR ap1,cal) to profile transcriptome change of meristem cells during inflorescence-to-floral phase transition by strand-specific RNA-sequencing. Overall design: Inflorescences of 35S:AP1-GR ap1,cal plants were treated with dexamethasone (Dex) for 2 hours as the actviator for induction of floral development as well as cycloheximide (Cyc) for 2 hours as mock treatment for inhibition of translation elongation. RNA libraries derived from non-treatment, 2-hour mock (Cyc) treatment and 2-hour inducer (Dex + Cyc) treatment samples with 3 biological replicates were sequenced by Illumina HiSeq 2500 with strand-specific RNA-sequencing protocol.