Integrated expression analysis to elucidate the role of miR394 during flowering in Arabidopsis thaliana

Differential domains of activity of MIR394A and MIR394B gene promoters together with transcriptomic analysis of mutant plants, indicate that miR394 participates in the fine tuning of Arabidopsis flower development through regulation of transcription factors and chromatin remodeling factors. The initiation of flowering is a highly coordinated process that requires synchronization of endogenous plant developmental program with environmental signals through a complex interplay of genetic regulatory networks. We had previously demonstrated a role for miR394 in the regulation of flowering time, since mir394a mir394b plants harboring insertional mutations in the two MIR394 Arabidopsis genes exhibited an early flowering phenotype correlated with modified expression of flowering genes. In the present study we provide transcriptomic RNA-seq data and histologic staining of reporter lines to give further insight into the role of miR394 in the regulation of flowering in Arabidopsis thaliana and present an initial bioinformatic characterization of a newly identified lncRNA, which partially overlaps the MIR394B locus, and therefore we named MIR394B-ASSOCIATED TRANSCRIPT (MIRAST). We found that MIRAST expression is generally low and does not differ significantly between Col-0 and mir394a mir394b mutant plants, allowing for the transcriptomic analysis to focus specifically on the role of miR394 in Arabidopsis flowering. We identified 2405 differentially expressed genes, including 13 transcription factors involved in flower organ development and 7 chromatin remodeling factors. Histologic staining of reporter lines further demonstrated distinct domains of expression for MIR394A and MIR394B genes during flower development. Taken together, our results support a role for miR394 in the fine tuning of Arabidopsis flower development, likely through the regulation of key transcriptional and chromatin remodeling regulators.