A multilayered regulation of stem cell gene expression by EMB1579 defines root meristem function.

In the Arabidopsis root meristem, stem cell maintenance relies on the combined activity of transcription factor networks. The transcriptional regulator EMBRYO DEFECTIVE 1579 (EMB1579) controls many aspects of plant growth. The molecular mechanisms underlying its function in root development, and tissue patterning remain elusive. Here, we show that EMB1579 is required for stem cell maintenance and cell division orientation in the root meristem. EMB1579 modulates the function of two root stem cells' regulatory modules, PLETHORAS and SCARECROW-SHORT-ROOT, in a process that involves transcriptional regulation and post-transcriptional modification. We demonstrate that EMB1579 acts as a catalyst for stem cell gene expression, and its activity is fine-tuned through physical association with the RNA splicing factors; importantly, we unveil that the formation of nuclear condensates is essential for regulating the expression of root stem cell genes. Our data unveil a mechanism by which EMB1579 regulates stem cell determinants in the root meristem. To investigate the role of EMB1579 in regulating the expression of genes involved in root growth and development, we performed RNA sequencing of wild-type (Col-0) and two emb1579 mutant lines (emb1579-1 and emb1579-3), using three biological replicates for each.