Gene Regulatory Networks Controlling Stem Cell Identity and Maintenance in the Arabidopsis thaliana Root

Development in multicellular organisms requires not only the production of specialized cell types but also mechanisms of coordination among them. Stem cells are ultimately the source of all cell types, and the balance between self-renewal and differentiation of their progeny regulates organ growth. Transcription factors and cell-to-cell signaling have a key role in coordinating these processes; however, how these transcriptional networks and signaling pathways control plant development is not completely understood. Thus, we aim to predict Gene Regulatory Networks (GRNs) important for stem cell identity and maintenance in the Arabidopsis thaliana root. We obtained a transcriptomic profile of all of the stem cell populations in the root using Fluorescence Activated Cell Sorting (FACS) coupled with RNA sequencing (RNA-seq). We then identified genes specifically expressed in one stem cell population as well as genes expressed in all or most of the stem cell populations. We hypothesized that the genes expressed in only one stem cell population have a role in stem cell identity, whereas genes expressed throughout the stem cell niche have a role in stem cell maintenance. To investigate how these identity and maintenance genes interact, we developed a computational pipeline that can infer GRNs from transcriptomic data. This pipeline combines spatial clustering, regression tree inference, and a directionality algorithm to predict the relationships between genes. By using this pipeline, we are able identify genetic pathways important for stem cell identity and maintenance.