Determining Ancient Gene Regulatory Networks by Systems Biology and Cross-Species Comparison

Transcription factors (TFs) trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. I will present a novel method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix (bHLH) TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. PpRSL1 is closely related to the A. thaliana TF RHD6 that is a regulator of root hair development. Interestingly, paralog pairs control root, respectively rhizoid development, in the two divergent lineages – yet only one of the two paralogs is involved in stem cell formation in the moss. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems.