Sustained-input switches for TFs and microRNAs in Plant Development

Our lab has recently developed an algorithm for identifying over-represented circuits involving transcription factors, miRNAs, and non-TF coding genes within genome-scale networks.  The algorithm was computationally validated using Arabidopsis networks and compared with outcomes in other model organisms.  This algorithm has enabled us to discover prevalent autoregulatory gene circuits associated with developmental patterning, and to observe that while miRNA-mediated feed forward loop is a predominant theme in large eukaryotic genomes, this pulse-generating circuit may be specific to tightly regulated TF and miRNA binding in plants.  We have also used the algorithm to identify a gene circuit capable of creating a sustained input switch for a downstream TF or miRNA, and examine instances of this circuit where all components are expressed in the same cell types of developing Arabidopsis roots.  In this talk I will explain current results and discuss validation cases that have emerged with strong interest in the literature.