Analysis of the whole Arabidopsis genome sequence revealed that approximately 5% of the genes encode TFs (Riechmann et al., 2000 ). Since TFs play major roles in the regulation of many biological processes, increasing our knowledge of their interactions with other regulatory proteins and with the other 95% of genes of the genome will provide strategic insights toward the understanding of these processes. In this Update, we present an overview of the TF networks known to control cell identity during the three main aspects of root development (primary root meristem establishment and maintenance, root hair differentiation, and lateral root formation; Fig. 2 ). As the comprehension of these processes improves, it becomes increasingly evident that TFs must be considered at a higher level not just for their DNA-binding functions, but rather as crucial members of regulatory networks responsible for the transmission of positional information required for coordinated plant development. In the shoot apical meristem, multilevel gene networks have been established to explain the formation of leaves and flowers (Soltis et al., 2002 ; Engstrom et al., 2004 ). TFs represent key intersections in these frameworks. Their study allowed the discovery of new participant genes and provides new cues
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