In the model plant Arabidopsis thaliana, the primary root is initiated during early embryogenesis by the specification of a single extra-embryonic suspensor cell as hypophysis. This root founder cell divides asymmetrically and generates the quiescent centre, the future organizer cells in the root apical meristem. Specification of the hypophysis critically depends on the activity of the MONOPTEROS (MP) protein. In micro-array experiments to identify genes that are controlled by MP during root initiation, the host group found a strong enrichment (10-fold) of basic Helix-Loop-Helix (bHLH) transcription factors. Out of a total of 8 MP-dependent bHLH genes, two were further characterized and both show MP-dependent expression in the embryo at stages or in cells relevant to primary root initiation. These genes were named TARGET OF MONOPTEROS (TOM) 5 and 7. The identification of the TOM5 and 7 transcription factors as biologically relevant targets of the important root regulator MONOPTEROS provides a unique entry into uncovering the transcriptional networks that govern cell-cell communication and cell fate specification in the embryo. While the function of TOM5 and 7 has been established in root initiation, their mechanisms of action are completely unknown. Furthermore, as single mutants do not have strong mp-like defects, the process likely involves redundant bHLH functions. In this project, I propose to study the role and detailed mechanism of action of bHLH family members in MP-dependent root initiation using a wide range of multi-disciplinary techniques, either familiar to me by my previous research or well established in the host group. On one hand this will involve detailed mechanistic action of TOM5 and TOM7; identifying the interaction partners of TOM7 and determining the downstream genes that are controlled by TOM5 and TOM7. On the other hand I will identify novel and redundant bHLH factors involved in the process of root initiation during early embryogenesis.