Transcriptome dynamics to unravel PC12 cell fate decisions Abstract: The PC12 cell line is a well established cell model system for analysing cell fate decisionmaking processes. When stimulated with the growth factor EGF the cells proliferate increasingly when stimulated with the nerve growth factor NGF the cells differentiate into sympathetic like neurons. Both processes are regulated via the ERK MAPK pathway. In this context signal duration of activated ERK seems to be the key mechanism for the emergence of the distinct cell fates. Whereas NGF stimulation results in sustained ERK activation and neuronal differentiation of the cell line EGF stimulation activates ERK transiently and results in enhanced cell proliferation. How the temporal dynamics of ERK signalling are encoded and translated in order to specify cell fates has not been fully understood yet. <br>This thesis is the first comparison of the EGF and NGF induced transcriptome of PC12 cells on a time scale of 24 hours with high sample density. It was shown that the EGF and NGF stimulus activate a very similar set of genes which initiates and modulates the cell fate decision. These genes’ expression dynamics however were different depending on the stimulus used: EGF stimulation induced a short impulse like gene expression pattern whereas NGF stimulation resulted in a long sustained response. In line with previous studies it was demonstrated that immediate early genes such as Egr1 Fos and Junb show an increased stability in the case of NGF stimulation. It was shown that this is most likely due to a delayed negative transcriptional feedback via Fosl1 Atf3 Maff Klf2 und Zfp36l2. Moreover it was demonstrated that both cell fates proliferation as well as differentiation are not solely dependent on the ERK MAPK pathway. Within the first hour after stimulation with EGF cross talk between the MAPK and PI3K pathways seems necessary in order to induce enhanced cell proliferation. After stimulation with NGF a more complex and sequential activation of different pathways was identified. In this context the activation of the Il6 pathway and the uPA uPAR complex seems to be of special importance. The activation of these two pathways was exclusively seen after NGF stimulation which encourages further research to gain a deeper understanding of their function in the process of neuronal differentiation. Additionally Dusp6 was identified as a potentially important modulator of the PC12 cell fate. In summary this thesis analyses and compares the EGF and NG ...