Identifizierung von Bifurkationspunkten der zellulären Reprogrammierung und reverse Engineering des Regulationsnetzwerkes der differentiellen Genexpression

Abstract

Cellular differentiation during sporulation of the lower eukaryote Physarum polycephalum (Amoebozoa) was investigated at the level of differential gene expression. During its life cycle this organism develops into a giant multinucleate cell, the so called plasmodium. All nuclei in this plasmodium behave synchronously concerning their state of cell cycle and transcription. This allows time series measurements of gene expression at the level of a single cell. By taking macroscopic samples from these plasmodia without disturbing their way to commitment and differentiation the gene expression levels of 35 sporulation relevant genes was analyzed at different time points during the sporulation process with the multiplex RT-PCR eXpress profiling method. Analyzing the time dependent changes in gene expression in Physarum polycephalum sporulation mutants revealed significant differences to wild type plasmodia. Individually different and stable states of gene expression in differentiating plasmodia could be identified by statistical data analysis. To study the co-regulation of genes an algorithm was implemented to assign the analyzed genes to jointly regulated groups. Based on the co-regulation the regulatory network was reconstructed and modeled as a Petri net. Different Physarum polycephalum sporulation mutants were fused with each other to search for somatic complementation effects. The gene expression levels in both halves of a fused plasmodium were analyzed separately and compared with the expression data of unfused plasmodia. We observed partial recovery of the wild type phenotype in fused plasmodia via effects of complementation. Based on the experimental data the hierarchy of certain differentiation specific blocks in the sporulation cascade has been analyzed and a model for regulation cascades in fused palasmodia was derived. The alternative ways of differentiation in individual Physarum polycephalum plasmodial cells during the sporulation process have been identified. These findings clearly support the theory of aWaddingtontype epigenetic landscape of gene regulation during commitment, cellular reprogramming and differentiation.