Transcriptional pioneering by PBX transcription factors in adult neurogenesis

• Applicant: Professorin Dr. Dorothea Schulte
• Subject Area: Developmental Neurobiology
• Term: from 2017 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 389410162

Pioneer transcription factors are a special class of transcriptional regulators that can penetrate condensed chromatin and bind regulatory regions at a time when the overall chromatin structure still prevents access of other transcription factors. They thus mark silent genes for their later activation. Published observations made by my group together with unpublished results collected in the course of preparing for this application implicate PBX1 as pioneer factor during neurogenesis in the adult ventricular-subventricular zone (V-SVZ) stem cell niche. This is important, because linking Pbx1 to transcriptional pioneering has important implications for understanding its role in stem cell biology. However, transcriptional pioneering by PBX1 has only been examined for few candidate genes to date and no genome-wide test of this hypothesis exists. The present research plan aims to fill this gap, using adult neurogenesis as model. This is an excellent system to study transcriptional pioneering, because here new neurons are produced 'on demand', which requires a rapid response of resident stem-/progenitor cells to external stimuli. In the current application, I propose to perform three sets of experiments, which logically build on each other. First, I plan to perform ChIP-seq (chromatin IP followed by massive parallel sequencing) to generate a genome-wide binding map for PBX1 in V-SVZ derived stem- and progenitor cells before and after neuronal differentiation. These maps will be compared with ChIP-seq data for two classical histone modifications indicative of transcriptionally active and repressed chromatin. This study will be the first to investigate PBX1 transcriptional pioneering on a genome-wide level and under physiological conditions. Second, I will use these results to examine whether PBX1 can mark inactive genes for their later activation and active genes for their repression. This concept would explain how the acquisition of one cell fate and can be directly linked to the shut-down or repression of competing fates. Evidence exists that this concept holds true for the Olig2 gene, but a genome-wide test is needed to build a unifying model. Based on our published results, I expect to identify genes that are involved in neuronal versus oligodendroglial differentiation, which may make our results also applicable to the study of demyelinating diseases. Thirdly, I plan to use our ChIP-seq results to test the hypothesis that commitment to neuronal differentiation in the two major stem cell niches in the adult brain, the V-SVZ and the subgranular zone (SGZ), is linked to the later specification of a GABAergic or glutamatergic neuron subtype. Preliminary data on the neuron-specific gene Doublecortin argue in favor of this theory but genome-wide approaches are needed for a clearer answer. When proven correct, this hypothesis will add important new aspects to our understanding of how cell fate decisions are made in the adult or embryonic brain.

• DFG Programme: Research Grants
• International Connection: United Kingdom
• Co-Investigator: Privatdozent Dr. Vijay Tiwari