Transcriptional pioneering by PBX transcription factors in adult neurogenesis
Final Report Abstract
Embryonic development requires the orchestrated expression of thousands of genes to achieve the emergence of increasingly complex patterns and cell fates. Developmental transcription factors (TFs) that provide spatial-temporal coordinates and functional identities to cells play a key role in this process. Only little over 1,600 genes in the human genome code for TFs of which an estimated 30-40% have a role in embryogenesis. Developmental TFs must thus form multimeric complexes and engage in self-regulating transcriptional networks to drive developmental progression forward. A lasting question is how these multimeric TF complexes form, how they achieve specificity for distinct developmental tasks, and whether any hierarchy exists among the individual components involved. The role of ubiquitously expressed developmental TFs is thereby particularly puzzling. In the research project, we investigated this question taking the TALE-homeodomain TF PBX1 in neurogenic differentiation as example. We used freshly isolated stem- and progenitor cell cultures from the V/SVZ mouse adult neurogenic stem cell niche as model because of their relatively simple differentiation potential compared to embryonic cortical progenitor cells. We applied a broad spectrum of genome-, transcriptome- and proteome-wide techniques to these cells, including ATAC-sequencing, ChIP-sequencing for PBX1 and histone modifications, RNA-sequencing following various genetic manipulations, spatial RNA analysis of the V-SZV stem cell niche and migrating and differentiating neurons produced from these stem cells, as well as mass spectrometry analysis of PBX1-interacting proteins isolated by immunoprecipiation. Together with extensive computational analysis of data taken from public repositories, our results argue that PBX1 serves as a platform on which different multi-TF complexes assemble as cells differentiate. We also uncovered a novel interaction of PBX1 with class I bHLH TFs TCF3 and TCF4. Presence of PBX1-TCF3/4 complexes seems to favor progenitor cell proliferation and counteract cellular differentiation. Interestingly, although physical interaction of PBX1 and TCF3/4 is new, t(1:19) chromosomal translocation resulting in genomic PBX1::TCF3 fusion is a known driver of a particularly aggressive subtype of acute lymphoblastic leukemia (ALL). We therefore argue that the forced heterodimer of TCF3 and PBX1 resulting from the t(1;19) translocation does not simply join two independent TFs but rather stabilizes the association of proven cooperators into a fatal symbiosis that serves as a turning point for malignant transformation. In the course of this work, we compiled a tool-box for computational analysis of sequencing data, which we published separately. Also data leading up to the NAR study were published.
Publications
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Transcriptional cooperation of PBX1 and PAX6 in adult neural progenitor cells. Scientific Reports, 11(1).
Hau, Ann-Christin; Mommaerts, Elise; Laub, Vera; Müller, Tamara; Dittmar, Gunnar & Schulte, Dorothea
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Bioinformatics for wet-lab scientists: practical application in sequencing analysis. BMC Genomics, 24(1).
Laub, Vera; Devraj, Kavi; Elias, Lena & Schulte, Dorothea
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Integrated multi-omics analysis of PBX1 in mouse adult neural stem- and progenitor cells identifies a transcriptional module that functionally links PBX1 to TCF3/4. Nucleic Acids Research, 52(20), 12262-12280.
Laub, Vera; Nan, Elisabeth; Elias, Lena; Donaldson, Ian J.; Bentsen, Mette; Rusling, Leona A.; Schupp, Jonathan; Lun, Jennifer H.; Plate, Karl H.; Looso, Mario; Langer, Julian D.; Günther, Stefan; Bobola, Nicoletta & Schulte, Dorothea
