Final Report Summary - NOTCH IN THYMOCYTES (Genome-wide dissection of the Notch-induced molecular program in developing T cells)
1. In contrast to the textbook view on Notch pathway, which suggests that Rbpj is constantly bound to DNA even in the absence of Notch signaling, our results revealed a Notch-dependent Rbpj binding in the majority of the sites.
2. We identified an unexpected group of ‘ephemeral’ Notch targets, which are induced in the earliest thymocytes but rapidly downregulated thereafter. Intriguingly, many of these genes were characteristic for transcriptional signatures of myeloid and/or NK cells.
3. We identified prominent Notch1 and Rbpj occupancy in the Tcrb enhancer which is likely to provide a missing molecular explanation of a previously described Tcrb recombination defect in Notch1-deficient mice. Consistently, short-term exposure of uncommitted progenitors to Notch ligands induced germline transcription of the Tcrb locus.
4. Although Notch signaling strength is known to drop upon pre-TCR expression, Notch acquires a mitogenic function at this transition, suggesting that a spectrum of its target genes may change. Our analysis suggests, that Notch targets in pre-TCR-expressing cells represent a subset of Notch targets prior to pre-TCR expression and no new Notch targets emerge at this transition.
In summary, these experiments resulted in the first systematic characterization of the Notch-induced molecular program in primary cells. The approaches pioneered in this study will allow characterization of Notch target genes in other primary cell types as well as in cancer models.