At the heart of neural tube patterning is a gene regulatory network (GRN). Graded Shh signalling regulates the expression of a group of transcription factors (TFs) that act as intermediaries in the interpretation of graded Shh signalling. Selective repressive and inductive interactions between pairs of transcription factors establish discrete changes in gene expression. This produces a transcriptional code that defines distinct progenitor domains and determines the subtype identity of neurons generated from each domain. Our goal is to identify the components and connections in this network and understand their function. Although many players are known, components and mechanisms remain to be discovered. We have contributed to this effort by determining the function of several TFs during neural development. We currently focus on understanding the underlying logic of the network and the structure of the functional sub-circuits that it contains.
Identifying and reconstructing the neural tube GRN
We are taking a systematic approach to identify the TFs that comprise the neural tube GRN by profiling the transcriptional responses of neural progenitors exposed to different levels and durations of Shh signalling. To obtain information about the network and to test predicted linkages we assay the effect of activating and inhibiting Shh signalling and perturbing the expression of specific transcription factors. Together these analyses allow us to understand the mechanism and underlying logic of gene regulation and to test these we construct and test mathematical models of the transcriptional network.
The comprehensive understanding of the neural tube GRN requires the identification of genomic targets of the key TFs, as well as of the regulatory regions that control their expression. To define the direct interactions between specific members of the network we are employing ChIP-seq and related techniques to identify sites bound by specific TFs in the GRN. These regions are investigated bioinformatically and tested using transgenic and gene editing approaches. We are interested in identifying the genomic elements in neural progenitors that are regulated by Shh and understanding how these elements function. These data, together with the transcriptome data will allow us to begin to reassemble the network that describes the transcriptional logic of the system