Transcriptional priming in neuronal diversification

Through her project Transcriptional priming in neuronal diversification, IMP group leader Luisa Cochella aims to understand the gene regulatory principles underlying the specification of cell types in an animal during embryonic development. In order to generate the many different cell types that form an animal from a single genome, each cell has to express a distinct set of genes, encoding specific structural and functional components that make each cell type unique. The expression of these gene sets is controlled by transcription factors that typically act in a combinatorial way, with two or more factors acting together to activate expression of a gene. The combinatorial activity of transcription factors enables the production of a large cellular diversity. Cochella and colleagues had previously described a novel mode of combinatorial activity of transcription factors, in which two transcription factors act on a gene at different timepoints during the development of a cell, several cell divisions apart. The first transcription factor primes the gene and the second can then boost its expression a few cell divisions later. This mechanism enables a new dimension in which transcription factor activity can be combined to increase cellular diversity. One example is the generation of morphologically symmetric pairs of neurons with asymmetric properties in the brain of the nematode worm C. elegans. But this mechanism likely acts in multiple developmental contexts, for example in the vertebrate retina in which different progenitor cells are primed early in development, biasing them towards the production of different types of retinal cells. The project of Luisa Cochella aims to illuminate our understanding of the mechanism and impact of transcriptional priming on the generation of neuronal diversity during development. Cochella and her Team will address this using C. elegans, a unique experimental system with a well-defined nervous system and a fully mapped developmental cell lineage. Apart from generating valuable knowledge for future research, the results will also be important for current efforts to directly generate different cell types in vitro.

Development of multicellular organisms relies on the generation of hundreds of diverse cell types, each with specialized properties and functions. Different cell types are defined by the expression of unique combinations of proteins called transcription factors (TFs). TFs activate transcription of multiple genes that together give each cell type its unique features. TFs work primarily in combinations of two or more, to achieve transcription of their target genes. Combinatorial activity enables the generation of a large cellular diversity, greater than the number of TFs encoded in the genome. Mechanistically, combinatorial function of TFs is achieved when two or more factors bind together the same piece of DNA to recruit and activate the transcription machinery, whereas binding of individual TFs is unable to promote transcription. However, we previously discovered that two TFs can act combinatorially on the same gene although one acts early in development and the second only acts hours later. This finding meant that the power of TF combinations should also be considered over time, having important implications for understanding how cellular diversity is generated during development. However, the molecular mechanism for this temporal combination was unknown and this is what we set out to explore here. The system we used is the nervous system of the nematode-worm Caenorhabditis elegans, consisting of 302 nerve cells, most of which occupy left/right symmetric positions in the worm brain. Our brains have different functions in the left and right hemispheres, similarly, the worm nervous system shows lateral asymmetry. Specifically, a pair of sensory neurons called ASE is functionally asymmetric, with the neuron on the left sensing different ions than the one on the right. This functional difference is established by the temporal combination of TFs described above and provided a tractable system to explore its mechanism. Specifically, both left and right ASE neurons express a TF called CHE-1. However, only the cell that gives rise to the left ASE also expresses another TF called TBX-37/38 much earlier during development. The combined activity of TBX-37/38 and CHE-1 over time, enable the left ASE to activate transcription of genes that is different from the right ASE (that never expresses TBX-37/38 during its development). We found that early TBX-37/38 activity changes the ability of a gene to be further activated by CHE-1. Specifically, TBX-37/38 binding to a gene locus makes the DNA more accessible such that when the TF CHE-1 comes on later, it can bind to that locus even though TBX-37/38 is no longer there. This means there is a molecular memory established by the early TF activity. We found some of the players for the establishment and maintenance of this memory, which forms the basis for temporal combinatorial activity of TFs.