We study the gene expression programmes that underlie the acquisition of different fates by neural stem cells.
Which genes are induced or repressed when stem cells remain dormant, or self-renew, or differentiate? How are these genes regulated in a coordinated manner? How is the timing of gene expression controlled during the progression of cellular differentiation?
We use large-scale genomic approaches (RNA-Seq, ChIP-Seq, proteomics) to characterise gene expression programmes in mouse and human neural stem cells and their differentiated progenies, obtained either by FACS-purification from the embryonic or postnatal brain or from neural stem cell culture.
We examine the contribution of different families of transcription factors in the regulation of these gene expression programmes, asking, for example, if master transcription factors implement stem cell fates by mobilising networks of more specialised transcription regulators or by directly regulating effector molecules that are involved in the acquisition of cellular phenotypes.
We also investigate the molecular mechanisms that determine the range of target genes that are regulated by a master transcription factor in a particular context. This includes the mechanisms that control the switch of activity of the same factor in mitotic progenitors versus postmitotic neurons and the mechanisms that control the regulation of different targets at different times during progression of a differentiation programme.
We focus in particular on epigenetic mechanisms, such as posttranslational modifications of histones influencing chromatin compaction at target loci and the role of master transcription factors and other components of neurogenic programmes in recruiting chromatin modifying enzymes.
We also examine the role of post-translational modifications such as phosphorylations by signalling pathways, in the regulation of the binding of transcription factors to the DNA and their interactions with transcriptional co-regulators.
In the publications listed below, we have systematically characterised the regulatory elements (enhancers and promoters) active in self-renewing mouse neural stem cells, by genome-wide mapping of accessible DNA and of several histone modifications.
We have predicted, with motif search algorithms and machine learning, the transcription factor network recruited at these active elements and we have validated these predictions by demonstrating a role of the transcription factor Olig2 in activation of proliferation genes and suppression of differentiation and quiescence genes (Mateo et al. 2015).
We have also compared the enhancer elements that are active in proliferating versus quiescent neural stem cells, by genome-wide mapping of a histone modification and a co-activator in mouse neural stem cells cultivated in the presence of different signaling molecules (EGF and BMP4, respectively).
We used bioinformatics to predict that different transcription factor families are recruited at proliferation-specific and quiescence-specific enhancers respectively. We also identified NFIX as an essential transcription factor for regulation of quiescence-specific genes in culture and for maintenance of quiescence in stem cells of the adult mouse hippocampus in vivo (Martynoga et al., 2014).
We have identified, on a genome scale, the genes regulated by the proneural transcription factor Ascl1/Mash1 in the mouse embryonic brain and in neural stem cell cultures. Analysis of the regulated genes unexpectedly identified core cell cycle regulators (e.g. cyclins, cdks, E2f genes), which led to the demonstration of a novel function of this important regulator of neurogenesis in promoting the proliferation of progenitor cells in the embryonic brain (Castro et al., 2011).
Figure 2: example of an enhancer element in the Ccnd2 gene identified by the recruitment of the co-activator p300 and the histone modification H3K27ac that is occupied by the proneural factor Ascl1.