Activity-dependent gene expression in male and female neurons: 3D genome architecture, transcription and chromatin mechanisms
Activity-regulated gene expression, the sequential expression of immediate early genes (IEG) and secondary response genes (SRG), facilitates the conversion of external stimuli into a transcriptional response which in turn impacts on e.g. synapses to modulate post-stimulus neuron function. Like other genes, IEG and SRG are regulated by transcription factors that bind to regulatory elements that interact with their respective target genes in the context of the various levels of 3D genome organization (e.g. topologically associating domains or TADs, high frequency looping interactions). How TF binding, chromatin changes and long range interactions feed into enhancer activation, enhancer-promoter interactions and gene activation at these loci remains less clear. Also, how specificity at the level of TF binding to regulatory elements and of enhancer-promoter communication is achieved is not well understood. Here we will delineate the molecular mechanisms underlying changes in genome topology and gene activity at activity-regulated loci. To gain mechanistic insights, we will perturb key transcription factors (e.g. CTCF, c-Fos) and chromatin modifiers (e.g. Polycomb Group proteins (PcG, e.g. Eed), Lsd1, CBP) involved in activity-dependent gene expression, enhancer biology and various aspects of 3D genome organization using targeted protein degradation in in vitro differentiated excitatory neurons. We also aim to explore sex-specific activity-dependent gene expression. Sex bias in neurodevelopmental disorders is known to be linked to the X chromosome and several X-linked genes have been linked to neurodevelopmental disorders (including important chromatin factors such as the histone lysine demethylase Utx and DNA methylation binding protein MeCP2). In female mammals, one of the two X chromosomes is almost completely epigenetically silenced by a process termed X-chromosome inactivation (XCI), but several genes can escape XCI. Due to escape from XCI, the protein products of these genes could thus be present in different doses in female and male neurons. In general, very little is known about sex-specific modulation of gene regulation. We will thus also study how activity-dependent expression impacts on gene expression on the X chromosome and vice versa how dosage differences of X-encoded gene regulators impact on stimulus response. We will also perturb gene dosage of X-encoded factors in female cells to assess the contribution of dosage to neuronal gene regulation in the context of chromatin state and 3D genome organization. This will include important transcriptional regulators and epigenetic factors such as MeCP2 or factors involved in enhancer-promoter communication such as Med14 for which sex-specific disease phenotypes have already been reported.
Dr. Edith Heard,Heidelberg
European Molecular Biology Laboratory (EMBL)