Spatial enhancer activation determines inhibitory neuron identity

Abstract

The mammalian telencephalon contains a tremendous diversity of GABAergic projection neuron and interneuron types, that originate in a germinal zone of the embryonic basal ganglia. How genetic information in this transient structure is transformed into different cell types is not yet fully understood. Using a combination ofin vivolineage tracing, CRISPR perturbation and ChIP-seq in mice, we found that the transcription factor MEIS2 favors the development of projection neurons through genomic binding sites in regulatory enhancers of projection neuron specific genes. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity towards these sites. In interneurons, the activation of projection neuron specific enhancers by MEIS2 and DLX5 is repressed by the transcription factor LHX6. When MEIS2 carries a mutation associated with intellectual disability in humans, it is less effective at activating enhancers involved in projection neuron development. This suggests that GABAergic differentiation may be impaired in patients carrying this mutation. Our research has uncovered a mechanism by which the selective activation of enhancers plays a crucial role in the establishment of neuronal identity, as well as in potential pathological mechanisms.

Nfib regulates progenitor competence in maturation of GABAergic neurons

“…NFI factors have been shown to regulate chromatin through various mechanisms, such as binding to nucleosomes (Chávez and Beato, 1997) and chromatin modifiers (Liu et al, 2001), opening chromatin (Adam et al, 2020), controlling chromatin loop boundaries, and directly altering histone modifications (Pjanic et al, 2013). In our data, Nfib promotes and forms partnerships with essential regulators of GABAergic IN and PN development, such as Tcf4 and Meis2 (Wang et al, 2022; Su et al, 2022; Dvoretskova et al, 2023), inducing more mature neuronal outcome as neurogenesis proceeds. We propose that Nfib may prime enhancer regions in APs of the GE, initiating chromatin remodelling and leading to stage-specific maturation competence.…”

“…If not through a sequential mechanism, what drives diversity within the GE? Other factors, such as the mode of cell-division (Petros et al, 2015;Kelly et al, 2018), cell-cycle length (Glickstein et al, 2007;Lodato et al, 2011;Zong et al, 2022), progenitor heterogeneity (van Heusden et al, 2021), spatial subdomains, and transcription factors that transduce patterning signals (Rubenstein and Puelles, 1994;Shimamura et al, 1995;Wichterle et al, 2001;Nery et al, 2002;Xu et al, 2004;Wonders and Anderson, 2006;Flames et al, 2007;Fragkouli et al, 2009;Flandin et al, 2010;Sandberg et al, 2016;Dvoretskova et al, 2023) et al, 2012), Gad2¡tm1(cre/ERT2)Zjh¿ (Gad2-CreER, JAX:010702) (Taniguchi et al, 2011), Ai65(RCFL-tdT)-D (Ai65D, JAX:021875) (Madisen et al, 2015). Embryos were staged in days post-coitus, with e0.5 defined as 12:00 of the day a vaginal plug was detected after overnight mating.…”

Massively parallelin vivoPerturb-seq reveals cell type-specific transcriptional networks in cortical development

“…hypPB enhances transgene expression in adult central and peripheral nervous system. The utility of applying Perturb-seq in vivo have been demonstrated in the past in embryonic brains (Dvoretskova et al, 2023;Jin et al, 2020). However, the need for a comprehensive in vivo screen platform for the adult central and peripheral nervous systems -especially pertinent to neurodegenerative diseases -still exists.…”

“…In vivo Perturb-seq uses a single-cell RNA-seq (scRNA-seq) readout in pooled CRISPR screens to assay transcriptomic changes in a systematic way: sampling the effect of each perturbation in each cell type. It has provided a scalable platform to dissect genetic mechanism with high-content, high-resolution transcriptomic readout in developing brains (Dvoretskova et al, 2023; Jin et al, 2020). Through gene expression analysis, this approach revealed convergent molecular networks and specific neuronal and glial cell types impacted by risk genes within the context of a developing brain.…”