Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes

Abstract

Developmental programs that generate the astonishing neuronal diversity of the nervous system are not completely understood and thus present a significant challenge for clinical applications of guided cell differentiation strategies. Using direct neuronal programming of embryonic stem cells, we found that two main vertebrate proneural factors, Ascl1 and Neurog2, induce different neuronal fates by binding to largely different sets of genomic sites. Their divergent binding patterns are not determined by the previous chromatin state but are distinguished by enrichment of specific E-box sequences which reflect the binding preferences of the DNA-binding domains. The divergent Ascl1 and Neurog2 binding patterns result in distinct chromatin accessibility and enhancer activity profiles that differentially shape the binding of downstream transcription factors during neuronal differentiation. This study provides a mechanistic understanding of how transcription factors constrain terminal cell fates, and it delineates the importance of choosing the right proneural factor in neuronal reprogramming strategies.

Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons

“…To understand the molecular mechanisms of general neuronal fate committed to CR neurons identities, we focus on the genetic network of some key transcription factors that may predominate the differentiation progression. Ebf2 is enriched in Cluster 2 and its target genes has been identified in Neurog2-induced neurogenesis from mESC assays recently (38). We found that 457 of the early phase C157 genes and 611 of the intermediate C0346 genes were the target genes of EBF2 during neural differentiation, implying that it might affect the molecular pathways of CR neuron differentiation (Table S1).…”

Next‐generation disease modeling with direct conversion: a new path to old neurons

“…Some data indicate that Ngn2, when using an appropriate conversion medium, not only binds most of the Ascl1 binding sites in fibroblasts, but also possesses many additional binding sites [30,33]. However, other data suggest that Ascl1 and Ngn2 possess divergent binding patterns that result in distinct chromatin states and different neuronal fates [34]. While further (meta-)analysis will likely shed more light on these different views, it is not surprising that the most efficient and reliable conversion strategies involve the combined expression of Ascl1 and Ngn2 [9,10,31,35].…”

“…1A). The epigenetic identity of the starting cell population and remnant signaling cues present during the fibroblast-to-iN transition state finally determine subtype identity [23,34]. In highly heterogeneous cell populations, such as astrocytes in the rodent brain or primary human fibroblasts, the subtype of the starting cell type was shown to determine subtype outcomes of the iNs [73].…”

“…Further, unlike for most other human cell types, primary human neuronal cultures of defined brain regions are not available for direct comparison, which further complicates the definition of gold standard criteria. By any means, the value of cell models should be measured by how well they perform their respective tasks, and these tasks might range from teaching us more about a complex disease, or how well they integrate into a neuronal circuit following transplantation [6,[33][34][35][36][37][38]114,115].…”

Atoh1 is repurposed from neuronal to hair cell determinant by Gfi1 acting as a coactivator without redistribution of its genomic binding sites

“…The advent of in vitro cell fate reprogramming has demonstrated that overexpression of specific TF combinations can be sufficient to drive specification of the same starting cells towards diverse cell types in the absence of other context-specific variables (Nakamori et al 2017;Pfisterer et al 2011;Zhao et al 2015;Masserdotti et al 2016). Therefore, cellular reprogramming provides a controlled system in which to investigate how TFs cooperate and modulate each other's functions for cell fate specificity in the absence of other differences in cellular context (Aydin et al 2019).…”