Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

Abstract

BackgroundCellular differentiation programs are controlled, to a large extent, by the combinatorial functioning of specific transcription factors. Cortical projection neurons constitute the major excitatory neuron population within the cortex and mediate long distance communication between the cortex and other brain regions. Our understanding of effector transcription factors and their downstream transcriptional programs that direct the differentiation process of cortical projection neurons is far from complete.ResultsIn this study, we carried out a ChIP-Seq (chromatin-immunoprecipitation and sequencing) analysis of NEUROD2, an effector transcription factor expressed in lineages of cortical projection neurons during the peak of cortical excitatory neurogenesis. Our results suggest that during cortical development NEUROD2 targets key genes that are required for Reelin signaling, a major pathway that regulates the migration of neurons from germinal zones to their final layers of residence within the cortex. We also find that NEUROD2 binds to a large set of genes with functions in layer-specific differentiation and in axonal pathfinding of cortical projection neurons.ConclusionsOur analysis of in vivo NEUROD2 target genes offers mechanistic insight into signaling pathways that regulate neuronal migration and axon guidance and identifies genes that are likely to be required for proper cortical development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1882-9) contains supplementary material, which is available to authorized users.

The transcription factor NeuroD2 coordinates synaptic innervation and cell intrinsic properties to control excitability of cortical pyramidal neurons

“…) Recent work, published during preparation and review of this article, has used ChIP‐seq to identify gene expression changes during embryonic development (E14.5) in NeuroD2 null embryos (Bayam et al . ). Interestingly, taken together with our results, the data suggest that NeuroD2 may affect expression of different genes depending upon developmental age of neurons.…”

“…It will be interesting to determine in future experiments what type of inhibition is specifically regulated by NeuroD2 transcription and discover exactly what the mechanism of stabilization is downstream of GRPR activation. Furthermore, are these processes recapitulated in adult-born neurons as it is believed that similar developmental processes must be evoked during circuit integration in the developed brain (Scobie et al 2009) Recent work, published during preparation and review of this article, has used ChIP-seq to identify gene expression changes during embryonic development (E14.5) in NeuroD2 null embryos (Bayam et al 2015). Interestingly, taken together with our results, the data suggest that NeuroD2 may affect expression of different genes depending upon developmental age of neurons.…”

Terminal neuron localization to the upper cortical plate is controlled by the transcription factor NEUROD2

“…To evaluate whether NEUROD2 interactions with specific genomic sites are temporally regulated, we compared NEUROD2 binding profiles between embryonic day 14.5 (E14.5) and postnatal day 0 (P0). We retrieved binding scores from our previously published NEUROD2 ChIP-Seq datasets that represent the amount of relative TF binding to target sequences and carried out a comparative analysis using the E14.5 and P0 results 26,27 . Based upon this comparison, we identified a large number of binding sites that were exclusively targeted at E14.5, and fewer sites that were targeted at both developmental stages or were specific to P0 (Supplemental Material 1) ( Fig.…”

“…Therefore, we decided to employ a target gene prediction approach, called the Closest Gene Method, which generates a score based on the number of TF binding sites and their proximity to the transcription start site of each gene 29 . We calculated Closest Gene scores for the P0 dataset and compared it to the E14.5 dataset which we had previously published (Supplemental Material 2) 27 . Genes with a Closest Gene score above a threshold value were predicted as targets.…”

“…We previously characterized the genetic targets of NEUROD2 in the cerebral cortex at two developmental timepoints: embryonic day 14.5 (E14.5), representing the peak of neurogenesis and migration in the mouse cortex; and postnatal day 0 (P0), representing the onset of neuronal differentiation, dendritic growth and synaptogenesis 26,27 . Here, we carry out a comparative analysis of these two datasets and overlay it with transcriptomics analysis of primary neurons where Neurod2 expression is knocked down.…”