Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers

Abstract

SUMMARY Generic spinal motor neuron identity is established by cooperative binding of programming transcription factors (TFs), Isl1 and Lhx3, to motor-neuron-specific enhancers. How expression of effector genes is maintained following downregulation of programming TFs in maturing neurons remains unknown. High-resolution exonuclease (ChIP-exo) mapping revealed that the majority of enhancers established by programming TFs are rapidly deactivated following Lhx3 downregulation in stem-cell-derived hypaxial motor neurons. Isl1 is released from nascent motor neuron enhancers and recruited to new enhancers bound by clusters of Onecut1 in maturing neurons. Synthetic enhancer reporter assays revealed that Isl1 operates as an integrator factor, translating the density of Lhx3 or Onecut1 binding sites into transient enhancer activity. Importantly, independent Isl1/Lhx3- and Isl1/Onecut1-bound enhancers contribute to sustained expression of motor neuron effector genes, demonstrating that outwardly stable expression of terminal effector genes in postmitotic neurons is controlled by a dynamic relay of stage-specific enhancers.

Genomic Analysis of a Transcriptional Networks Directing Progression of Cell States During MGE development

“…In addition, our data show a combination of NKX2-1 and LHX6 binding to aREs that have an enrichment of E-box motifs. This combination of TFs (HD, LIM and E-box binding) is consistent with the transcriptional program governing the development and establishment of terminal effector gene expression in motor neurons [8,9]. These beautiful studies show that TFs are shuttled between different REs along the progression of motor neuron development.…”

“…Distantly acting REs have been identified based on conservation and activity [3,4]. Their spatial activity and dynamic genomic contacts can be predicted using a combination of TF binding profiling, genomewide 3D chromosome organization mapping and CRISPR/Cas9 editing [5][6][7][8][9][10] Mouse genetic experiments have elucidated the functions of many TFs in the development of the subpallial telencephalon [11,12]. These studies show that the HD protein NKX2-1 is required for regional specification of the MGE by repressing alternative identities, as well as promoting GABAergic and cholinergic cell fates via the induction of TFs such as LHX6 and LHX8 [13][14][15][16][17].…”

Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons

“…Both iPSC reprogramming and normal development are thought to proceed through stepwise and gradual transitions, where prior steps bookmark enhancers for activation in subsequent stages (Lara-Astiaso et al, 2014). Recent studies of enforced ESC programming to motor neurons also revealed dynamic multi-step chromatin remodeling (Rhee et al, 2016; Velasco et al, 2016). It should be noted, though, that conventional Yamanaka-factor iPSC reprogramming is a slow and stochastic process (Buganim et al, 2012; Hanna et al, 2009; Smith et al, 2016).…”

The transcription factor Pou3f1 provides a new map to the glutamatergic neurons of the cerebellar nuclei

“…Mechanistically, the molecular hand-off between Pou3f1 and Atoh1 may be mediated at the level of transcriptional regulation. Namely, analogous to the regulatory model that governs mouse motor neuron differentiation proposed by Rhee et al (2016), we suspect that, as cells leave the RL, the enhancer driving Atoh1 expression at the RL is transcriptionally silenced. This silencing event frees up a yet to be identified transcription factor, now able to bind to another enhancer that drives the expression of Pou3f1 along the SS.…”