Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons

Abstract

SUMMARY How transcription factors (TFs) reprogram one cell lineage to another remains unclear. Here, we define chromatin accessibility changes induced by the proneural TF Ascl1 throughout conversion of fibroblasts into induced neuronal (iN) cells. Thousands of genomic loci are affected as early as 12 hours after Ascl1 induction. Surprisingly, over 80% of the accessibility changes occur between days 2 and 5 of the 3-week reprogramming process. This chromatin switch coincides with robust activation of endogenous neuronal TFs and nucleosome phasing of neuronal promoters and enhancers. Subsequent morphological and functional maturation of iN cells are accomplished with relatively little chromatin reconfiguration. Integrating chromatin accessibility and transcriptome changes, we built a network model of dynamic TF regulation during iN cell reprogramming, and identified Zfp238, Sox8 and Dlx3 as key TFs downstream of Ascl1. These results reveal a singular, coordinated epigenomic switch during direct reprogramming, in contrast to step-wise cell fate transitions in development.

Potential application of cell reprogramming techniques for cancer research

“…Chromatin modifiers, such as the EZH2 and ASCL1 components, are also useful for DR to iNSCs or motor neurons [183, 201–203]. JMJD3 has been reported as an epigenetic enhancer of lineage conversion from bone marrow progenitors to liver cells [204].…”

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

“…Pioneer TFs induce the expression of endogenous secondary pro-neuronal TFs or of factors that repress the starting cell type-specific transcriptome, which further contributes to establishing neuronal identity [27]. Chromatin accessibility and transcriptome data have suggested that Zfp238, Sox8, and Dlx3 are among the most important endogenous secondary TF genes downstream of Ascl1 [32]. 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].…”

Dual modulation of neuron‐specific microRNAs and the REST complex promotes functional maturation of human adult induced neurons

“…One of the most commonly used TFs is the proneuronal gene achaete-scute homolog 1 (Ascl1). Many other TFs can also contribute to the reprogramming, such as brain-specific homeobox/POU domain protein 2 (Brn2) that does not access fibroblast chromatin actively on their own but it is recruited by Ascl1 [11,12]. Ascl1 alone can act as a pioneer factor occupying specific sites of the fibroblast genome [11].…”

“…Ascl1 belongs to the family of the basic helix-loop-helix family, and it specifically binds DNA sequences containing an E-box motif [10]. Ascl1 alone can act as a pioneer factor occupying specific sites of the fibroblast genome [11]. Many other TFs can also contribute to the reprogramming, such as brain-specific homeobox/POU domain protein 2 (Brn2) that does not access fibroblast chromatin actively on their own but it is recruited by Ascl1 [11,12].…”

“…Ascl1 alone can act as a pioneer factor occupying specific sites of the fibroblast genome [11]. Many other TFs can also contribute to the reprogramming, such as brain-specific homeobox/POU domain protein 2 (Brn2) that does not access fibroblast chromatin actively on their own but it is recruited by Ascl1 [11,12]. Also, microRNAs [13][14][15][16] and small molecules [17][18][19][20] have been shown to play a critical role in the conversion process.…”