Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons

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 hr 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 is accomplished with relatively little chromatin reconfiguration. By 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 stepwise cell fate transitions in development. [Display omitted] •Pioneer factor Ascl1 opens closed chromatin at its target sites within 12 hr•Rapid chromatin remodeling in reprogramming precedes neuronal maturation•Ascl1 induces well-structured and stable nucleosome positioning by day 5•Network model identifies Zfp238, Sox8, and Dlx3 as critical TFs for iN cell reprogramming Wapinski et al. find that “on-target” pioneer factor Ascl1 induces rapid, genome-wide chromatin remodeling and nucleosome phasing that precedes other indicators of neuronal maturation. Building a network model incorporating chromatin accessibility and transcriptomic changes allows identification of Zfp238, Sox8, and Dlx3 as critical downstream factors for iN cell reprogramming.