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 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. Examination of changes of the chromatin accessibility landscape during Ascl1-mediated reprogramming of mouse embryonic fibroblasts (MEFs) into neurons, at distinct timepoints during the reprogramming process. Chromatin changes were correlated with previously published RNA-seq data for control rtTA 48hr and Ascl1 48hr (GSE43916: GSM1074345-8), and newly generated RNA-seq data for Ascl1 7d.