Genome-wide profiling of chromatin accessibility during microRNA-mediated neuronal reprogramming [ATAC-seq]

Neuronal microRNAs, miR-9/9* and miR-124 (miR-9/9*-124), exert reprogramming activities to direct cell-fate conversion of adult human fibroblasts to post-mitotic neurons and enable the generation of discrete neuronal subtypes with additional transcription factors. Previously, the molecular events underlying the neurogenic switch mediated by microRNAs during neuronal reprogramming were unknown. Here, we systematically dissected the neurogenic state induced by miR-9/9*-124 alone and reveal the surprising capability of miR-9/9*-124 in coordinately stimulating the reconfiguration of chromatin accessibilities, DNA methylation and transcriptome, leading to the generation of functionally excitable neurons, yet unbiased towards a particular subtype-lineage. We show that the microRNA-induced neuronal state enables additional transcription factors, ISL1 and LHX3, to selectively commit conversion to a highly homogenous population of human spinal cord motor neurons. Taken together, our study reveals a modular synergism between microRNAs and transcription factors that allows lineage-specific neuronal reprogramming, providing a platform for generating distinct subtypes of human neurons. Overall design: Human fibroblasts were reprogrammed by microRNAs miR-9/9* and miR-124 (miNs) or transduced with a non-specific microRNA control (Ctrl). To profile chromatin accessibility during neuronal reprogramming, samples were collected at Ctrl day 10, miNs day 10 and miNs day 20. For Brg1 knockdown in reprogrammed cells, miNs were transduced with shBRG1 or shEGF and samples were collected at shBRG1 day 20 and shEGFP day 20. ATAC-seq was performed as previously described (Buenrostro et al., 2013).