Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.
Nucleic Acids Res. 2019 Jun 20;47(11):5587-5602. doi: 10.1093/nar/gkz273.
Remodeling of chromatin accessibility is necessary for successful reprogramming of fibroblasts to neurons. However, it is still not fully known which transcription factors can induce a neuronal chromatin accessibility profile when overexpressed in fibroblasts. To identify such transcription factors, we used ATAC-sequencing to generate differential chromatin accessibility profiles between human fibroblasts and iNeurons, an in vitro neuronal model system obtained by overexpression of Neurog2 in induced pluripotent stem cells (iPSCs). We found that the ONECUT transcription factor sequence motif was strongly associated with differential chromatin accessibility between iNeurons and fibroblasts. All three ONECUT transcription factors associated with this motif (ONECUT1, ONECUT2 and ONECUT3) induced a neuron-like morphology and expression of neuronal genes within two days of overexpression in fibroblasts. We observed widespread remodeling of chromatin accessibility; in particular, we found that chromatin regions that contain the ONECUT motif were in- or lowly accessible in fibroblasts and became accessible after the overexpression of ONECUT1, ONECUT2 or ONECUT3. There was substantial overlap with iNeurons, still, many regions that gained accessibility following ONECUT overexpression were not accessible in iNeurons. Our study highlights both the potential and challenges of ONECUT-based direct neuronal reprogramming.
染色质可及性的重编程对于成功将成纤维细胞重编程为神经元是必要的。然而，目前仍不完全清楚哪些转录因子在成纤维细胞中过表达时可以诱导神经元染色质可及性特征。为了鉴定这种转录因子，我们使用 ATAC-seq 技术在人成纤维细胞和 iNeurons 之间生成了差异染色质可及性图谱，iNeurons 是通过在诱导多能干细胞 (iPSC) 中过表达 Neurog2 获得的体外神经元模型系统。我们发现，ONECUT 转录因子序列基序与 iNeurons 和成纤维细胞之间的差异染色质可及性密切相关。与该基序相关的三个 ONECUT 转录因子（ONECUT1、ONECUT2 和 ONECUT3）在成纤维细胞中转基因表达两天内诱导出神经元样形态和神经元基因的表达。我们观察到染色质可及性的广泛重塑；特别是，我们发现包含 ONECUT 基序的染色质区域在成纤维细胞中是处于或低可及状态的，而在过表达 ONECUT1、ONECUT2 或 ONECUT3 后变得可及。与 iNeurons 有大量重叠，但在 ONECUT 过表达后获得可及性的许多区域在 iNeurons 中不可及。我们的研究强调了基于 ONECUT 的直接神经元重编程的潜力和挑战。
