Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA.
Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
Cell Rep. 2017 Sep 26;20(13):3236-3247. doi: 10.1016/j.celrep.2017.09.011.
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.
转录因子 (TFs) 如何将一种细胞谱系重编程为另一种细胞谱系尚不清楚。在这里,我们定义了在成纤维细胞向诱导性神经元 (iN) 细胞转化过程中,神经前体细胞 TF Ascl1 诱导的染色质可及性变化。在 Ascl1 诱导后 12 小时内,数千个基因组位点就受到影响。令人惊讶的是,超过 80%的可及性变化发生在 3 周重编程过程的第 2 天到第 5 天之间。这种染色质转换与内源性神经元 TF 的强烈激活以及神经元启动子和增强子的核小体相位相一致。随后,iN 细胞的形态和功能成熟伴随着相对较少的染色质重新配置。通过整合染色质可及性和转录组变化,我们构建了 iN 细胞重编程过程中动态 TF 调控的网络模型,并确定了 Zfp238、Sox8 和 Dlx3 作为 Ascl1 下游的关键 TF。这些结果揭示了在直接重编程过程中存在一个独特的、协调的表观基因组开关,而不是发育过程中逐步的细胞命运转变。