Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction
Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction
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DOI：
10.1016/j.stem.2019.09.010
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发表时间：
2019-11-07
期刊：
影响因子：
23.9
通讯作者：
Yosef, Nir
中科院分区：
文献类型：
--
作者：
Inoue, Fumitaka;Kreimer, Anat;Yosef, Nir
表观基因组调控和谱系特异性基因表达协同作用以驱动细胞分化，但这些过程之间的时间相互作用在很大程度上是未知的。以人类多能干细胞 (hPSC) 的神经诱导为范例，我们通过在早期神经分化过程中的七个时间点进行 RNA 测序 (RNA-seq)、染色质免疫沉淀测序 (ChIP-seq) 以及转座酶可及染色质测序 (ATAC-seq) 来探究这些动态。我们发现 DNA 可及性的变化先于 H3K27ac，随后是基因表达的变化。使用大规模并行报告分析 (MPRA) 来测试 2,464 个候选调控序列在所有七个时间点的活性，我们发现其中许多序列具有与其各自的细胞内源基因表达和染色质变化相关的时间活性模式。结合所有基因组和 MPRA 数据的优先排序方法进一步确定了参与驱动神经命运的关键转录因子。这些结果提供了基因和调控元件的综合资源，可协调神经诱导并阐明分化过程中的时间框架。
Epigenomic regulation and lineage-specific gene expression act in concert to drive cellular differentiation, but the temporal interplay between these processes is largely unknown. Using neural induction from human pluripotent stem cells (hPSCs) as a paradigm, we interrogated these dynamics by performing RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and assay for transposase accessible chromatin using sequencing (ATAC-seq) at seven time points during early neural differentiation. We found that changes in DNA accessibility precede H3K27ac, which is followed by gene expression changes. Using massively parallel reporter assays (MPRAs) to test the activity of 2,464 candidate regulatory sequences at all seven time points, we show that many of these sequences have temporal activity patterns that correlate with their respective cell-endogenous gene expression and chromatin changes. A prioritization method incorporating all genomic and MPRA data further identified key transcription factors involved in driving neural fate. These results provide a comprehensive resource of genes and regulatory elements that orchestrate neural induction and illuminate temporal frameworks during differentiation.