Profiling of Pluripotency Factors in Single Cells and Early Embryos
Profiling of Pluripotency Factors in Single Cells and Early Embryos
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DOI：
10.1016/j.cell.2019.03.014
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发表时间：
2019-05-16
期刊：
影响因子：
64.5
通讯作者：
Fazzio, Thomas G.
中科院分区：
文献类型：
--
作者：
Hainer, Sarah J.;Boskovic, Ana;Fazzio, Thomas G.
细胞命运决定由序列特异性转录因子（TF）控制，这些转录因子在发育中的胚胎内的小细胞群中起作用。为了了解它们在体内的功能，重要的是要确定这些细胞中的TF结合位点。然而，目前的方法不能在单细胞水平或接近单细胞水平上对TF进行全基因组分析。在这里，我们采用靶下切割和使用核酸酶（CUT&RUN）方法释放来分析低细胞数量中的TF，包括单细胞和单个植入前胚胎。单细胞实验表明，在大多数细胞中，只有一小部分TF结合位点被占据，其方式与多细胞研究的峰强度测量大致一致。我们进一步表明，染色质结合的多能性TF NANOG是高度依赖于SWI/SNF染色质重塑复合物在个别囊胚，但不是在培养的细胞。因此，超低输入CUT&RUN（uliCUT&RUN）能够从发育或疾病中特别重要的稀有细胞群中询问TF结合。
Cell fate decisions are governed by sequence-specific transcription factors (TFs) that act in small populations of cells within developing embryos. To understand their functions in vivo, it is important to identify TF binding sites in these cells. However, current methods cannot profile TFs genome-wide at or near the single-cell level. Here we adapt the cleavage under targets and release using nuclease (CUT&RUN) method to profile TFs in low cell numbers, including single cells and individual pre-implantation embryos. Single-cell experiments suggest that only a fraction of TF binding sites are occupied in most cells, in a manner broadly consistent with measurements of peak intensity from multi-cell studies. We further show that chromatin binding by the pluripotency TF NANOG is highly dependent on the SWI/SNF chromatin remodeling complex in individual blastocysts but not in cultured cells. Ultra-low input CUT&RUN (uliCUT&RUN) therefore enables interrogation of TF binding from rare cell populations of particular importance in development or disease.