Profiling of Pluripotency Factors in Single Cells and Early Embryos

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. [Display omitted] •A modified CUT&RUN method allows chromatin profiling from small numbers of cells•Transcription factors are profiled from single cells and blastocyst-stage embryos•NANOG binding in vivo depends on SWI/SNF function A modified CUT&RUN method makes it possible to map chromatin proteins in very low cell numbers, including profiling of several transcription factors in single cells, enabling interrogation of rare cell populations of particular importance in development or disease.