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 CUT&RUN method to profile TFs in low cell numbers, including single cells and individual pre-implantation embryos. Single-cell experiments demonstrate that only a fraction of TF binding sites appear to be 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. Overall design: ultra-low input CUT&RUN. Antibody enriched DNA was fragmented using proteinA-Mnase, and libraries were generated.