Using single-cell techniques, the behaviors of individual stem cells are coming under ever-greater scrutiny. Such efforts are pushing the boundaries of technology development in cell biology and are getting to the heart of what defines cellular states, what drives cell-state changes, and what can we learn about biological systems from cell-to-cell variability. A prime example of this trend comes from recent work by Takahashi et al., 2019Takahashi S. Miura H. Shibata T. Nagao K. Okumura K. Ogata M. Obuse C. Takebayashi S.I. Hiratani I. Genome-wide stability of the DNA replication program in single mammalian cells.Nat Genet. 2019; 51: 529-540Crossref PubMed Scopus (40) Google Scholar, who have addressed whether replication timing across the genome is stereotyped between individual cells of the same cell type, and their results raise questions about the potential role of replication timing in the decision-making of differentiating stem cells. Previous studies with bulk sequencing of cell populations have revealed the basic principle that regions that replicate early tend to be euchromatic, actively transcribed, and in the nuclear interior, whereas late-replicating regions tend to be heterochromatic and at the nuclear periphery. Takahashi et al. have now designed and tested an approach to profile early- versus late-replicating regions at the single-cell level in mouse embryonic stem cells (mESCs), before and after differentiation and in an immortalized human retinal pigment epithelial cell line. Similar to another recent study by Dileep and Gilbert, 2018Dileep V. Gilbert D.M. Single-cell replication profiling to measure stochastic variation in mammalian replication timing.Nat. Commun. 2018; 9: 427Crossref PubMed Scopus (41) Google Scholar, the authors find that overall genome-wide replication timing is highly consistent between individual cells in a given state and that some regions exhibit more intrinsic variability than others. Going deeper, they reveal an interesting corollary: developmentally regulated genes exhibit higher-than-average variability in replication timing. Does this suggest a link between replication timing variability and developmental plasticity? The variability at these genes does in fact go away upon mESC differentiation. Future work may explore this facet of nuclear organization in stem cell “decision-making” or how this might be exploited to direct different differentiation endpoints. Getting to the molecular basis of the observations of studies such as Takahashi et al. will likely be aided by new approaches to study the behavior of proteins and protein complexes in single cells. In this vein, a recent study in our journal (Hainer et al., 2019Hainer S.J. Bošković A. McCannell K.N. Rando O.J. Fazzio T.G. Profiling of Pluripotency Factors in Single Cells and Early Embryos.Cell. 2019; 177: 1319-1329Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar) adapts a nuclease-based method for mapping the binding of transcription factors, known as CUT&RUN (Skene and Henikoff, 2017Skene P.J. Henikoff S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites.Elife. 2017; 6: e21856Crossref PubMed Scopus (584) Google Scholar), for use with very small cell numbers, even single cells. With this modified protocol, called ultra-low input CUT&RUN (uliCUT&RUN), Hainer and colleagues probe the distribution of transcription factors in mESCs and in vivo in pre-implantation embryos. In mESCs, they substantiate the long-standing conjecture that the fractional occupancy of transcription factors such as the pluripotency enabling NANOG and SOX2 in single cells is what underpins variable ChIP-seq (chromatin immunoprecipitation sequencing) peaks in bulk analyses. In early embryos, they further establish that NANOG binding in the inner cell mass requires the SWI/SNF chromatin remodeler, a feature not observed in similar analyses from cultured cells. This technological development will enable more accurate temporal reconstructions of transcription factor activity in individual cells and provides a new means of probing heterogeneity in vivo when tissue samples are limiting. One of the most powerful quantitative and high-throughput means of assessing levels of individual proteins in single stem cells comes from mass cytometry (cyTOF), in which antibodies to proteins of interest are conjugated to heavy metals to enable coupling of flow cytometry and time-of-flight mass spectrometry. A key advantage of cyTOF is the ability to monitor many proteins at once. Palii et al., 2019Palii C.G. Cheng Q. Gillespie M.A. Shannon P. Mazurczyk M. Napolitani G. Price N.D. Ranish J.A. Morrissey E. Higgs D.R. et al.Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-SpecificTranscription Factors Determine Cell Fate.Cell Stem Cell. 2019; 24: 812-820Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar use this to impressive effect to assay the levels of 27 proteins across 13 time points (using temporal barcoding) during the differentiation of hematopoietic stem/progenitor cells (HSPCs). They specifically examine the trajectories of megakaryocyte-erythroid progenitors and find that both KLF1, which biases red blood cell fate, and FLI1, which biases megakaryocyte fate, are expressed in the same bipotential progenitors. They further show that the change in these lineage-specific transcription factors is gradual and not switch-like, as might be expected by a more rigid conceptualization of cell-fate decision-making. One anticipates that these gradual shifts in gene expression in developmental transitions (as observed by Palii et al.), the replication timing variability reported by Takahashi et al., and the conditional binding of transcription factors in early embryos (as seen by Hainer and colleagues) will all be reflected in changes in nuclear organization affecting the relevant loci. To confirm this and attain a more complete biophysical understanding of these transitions and their dynamics, will it one day be possible to track the compartmentalization and transcription factor occupancy of multiple developmentally important genetic loci in a single cell over time?