Cell-cycle control of developmentally regulated transcription factors accounts for heterogeneity in human pluripotent cells

Abstract

Heterogeneity within pluripotent stem cell (PSC) populations is indicative of dynamic changes that occur when cells drift between different states. Although the role of metastability in PSCs is unclear, it appears to reflect heterogeneity in cell signaling. Using the Fucci cell-cycle indicator system, we show that elevated expression of developmental regulators in G1 is a major determinant of heterogeneity in human embryonic stem cells. Although signaling pathways remain active throughout the cell cycle, their contribution to heterogeneous gene expression is restricted to G1. Surprisingly, we identify dramatic changes in the levels of global 5-hydroxymethylcytosine, an unanticipated source of epigenetic heterogeneity that is tightly linked to cell-cycle progression and the expression of developmental regulators. When we evaluated gene expression in differentiating cells, we found that cell-cycle regulation of developmental regulators was maintained during lineage specification. Cell-cycle regulation of developmentally regulated transcription factors is therefore an inherent feature of the mechanisms underpinning differentiation.

Figure 1

Establishment and Characterization of Fucci hESCs (A) Diagram of Fucci reporters. (B) Diagram of cell-cycle phase-specific fluorescent protein expression patterns. (C) WA09 Fucci hESCs were imaged every 15 min over a 24 hr period. Micron bar: 50 μm. Arrowheads: cell progression from G1 to S to G2. (D and E) WA09 Fucci hESCs were treated with Violet Vybrant DyeCycle for 2 hr and then analyzed on the MoFlo. The approximate percentage of cells in each cell-cycle phase is shown. Data are representative of biological replicates.

Figure 2

Gene-Expression Profiling of Human Fucci ESCs (A) Following RNA-seq, cluster analysis was performed on cell-cycle-regulated transcripts in WA09 Fucci hESCs, represented by a heatmap. (B) GO analysis of cell-cycle-regulated genes from human Fucci RNA-seq. (C) Percentage of genes by GO analysis in the transcriptional regulation or cell-cycle categories according to RNA-seq cluster analysis. Developmental transcription factors were heavily enriched in cluster 6, and mitotic genes were enriched in clusters 2 and 7. (D–F) WA09 Fucci hESCs were separated into cell-cycle phases by FACS, and RNA levels were then determined by qRT-PCR for (D) pluripotency genes, (E) cell-cycle mitotic genes, and (F) developmental transcription factors. Data are representative of biological triplicate experiments displayed as mean ± SEM. ^∗p < 0.05, ^∗∗p < 0.01. See also Figure S1.

Figure 3

WNT and ERK Signaling Promote Heterogeneity in Late G1 Cells (A) WA09 Fucci hESCs grown in self-renewal media were treated with U0126 (20 μM) or DKK1 (150 ng/ml) for 3 days and then separated into cell-cycle phases by FACS. RNA expression analysis by qRT-PCR was performed for endoderm markers. All experiments were performed in technical triplicate and are representative of multiple experiments. (B and C) WA09 Fucci hESCs were treated with U0126 (20 μM) or DKK1 (150 ng/ml) for 3 days and immunostaining was performed for indicated proteins and quantitated in (C) as the ratio of Alexa Fluor 647+ (for indicated proteins) to KO2+ cells. Data represent analyses from five different fields of view, and the total number of cells counted per condition was >350. Arrowheads: KO2+ cells that express endoderm markers in self-renewal media, but not in the presence of the MEK/ERK inhibitor (U0126). Data are representative of multiple experiments. Micron bar: 50 μm. (D) Immunoblotting (20 μg/lane) for FACS-isolated Fucci fractions for the indicated signaling molecules. (E) Schematic diagram indicating that cells in G1 are most responsive to differentiation-inducing signals. Colors are representative of Fucci fractions (gray, early G1; red, late G1; yellow, G1/S; green, S-G2/M). Circles depict cells progressing through the cell cycle, with solid circles representing cells that express developmental regulators. Data are representative of biological triplicate experiments displayed as mean ± SEM. ^∗p < 0.05, ^∗∗p < 0.01. See also Figure S2.

Figure 4

Developmental Regulators Retain Cell-Cycle Regulation during Differentiation (A) Schematic for examination of DE cell-cycle-regulated transcripts. Fucci hESCs were differentiated to DE for 2 or 4 days, cell-cycle fractions were isolated by FACS, and RNA expression analysis was performed. (B) Flow-cytometry plots of undifferentiated ESCs, 2-day DE, and 4-day DE. (C) RNA expression analysis of Fucci cell-cycle fractions after differentiation to DE. All experiments were performed in technical triplicate and are representative of multiple experiments. (D and E) Immunostaining upon differentiation of Fucci ESCs for 2 or 4 days to DE is quantitated in (E) as the percentage of positive cells in each cell-cycle fraction. Data are representative of multiple independent experiments. Micron bar: 50 μm. (F) Immunoblotting (20 μg/lane) for the indicated proteins from cell-cycle fractions in undifferentiated ESC or after 2 days of DE differentiation. Data are representative of biological triplicate experiments displayed as mean ± SEM. ^∗p < 0.05, ^∗∗p < 0.01. See also Figures S3 and S4.

Figure 5

The Epigenetic Mark 5hmC Is Cell-Cycle Regulated (A) Dot blot analysis reveals a loss of 5hmC in S phase. Representative of assays performed in biological triplicate. (B) MS analysis for 5hmC performed in technical triplicate and representative of experiments in biological duplicate. (C) 5hmC-capture qPCR for upstream regions of TSS. (D) Sequencing of 5hmC-enriched regions reveals enrichment for DhMRs at TSSs and TESs. The experiment was performed in technical triplicate and is representative of duplicate experiments. (E) DhMRs are colocated with enhancer marks (H3K4me1 and K3K9ac) and bivalent marks (H3K4me3 and H3K27me3). (F) TAB-seq for promoter regions in Fucci fractions, with diagram indicating primer location. Data are representative of biological triplicate experiments displayed as mean ± SEM. ^∗p < 0.05, ^∗∗p < 0.01. See also Figure S5.

Figure 6

PSC Heterogeneity Is Contingent upon the Cell-Cycle Position As cells pass through G1 phase, they become sensitized to signaling pathways and exhibit increased levels of developmental regulators (“lineage primed”). During differentiation, the expression of developmentally important transcription factors increases, but they maintain periodicity during the cell cycle. Expansion of the G1 phase is likely to be a factor in this. Colors are representative of Fucci fractions (gray, early G1; red, late G1; yellow, G1/S; green, S-G2/M). Circles depict cells progressing through the cell cycle, with solid gray circles representing cells that weakly express developmental regulators, and solid black circles indicating cells that strongly express developmental regulators.