Single-Cell Profiling of Epigenetic Modifiers Identifies PRDM14 as an Inducer of Cell Fate in the Mammalian Embryo

Abstract

Cell plasticity or potency is necessary for the formation of multiple cell types. The mechanisms underlying this plasticity are largely unknown. Preimplantation mouse embryos undergo drastic changes in cellular potency, starting with the totipotent zygote through to the formation of the pluripotent inner cell mass (ICM) and differentiated trophectoderm in the blastocyst. Here, we set out to identify and functionally characterize chromatin modifiers that define the transitions of potency and cell fate in the mouse embryo. Using a quantitative microfluidics approach in single cells, we show that developmental transitions are marked by distinctive combinatorial profiles of epigenetic modifiers. Pluripotent cells of the ICM are distinct from their differentiated trophectoderm counterparts. We show that PRDM14 is heterogeneously expressed in 4-cell-stage embryos. Forced expression of PRDM14 at the 2-cell stage leads to increased H3R26me2 and can induce a pluripotent ICM fate. Our results shed light on the epigenetic networks that govern cellular potency and identity in vivo.

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

“…Although it has previously been thought that cells are homogenous until generation of inside and outside cells, more recent studies have opened a new possibility that cells at the 4-cell stage can already exhibit differences in cell fate Tabansky et al, 2013) and developmental potential (Morris et al, 2012;. This led to the suggestion that the differential activity of epigenetic regulators such as CARM1 (Torres-Padilla et al, 2007) or PRDM14 (Burton et al, 2013), or the differential behavior of transcription factors such as Oct4 (Plachta et al, 2011), at the 4-cell stage could be linked to differential cell fate and potential. Here, we sought to address this by first investigating and directly comparing global differences in gene expression between individual cells within the embryo during the first days of development.…”

“…Historically, cells of the early mouse embryo were considered identical in their ability to give rise to embryonic or extra-embryonic lineages, due to the regulative ability of the embryo to compensate for alterations in cell arrangement (Hillman et al, 1972;Tarkowski, 1959). However, more recent evidence has suggested that cells as early as the 4-cell stage become heterogeneous, exhibiting differences in developmental fate and potential (Bischoff et al, 2008;Tabansky et al, 2013) and in the activity of specific cell-fate regulators (Burton et al, 2013;Plachta et al, 2011;Torres-Padilla et al, 2007). This heterogeneity indicates the possibility that the breaking of embryo symmetry starts earlier than expected, prior to differences in cell position and polarity evident from the 16-cell-stage onward (Fleming, 1987;Johnson and Ziomek, 1981).…”

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

“…However, such approaches can examine the expression of only a small number of genes in each experiment, thus restricting our ability to examine co-expression patterns and to robustly identify subpopulations of cells. Protocols have been developed to overcome these limitations by amplifying small quantities of mRNA 4,5 , which, in combination with microfluidics approaches for isolating individual cells 6,7 , have been used to analyze the co-expression of tens to hundreds of genes in single cells 8,9 . These protocols also allow the entire transcriptome of large numbers of single cells to be assayed in an unbiased way.…”

The molecular underpinnings of totipotency

“…During early embryonic cleavage stages, many chromatin modifiers, co-activators and repressors are expressed in discrete and highly dynamic expression patterns [60]. At the 8-cell stage a unique set of these regulators are expressed, including the demethylases Kdm5a, Kdm6a and Dnmt3l, and these factors are also expressed in later trophoblast cells.…”