DNA and Chromatin Modification Networks Distinguish Stem Cell Pluripotent Ground States

Abstract

Pluripotent stem cells are capable of differentiating into all cell types of the body and therefore hold tremendous promise for regenerative medicine. Despite their widespread use in laboratories across the world, a detailed understanding of the molecular mechanisms that regulate the pluripotent state is currently lacking. Mouse embryonic (mESC) and epiblast (mEpiSC) stem cells are two closely related classes of pluripotent stem cells, derived from distinct embryonic tissues. Although both mESC and mEpiSC are pluripotent, these cell types show important differences in their properties suggesting distinct pluripotent ground states. To understand the molecular basis of pluripotency, we analyzed the nuclear proteomes of mESCs and mEpiSCs to identify protein networks that regulate their respective pluripotent states. Our study used label-free LC-MS/MS to identify and quantify 1597 proteins in embryonic and epiblast stem cell nuclei. Immunoblotting of a selected protein subset was used to confirm that key components of chromatin regulatory networks are differentially expressed in mESCs and mEpiSCs. Specifically, we identify differential expression of DNA methylation, ATP-dependent chromatin remodeling and nucleosome remodeling networks in mESC and mEpiSC nuclei. This study is the first comparative study of protein networks in cells representing the two distinct, pluripotent states, and points to the importance of DNA and chromatin modification processes in regulating pluripotency. In addition, by integrating our data with existing pluripotency networks, we provide detailed maps of protein networks that regulate pluripotency that will further both the fundamental understanding of pluripotency as well as efforts to reliably control the differentiation of these cells into functional cell fates. Molecular & Cellular Proteomics

Cited2, a Transcriptional Modulator Protein, Regulates Metabolism in Murine Embryonic Stem Cells

“…Indeed, measurement of glycolytic activity by the percentage of glucose converted to lactate revealed that ϳ40% of glucose was converted to lactate in WT EBs (Fig. 5D), whereas undifferentiated WT ESCs consumed ϳ80% of glucose for glycolysis, indicating that WT EBs experienced a metabolic switching during differentiation in agree- ment with a previous study (46). In contrast, the majority of glucose (ϳ95%) was still converted to lactate in Cited2 ⌬/Ϫ EBs (Fig.…”

Chromatin features and the epigenetic regulation of pluripotency states in ESCs

“…In this regard, it was postulated that conventional human ESCs might bear a greater resemblance to the mouse epiblast stem cells (EpiSCs), which originate from a developmentally more advanced post-implantation epiblast that has undergone X chromosome inactivation and cannot efficiently form germline chimeras when injected into blastocysts (Brons et al, 2007;Tesar et al, 2007). This diminished potency may be due to the differences in transcriptional and chromatin constituency between mouse EpiSCs and ESCs (Song et al, 2012).…”

Cdx2Efficiently Induces Trophoblast Stem-Like Cells in Naïve, but Not Primed, Pluripotent Stem Cells

“…Interestingly, ESC-derived TSClike cells fail to acquire genomic methylation features of TSCs [21], arguing that epigenetic differences between ESCs and EpiSCs could limit the developmental potential of EpiSCs to become TSCs. Differences in the transcriptomes, proteomes, and chromatin states of ESCs and EpiSCs have been compared [62][63][64][65]. Notably, NuRD-dependent methylation prevents ESCs from spontaneously acquiring trophoblast fate [66][67][68][69].…”