Pluripotent stem cells can potentially differentiate into any given cell type. They commonly exhibit mechanically softer nuclei , lack type-A lamins  and have a poorly defined cytoskeleton .
Embryonic stem cells are pluripotent in early organism development, but gradually undergo lineage restriction and transform into the stem cells with limited differentiation capacities (e.g., hematopoietic stem cells, neural stem cells). These stem cells divide to give rise to specialized cells and tissues, but half of the new generation does not differentiate, retaining their stem cell identity. This type of division cycles is possible due to both epigenetic inheritance (i.e., DNA methylation, chromatin modifiers, histone variants) and chromatin plasticity of stem cells (reviewed in ).
Generally, stem cell chromatin is less compact and more transcription-permissive when compared to differentiated cells. Fluorescent recovery after photobleaching (FRAP) experiments showed high exchange rate of several chromatin-associated proteins (e.g., histones H2B and H3, heterochromatin-associated protein HP1 and linker histone H1) in embryonic stem cells . However, a search for molecular “signature” of stem cells failed to retrieve much: only Oct4, Sox2 and Nanog were identified as commonly expressed embryonic stem cell-specific genes (reviewed in ). In terms of localization, a region of 12p chromosome that contains clustered pluripotency genes (including Nanog) is confined to more central nuclear regions in human embryonic stem cells as compared to differentiated cells . Furthermore, Oct4 locus was found to loop out from its chromosome territory (chromosome 6p) in human embryonic stem cells . The same study demonstrated that centromeric regions of chromosomes in stem cells are not as much confined to the nuclear periphery as they are in differentiated cells .
To describe the transcriptional regulation in embryonic stem cells, Meshorer and Misteli proposed the following models :
- The hierarchical activation (HA) model emphasizes the existence of “stemness” genes, responsible for self-renewal and maintenance of pluripotency. These genes are silenced during cell commitment, while lineage-specific genes are activated.
- The promiscuous transcription (PT) model is similar to HA model in that specific “stemness” genes are expressed; however, many other genes, including lineage-specific, are also indiscriminately expressed at the low “background” level. During cell differentiation, these “background” and “stemness” genes are silenced, and tissue-specific genes are activated.
- The early transcription competence marks (ETCM) model is based on the observation that in embryonic stem cells several tissue-specific genes, albeit repressed, still contain markers of active chromatin (the so-called “bivalent domains” ), suggesting that they are marked for expression at a later stage of differentiation.
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