Importantly, there is currently no evidence that either fluctuating expression of pluripotency factors or state reversion occurs during epiblast progression and lineage commitment in vivo. Instead, the variation that many have observed may simply be a culture epiphenomenon: an attractive playbox for experimentalists and modellers, but with questionable relevance for the way in which pluripotent cells really make fate decisions.
Epigenetic mechanisms underlying somatic reprogramming have been extensively studied, but little is known about the nuclear architecture of pluripotent stem cells (PSCs). Using circular chromosome conformation capture with high-throughput sequencing (4C-seq) and fluorescence in situ hybridization (FISH), we identified chromosomal regions that colocalize frequently with the Oct4 locus in PSCs. These PSC-specific long-range interactions are established prior to transcriptional activation of endogenous Oct4 during reprogramming to induced PSCs and are facilitated by Klf4-mediated recruitment of cohesin. Depletion of Klf4 leads to unloading of cohesin at the Oct4 enhancer and disrupts long-range interactions prior to loss of Oct4 transcription and subsequent PSC differentiation, suggesting a causative role for Klf4 in facilitating long-range interactions independent of its transcriptional activity. Taken together, our results delineate the basic nuclear organization at the Oct4 locus in PSCs and suggest a functional role for Klf4-mediated higher-order chromatin structure in maintaining and inducing pluripotency.
Stemgent has been working alongside some of the world's leading stem cell scientists in developing innovative technology and application solutions for the advancement of stem cell and iPS cell research.
This review is to provide the reader with information on where to find many of the data sets and how to utilize the various (epi)genome browsers for display and initial analysis. We provide selected examples to highlight key features and demonstrate the application of these browsers to stem cell biology.
Permanent cell lines of pluripotent ESCs and iPSCs and our increasing ability to direct them into any cell type for therapeutic potential holds enormous promise for future regenerative medicine. ESCs are considered to be the gold standard of pluripotency, while iPSCs offer the development of cells from any adult individual, which advances the possibility of curing devastating degenerative diseases using cell or tissue grafts with perfect histocompatibility match. This potential calls for efforts to characterize and compare the nature of these pluripotent cell types in great detail. Only such deep studies can give us sufficient insight into the potential, efficacy, and safety to reach a decision; which one will be more favorable for future clinical applications. At the current state of knowledge, we are not in a position to make such a decision. The game between ESCs and iPSCs is still on with no obvious indication of the winner.
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