Epigenetic phenomena reflect alternative gene expression states that are maintained through multiple rounds of mitosis, and sometimes through meiosis.
The central dogma of gene expression states that information moves from DNA to RNA to protein, where mRNA translation represents a final step in protein expression.
We have shown that the size of a k-function's latent repertoire depends only on the number of unique expression states that occur in the k-function.
Additionally, this rapid development is precisely coordinated through expression states that are predictable within the in vitro setting over 48 h [ 3, 4].
Thus, the majority of ES cells overexpressing Prdm14 reside within the Rex1-high expression state that indicates naive pluripotency (supplementary Fig S3D online).
First, by arbitrarily dividing read coverage values of genes into several bins, the earlier HMM [ 94] contains multiple expression states that are not directly connected, thus in principle it cannot assemble transcripts with highly non-uniform coverage.
In addition to establishing a functional link between chromatin structure and gene expression state, these studies demonstrated that genetically identical cells can achieve alternate gene expression states that are stably maintained through cell division, thereby supporting an epigenetic mechanism of inheritance.
Within the context of our 11 gene HSPC network topology, several expression states that correspond to the differentiated cell types shown in Figure 3 can automatically revert to the stem cell state, suggesting a potential for spontaneous reversion of differentiated cells to the immature stem cell phenotype (details in Supplementary Table S3).
An expression state that is not influenced by constant inputs thanks to adaptation is robust with respect to the ubiquitous cell-to-cell variability in TF concentrations, but it is still responsive to signals that induce dynamical variations of TF levels.
The apocarotenoid accumulation varies with developmental stages and thus in order to fit into this narrow window of developmental changes, chromatin needs to be flexibly regulated so as to confer stable expression states that can be reset owing to changes in the progression of development.
