Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape

Abstract

In 2006, the "wall came down" that limited the experimental conversion of differentiated cells into the pluripotent state. In a landmark report, Shinya Yamanaka's group described that a handful of transcription factors (Oct4, Sox2, Klf4 and c-Myc) can convert a differentiated cell back to pluripotency over the course of a few weeks, thus reprograming them into induced pluripotent stem (iPS) cells. The birth of iPS cells started off a rush among researchers to increase the efficiency of the reprogramming process, to reveal the underlying mechanistic events, and allowed the generation of patient- and disease-specific human iPS cells, which have the potential to be converted into relevant specialized cell types for replacement therapies and disease modeling. This review addresses the steps involved in resetting the epigenetic landscape during reprogramming. Apparently, defined events occur during the course of the reprogramming process. Immediately, upon expression of the reprogramming factors, some cells start to divide faster and quickly begin to lose their differentiated cell characteristics with robust downregulation of somatic genes. Only a subset of cells continue to upregulate the embryonic expression program, and finally, pluripotency genes are upregulated establishing an embryonic stem cell-like transcriptome and epigenome with pluripotent capabilities. Understanding reprogramming to pluripotency will inform mechanistic studies of lineage switching, in which differentiated cells from one lineage can be directly reprogrammed into another without going through a pluripotent intermediate.

Figure 1

The “labyrinth to pluripotency” represents the transcriptional and morphological changes during reprogramming to the iPS cell state. (Center) Reprogramming starts from somatic cells induced to ectopically express Oct4, Sox2, Klf4 and c-Myc. The green line leads via indicated cornerstones to the faithfully reprogrammed iPS cell state. Many cells do not succeed in reprogramming as indicated by lines ending in the labyrinth at different steps. The gray line, parallel to the green, shows that pre-iPS cells, a stalled reprogramming intermediate, can be converted to the iPS stage by diverse treatments.

Figure 2

A comparison of genome reorganization in differentiation and reprogramming in the mouse system. Top and bottom: main characteristics of the starting/end point cell types of the indicated processes are shown. (Left) events occurring during differentiation of ES cells and in early mouse embryonic development are given. Note that it reads top to bottom. (Right) steps of factor-induced reprogramming to pluripotency, reading from bottom to top. Note that some of the steps are similar between the differentiation and reprogramming processes, just happening in reverse order. See main text for more details.