Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

Davide Cacchiarelli*, Cole Trapnell*, Michael J. Ziller*, Magali Soumillon, Marcella Cesana, Rahul Karnik, Julie Donaghey, Zachary D. Smith, Sutheera Ratanasirintrawoot, Xiaolan Zhang, Shannan J. Ho Sui, Zhaoting Wu, Veronika Akopian, Casey A. Gifford, John Doench, John L. Rinn, George Q. Daley, Alexander Meissner, Eric S. Lander, Tarjei S. Mikkelsen 2015.
Cell 162:2 412–424


Induced pluripotency is a promising avenue for disease modeling and therapy, but the molecular principles underlying this process, particularly in human cells, remain poorly understood due to donor-to-donor variability and intercellular heterogeneity. Here, we constructed and characterized a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process. This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. We observed distinct waves of gene network activation, including the ordered re-activation of broad developmental regulators followed by early embryonic patterning genes and culminating in the emergence of a signature reminiscent of pre-implantation stages. Moreover, complementary functional analyses allowed us to identify and validate novel regulators of the reprogramming process. Altogether, this study sheds light on the molecular underpinnings of induced pluripotency in human cells and provides a robust cell platform for further studies.

* equal contribution