Elucidating the mechanism of reprogramming of somatic cells to induced pluripotency is confounded by heterogeneity. Here, we used a combination of four small molecules that converted somatic cells at very high efficiency and profiled the transcriptomes of single reprogramming fibroblasts (MEFs) and postnatal brain cells. Reprogramming MEFs formed a single trajectory with two branch points of stalled cells that either fail to downregulate cell motility genes or upregulate embryonic transcription and cell division related genes. We identify factors that are associated with specific transitions including Phlda2 and Zfp985 as novel markers for the final conversion to the ESC-like state. Postnatal brain cells reprogram faster than MEFs partly because they are able to increase expression of cell cycle related genes. Dissecting the contribution of each component of the small molecule combination we are able to link 2i function to downregulation of lineage specific genes, while inhibition of Dot1l in conjunction with ascorbic acid enhances pluripotent gene expression. SOURCE: Rupa Sridharan (slab@discovery.wisc.edu) - Sridharan University of Wisconsin

Pluto Bioinformatics

GSE108222: Defining reprogramming checkpoints from single cell analysis of induced pluripotency