Low CAG promoter activity enriches for reprogramming progressive cells

The variability in reprogramming propensity is associated with the activity of the MKL1/SRF transcription factor and concurs with small cell size as well as rapid cell cycle. Reprogramming progressive cells can be prospectively identified by their low activity of a widely used synthetic promoter, CAG. CAG low cells arise and expand during cell cycle acceleration in the early reprogramming culture of both mouse and human fibroblasts. Here, CAG low and CAG high cells from reprogramming culture were FACS-sorted and subject to RNA-sequencing. Data support the notion that Low CAG promoter activity enriches for reprogramming progressive cells. Our work illustrates a molecular scenario underlying the distinct reprogramming propensities and demonstrates a convenient practical approach for their enrichment. For mouse cells, CAG:H2B-GFP transgenic MEFs were transduced with Dox-inducible Yamanaka factors OSKM, and induced for reprogramming. Cells with highest (10%) and lowest (10%) H2B-GFP intensity were FACS-sorted on reprogramming day 4 and subject to RNA-sequencing. For human cells, human secondary fibroblasts (with Dox-inducible Yamanaka factors) were transduced with CAG:GFP virus, and induced for reprogramming. Cells with highest (10%) and lowest (10%) GFP intensity were FACS-sorted on reprogramming day 7 and subject to RNA-sequencing.