Summary The combined activity of three transcription factors can reprogram adult cells into induced pluripotent stem (iPS) cells. However, the transgenic methods used to deliver reprogramming factors have raised concerns regarding the future utility of the resulting stem cells. These uncertainties could be overcome if each transgenic factor were replaced with a small molecule that either directly activated its expression from the somatic genome or in some way compensated for its activity. To this end, we have used high-content chemical screening to identify small molecules that can replace Sox2 in reprogramming. We show that one of these molecules functions in reprogramming by inhibiting Tgf-β signaling in a stable and trapped intermediate cell type that forms during the process. We find that this inhibition promotes the completion of reprogramming through induction of the transcription factor Nanog.

Current DNA methylation assays are limited in the flexibility and efficiency of characterizing a large number of genomic targets. We report a method to specifically capture an arbitrary subset of genomic targets for single-molecule bisulfite sequencing for digital quantification of DNA methylation at single-nucleotide resolution. A set of ~30,000 padlock probes was designed to assess methylation of 66,000 CpG sites within 2,020 CpG islands on human chromosome 12, chromosome 20, and 34 selected regions. To investigate epigenetic differences associated with dedifferentiation, we compared methylation in three human fibroblast lines and eight human pluripotent stem cell lines. Chromosome-wide methylation patterns were similar among all lines studied, but cytosine Correspondence should be addressed to K.Z. (E-mail: kzhang@bioeng.ucsd.edu) or Y.G. (E-mail: ygao@vcu.edu). Accession numbers. All sequence reads and methylation data have been deposited at GEO, with accession number GSE15007.Note: Supplementary information is available on the Nature Biotechnology website. AUTHOR CONTRIBUTIONS NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript methylation was slightly more prevalent in the pluripotent cells than in the fibroblasts. Induced pluripotent stem (iPS) cells appeared to display more methylation than embryonic stem cells. We found 288 regions methylated differently in fibroblasts and pluripotent cells. This targeted approach should be particularly useful for analyzing DNA methylation in large genomes.DNA methylation is a primary epigenetic mechanism for transcriptional regulation during normal development and goes awry in many diseases, including cancers. Genome-scale patterns of DNA methylation have been characterized by microarray hybridization or bisulfite sequencing 1 . Microarray methods have enabled methylation to be quantified at 1,536 discrete CpG sites in the human genome with the GoldenGate assay 2,3 . They have also been coupled with methylated DNA immunoprecipitation or methyl-specific restriction enzyme digestion to quantify relative levels of DNA methylation, although the read-outs of such approaches are only averages of the levels of methylation of multiple adjacent CpG sites [4][5][6] .More recently, next-generation sequencing has enabled absolute quantification of DNA methylation with single-nucleotide resolution on a larger scale than previously possible. These efforts include bisulfite sequencing of PCR amplicons from human tissues and cancer cell lines 7-9 , single-molecule sequencing of reduced representation libraries from mouse embryonic stem cells 10,11 and whole-genome bisulfite sequencing of Arabidopsis thaliana 12,13 . Although whole-genome bisulfite sequencing of a mammalian genome should be technically feasible, the large genome sizes pose a considerable challenge 14 .Selection or enrichment of genomic targets prior to sequencing would substantially reduce sequencing cost. PCR-based target selection is highly specific, but cannot be multiplexed easily for...

Highlights d Adult human pancreatic beta cells can be induced to proliferate at high rates d Driven by synergy between DYRK1A inhibitors and TGFb superfamily inhibitors d Reflects activation of cyclins and CDKs accompanied by CDK inhibitor suppression d Proliferation occurs in type 2 diabetic beta cells, with enhanced differentiation SUMMARYSmall-molecule inhibitors of dual-specificity tyrosine-regulated kinase 1A (DYRK1A) induce human beta cells to proliferate, generating a labeling index of 1.5%-3%. Here, we demonstrate that combined pharmacologic inhibition of DYRK1A and transforming growth factor beta superfamily (TGFbSF)/SMAD signaling generates remarkable further synergistic increases in human beta cell proliferation (average labeling index, 5%-8%, and as high as 15%-18%), and increases in both mouse and human beta cell numbers. This synergy reflects activation of cyclins and cdks by DYRK1A inhibition, accompanied by simultaneous reductions in key cell-cycle inhibitors (CDKN1C and CDKN1A). The latter results from interference with the basal Trithorax-and SMAD-mediated transactivation of CDKN1C and CDKN1A.Notably, combined DYRK1A and TGFb inhibition allows preservation of beta cell differentiated function. These beneficial effects extend from normal human beta cells and stem cell-derived human beta cells to those from people with type 2 diabetes, and occur both in vitro and in vivo.