Many adult regenerative cells divide infrequently but have high proliferative capacity. We developed a strategy to fluorescently label slow-cycling cells in a cell type-specific fashion. We used this method to purify the label-retaining cells (LRCs) that mark the skin stem cell (SC) niche. We found that these cells rarely divide within their niche but change properties abruptly when stimulated to exit. We determined their transcriptional profile, which, when compared to progeny and other SCs, defines the niche. Many of the >100 messenger RNAs preferentially expressed in the niche encode surface receptors and secreted proteins, enabling LRCs to signal and respond to their environment.Epidermis and its appendages undergo continuous renewal and maintain reservoirs of multipotent SCs whose descendants are organized spatially and temporally. The epidermal basal layer (BL) contains putative SCs in addition to the transiently amplifying (TA) cells, which give rise to terminally differentiating suprabasal layers (1-3). The BL and the hair follicle outer root sheath (ORS) are contiguous and biochemically similar ( fig. S1A). In the hair bulb, the dermal papilla (DP) maintains contact with matrix TA cells until they differentiate to form the inner root sheath (IRS) and hair shaft. Follicles periodically undergo cycles of growth (anagen), destruction (catagen), and rest (telogen). The zone between noncycling and cycling segments is a SC niche, the ORS "bulge" (4,5).Multipotent epithelial SCs with high proliferative potential reside in the bulge (6,7). The bulge contains the majority of infrequently cycling, label-retaining cells (LRCs), which can respond to anagen DP signals to regenerate the follicle. After wounding or transplantation, bulge cells give rise to epidermis, follicles, and sebaceous glands. Additionally, when dissected from rat whiskers and cultured, bulge cells yield more colonies than other follicle segments (7). It is not known what features define this specialized SC niche, what its interactions with bulgeLRCs are, and whether all LRCs are SCs. To begin to address these issues, we devised a strategy based on the prediction that bulge SCs are uniquely both slow-cycling and active for a keratinocyte-specific promoter. With this strategy, we purify and characterize bulge LRCs and related keratinocyte progeny in the BL and ORS. Analyses of their transcriptional profiles reveal the skin LRC mRNAs; some of these mRNAs are found in SCs of other tissues, whereas others specify the unique environment of the skin SC niche.To mark infrequently cycling cells of adult skin epithelium, we engineered transgenic mice to express histone H2B-green fluorescent protein (GFP) (8) controlled by a tetracyclineresponsive regulatory element (TRE). A tightly regulated TRE-mCMV-H2B-GFP founder animal was crossed with mice harboring a keratin 5 (K5) promoter-driven tet repressor-VP16

In adult skin, each hair follicle contains a reservoir of stem cells (the bulge), which can be mobilized to regenerate the new follicle with each hair cycle and to reepithelialize epidermis during wound repair. Here we report new methods that permit their clonal analyses and engraftment and demonstrate the two defining features of stem cells, namely self-renewal and multipotency. We also show that, within the bulge, there are two distinct populations, one of which maintains basal lamina contact and temporally precedes the other, which is suprabasal and arises only after the start of the first postnatal hair cycle. This spatial distinction endows them with discrete transcriptional programs, but surprisingly, both populations are growth inhibited in the niche but can self-renew in vitro and make epidermis and hair when grafted. These findings suggest that the niche microenvironment imposes intrinsic "stemness" features without restricting the establishment of epithelial polarity and changes in gene expression.

SUMMARY Induced pluripotent stem cells (iPSCs) outwardly appear to be indistinguishable from embryonic stem cells (ESCs). A study of gene expression profiles of mouse and human ESCs and iPSCs suggests that, while iPSCs are quite similar to their embryonic counterparts, a recurrent gene expression signature appears in iPSCs regardless of their origin or the method by which they were generated. Upon extended culture, hiPSCs adopt a gene expression profile more similar to hESCs; however, they still retain a gene expression signature unique from hESCs that extends to miRNA expression. Genome-wide data suggested that the iPSC signature gene expression differences are due to differential promoter binding by the reprogramming factors. High-resolution array profiling demonstrated that there is no common specific subkaryotypic alteration that is required for reprogramming and that reprogramming does not lead to genomic instability. Together, these data suggest that iPSCs should be considered a unique subtype of pluripotent cell.