Adult stem cells occur in niches that balance self-renewal with lineage selection and progression during tissue homeostasis. Following injury, culture or transplantation, stem cells outside their niche often display fate flexibility1,2,3,4. Here we show that super-enhancers5 underlie the identity, lineage commitment and plasticity of adult stem cells in vivo. Using hair follicle as a model, we map the global chromatin domains of hair follicle stem cells and their committed progenitors in their native microenvironments. We show that super-enhancers and their dense clusters (‘epicentres’) of transcription factor binding sites undergo remodelling upon lineage progression. New fate is acquired by decommissioning old and establishing new super-enhancers and/or epicentres, an auto-regulatory process that abates one master regulator subset while enhancing another. We further show that when outside their niche, either in vitro or in wound-repair, hair follicle stem cells dynamically remodel super-enhancers in response to changes in their microenvironment. Intriguingly, some key super-enhancers shift epicentres, enabling their genes to remain active and maintain a transitional state in an ever-changing transcriptional landscape. Finally, we identify SOX9 as a crucial chromatin rheostat of hair follicle stem cell super-enhancers, and provide functional evidence that super-enhancers are dynamic, dense transcription-factor-binding platforms which are acutely sensitive to pioneer master regulators whose levels define not only spatial and temporal features of lineage-status but also stemness, plasticity in transitional states and differentiation.
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We thank S. Mazel, L. Li, S. Semova, and S. Tadesse for FACS sorting (Rockefeller University FACS facility); and C. Lai for assistance in high-throughput sequencing (Rockefeller University Genomics Resource Center). We thank E.F. laboratory members A. Aldeguer, S. Hacker, M. Sribour and J. Levorse for assistance in mouse research; I. Matos for advice on image acquisition; J. Racelis, S. Chai, and E. Wong for technical assistance; and Y. Ge, S. Naik, A. Kulukian, and N. Oshimori for discussions. R.C.A. was supported by the Anderson Cancer Center Graduate Student Fellowship. E.F. is an HHMI Investigator. This work was supported by grants from the National Institutes of Health (R01-AR31737 to E.F. and R21MH099452 to D.Z.).
The authors declare no competing financial interests.
Extended data figures and tables
a, FACS purification of wild-type hair follicle stem cells for ChIP-seq according to established markers α6hi and CD34+26. Sca1 is used to remove basal epidermal cells. b, FACS purification of TACs from Krt14-H2B–GFP mice29. TACs are GFPloSca1−α6lo/−CD34−. c, Epifluorescence of Krt14-driven H2B–GFP. Hair follicle stem cells and epidermal cells are GFPhi, whereas TACs are GFPlo. d, q-PCR to verify the FACS sorting strategy and measure enrichment of cell-type-specific marker genes. Mean and standard deviation are shown (n = 3). P values from t-test: P < 0.05; P < 0.01; P < 0.001, relative to hair follicle stem cells.
a, Distribution of H3K27ac occupancy at promoter and enhancers in hair follicle stem cells. b, Distribution of typical-enhancers and super-enhancers in hair follicle stem cells. c, Enhancer size distribution in hair follicle stem cells. d, Number of individual H3K27ac peaks per gene. Super-enhancers are clusters of H3K27ac peaks and mainly consist of ≥ 5 peaks per gene. e, f, Enhancer-gene assignments, exemplified by hair follicle stem cell super-enhancers Fzd6 and Btg2. FPKM, fragments per kilobase of transcript per million mapped reads (RNA-seq). g, Differential expression for genes driven by hair follicle stem cell super-enhancers and typical-enhancers. P values from t-test: P < 0.001. h, Density plot, contrasting expression levels of typical-enhancer versus super-enhancer associated hair follicle stem cell genes in hair follicle stem cells compared to epidermal progenitors. Note cell type-specific differences in expression for hair follicle stem cell genes controlled by super-enhancers but not typical-enhancers. i, Gene Ontology analysis of genes controlled by hair follicle stem cell enhancers. j, List of selected super-enhancer regulated hair follicle stem cell genes. SE, super-enhancer; TE, typical-enhancer.
Extended Data Figure 3 Hair follicle stem cell TFs are enriched within super-enhancers and cluster in epicentres.
a, b, Enrichment of hair follicle stem cell TFs within chromatin of super-enhancers, but not typical-enhancers. Comparisons were made with 377 randomly selected typical-enhancers and their flanking sequence extended 5′ and 3′ to match the average length of super-enhancers (average of 3 analyses is shown). Each ‘TF event’ (a) represents one hair follicle stem cell TF bound within a super-enhancer. ‘TF peaks’ (b) refers to the absolute amount of TFs occupying the super-enhancer. c, Heatmap showing ChIP-seq read densities (from −5 kb to +5 kb of peak centre) across H3K27ac peaks located in super-enhancers. Note that hair follicle stem cell TFs frequently bound densely together with strong H3K27ac peaks. d, Motif analysis of hair follicle stem cell super-enhancers for putative TF binding sites. e, Analysis of distance of H3K27ac peaks to their nearest transcription factor ChIP-seq peaks in hair follicle stem cells in vivo (distance of the two peak centres). Note that enrichment of TF binding occurs within 1-kb regions of H3K27ac peaks (‘epicentres’). f, Frequency and distribution of hair follicle stem cell super-enhancer epicentres. g, Rare ‘atypical’ enhancers co-bound by 7 hair follicle stem cell TFs are more highly expressed in hair follicle stem cells versus committed progenitors.
a, Distribution of H3K27ac ChIP-seq signal across all enhancers in transit-amplifying cells (TACs) reveals 381 super-enhancers of little overlap with hair follicle stem cell super-enhancers. b, Tracking the status of TAC super-enhancers in hair follicle stem cells indicates striking enhancer remodelling upon lineage progression. Example shows the appearance of a de novo super-enhancer for the Dlx3/4 locus as hair follicle stem cells commit to a TAC fate. c, Examples of super-enhancer associated genes in TACs. Genes in green have a reported function in hair follicles.
a, The lentiviral control (CTRL) reporter construct (containing no enhancer) is silent throughout all stages of the hair cycle, despite efficient infection (as evidenced by H2B–mRFP1). b, Immunofluorescence showing that Cxcl14-eGFP super-enhancer reporter activity co-localizes with Krt24+ hair follicle stem cells. DP, dermal papilla; Bu, Bulge. White dashed lines denote the epidermal–dermal border; solid lines delineate the DP. c, H3K27ac and MED1 ChIP-seq occupancy at the Cux1 locus in TACs. Red box shows the super-enhancer epicentre that was cloned for reporter assays. Note that epicentres bound by MED1 are sufficient to identify cell-stage specific loci, even without prior information about lineage-specific TFs. d, CUX1 expression pattern in hair follicles.
Extended Data Figure 6 Hair follicle stem cells adapt to microenvironmental changes by reversible remodelling of super-enhancers.
a, Absence of Cxcl14-SE-eGFP reporter activity in transduced cultured hair follicle stem cells. b, Transplanted cultured hair follicle stem cells establish de novo hair follicles and regain expression of hair follicle stem cell TFs. c, Note extensive hair follicle stem cell super-enhancer remodelling upon culture conditions. d, Hair follicle stem cells in vitro are molecularly distinct from activated hair follicle stem cells (aHFSC) in vivo. e–h, H3K27ac levels at the Cxcl14, Sfrp1, Lhx2 and Ehf loci in hair follicle stem cells in vivo and in vitro. Note the dynamic regulation of super-enhancers and the resulting changes in gene expression. i, Selected list of super-enhancer associated genes in hair follicle stem cells in vitro. j, Note hair follicle stem cell super-enhancer plasticity in vitro and during wound repair: Fhl2 and Prrg4 display super-enhancer-mediated activity in vitro. Upon transplantation, hair follicle stem cells silence in vitro induced genes concomitant with hair follicle regeneration. However, during wounding, hair follicle stem cells (lineage marked with K19-CreER/R26YFP) regain expression of Fhl2 and Prrg4.
Extended Data Figure 7 Hair follicle stem cells activate different epicentres within super-enhancers to sustain expression of critical genes in different microenvironments.
a, b, H3K27ac and hair follicle stem cell TF ChIP-seq occupancies at the Macf1 and Rad51b loci in hair follicle stem cells in vivo and in vitro. Regions C, E and F mark epicentres active in vivo, richly bound by hair follicle stem cell TFs; adjacent regions D and G are novel epicentres active in vitro. Relative luciferase activities were driven by the 1–1.5 kb encompassing these epicentres. Mean and standard deviation are shown (n = 3). P values from t-test: P < 0.001. Functional validation of epicentre shifts in vivo. eGFP-reporter activity of in vitro epicentres is highly active in the epidermis, while physiological hair follicle stem cell epicentres are restricted to the hair follicle niche. c, Motif analysis of Macf1 epicentres (regions A and B, Fig. 3e) for putative TF binding sites. d, Number and distribution of hair follicle stem cell super-enhancer epicentres in vitro. e, Frequency of epicentre shifts in hair follicle stem cell super-enhancers (in vivo versus in vitro). Note that corresponding to the loss of hair follicle stem cell TFs in vitro, many super-enhancers display epicentre shifts to maintain expression of critical genes (for example, Macf1) in different microenvironments.
Extended Data Figure 8 Hair follicle stem cell TFs are reduced outside the niche but are sensitive to Sox9 levels.
a, SOX9 is expressed and displays nuclear localization in hair follicle stem cells in vitro. b, Colony formation assays on wild-type and Sox9-cKO hair follicle stem cells. Sox9fl/fl Rosa26YFPfl/+ hair follicle stem cells were seeded at 2,000 and 4,000 and transduced with lentiviral-Cre to achieve Sox9 ablation in vitro. All yellow and green colonies were not effectively targeted and are still SOX9+. All red colonies (SOX9-negative) aborted, as revealed by quantifications of colony numbers and sizes shown at right. c, Sox9-overexpression in cultured hair follicle stem cells. SOX9 induces the expression of Tle4, Tcf7l1, Tcf7l2 and Lhx2. d, e, Hair follicle stem cell TFs are expressed at substantially lower levels in basal epidermal progenitors in vivo or in cultured epidermal keratinocytes relative to hair follicle stem cells. f, Downregulation of hair follicle stem cell TFs in Sox9-cKO hair follicle stem cells in vivo before hair follicle stem cells are lost. g, Doxycycline-inducible overexpression of Lhx2 in cultured epidermal keratinocytes does not induce hair follicle stem cell TFs. For b–g, mean and standard deviation are shown (n = 3). P values from t-test: P < 0.05; P < 0.01; P < 0.001; n.d., not detected; n.s., not significant.
Extended Data Figure 9 Sustained Sox9 expression in committed progenitors perturbs lineage progression.
a, Sustained Sox9 in adult mice (doxycycline for 3 weeks in adult mice, starting at P21) leads to de novo formation of minibulge-like structures along the ORS. b, Immunofluorescence showing that Lef1 (normally H3K27me3 repressed in hair follicle stem cells, but H3K27ac super-enhancer induced in TACs) remains repressed in mycSOX9+ hair follicles.
This file comprises of 3 sheets as follows: sheet 1- ‘HFSC SE in vivo’ list of H3K27ac super-enhancers of hair follicle stem cells (HFSCs) in vivo: chromosomal coordinates and corresponding gene assignments. The table also contains the criteria for enhancer-gene assignments; sheet 2 - ‘TAC SE in vivo’ list of H3K27ac super-enhancers of transit-amplifying cells (TACs) in vivo: chromosomal coordinates and corresponding gene assignments. The table also contains the criteria for enhancer-gene assignments; and sheet 3 - ‘HFSC SE in vitro’ list of H3K27ac super-enhancers of hair follicle stem cells (HFSCs) in vitro: chromosomal coordinates and corresponding gene assignments. The table also contains the criteria for enhancer-gene assignments. (XLSX 127 kb)
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Adam, R., Yang, H., Rockowitz, S. et al. Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice. Nature 521, 366–370 (2015). https://doi.org/10.1038/nature14289
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