Student Theses and Dissertations


Rene C. Adam

Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)

RU Laboratory

Fuchs Laboratory


Adult stem cells reside in niches, which control their long-term ability to selfrenew and produce the differentiated cell lineages necessary to regenerate and repair their tissues. Following injury, culture or transplantation, stem cells outside their niche often acquire broader plasticity in fates. In my graduate work, I showed that super-enhancers underlie the identity, lineage commitment and plasticity of adult stem cells in vivo. My chosen model is the hair follicle, where its stem cells (HFSCs), niche and master regulators are well-characterized. By mapping global chromatin domains of HFSCs in their native niche, and of committed progenitors, I discovered that super-enhancers and their dense clusters (‘epicenters’) of transcription factor binding sites change dramatically upon lineage progression. New fate is acquired by decommissioning old and establishing new super-enhancers, an auto-regulatory process that abates one master regulator subset while enhancing another. I showed that epicenters dictate tissue-specific and lineagespecific reporter expression in vivo, yielding powerful genetic tools to drive unprecedented lineage-specificity. Exploiting the ability to culture and transplant HFSCs, I found that intriguingly, when outside their niche and faced with a new environment, HFSCs dynamically remodel super-enhancers, including those driving master identity genes. In vitro, new super-enhancers emerge which drive genes induced upon woundhealing in vivo. Cultured HFSCs adapt to this perceived wounding state by activating different epicenters within the super-enhancers of key SC-identity genes. Probing mechanism, I identified SOX9 as the crucial chromatin regulator of super-enhancers. While high levels maintain HFSC fate and absence results in alternative fates, low levels, e.g. during wound-repair, early lineage progression or culturing, permit fate plasticity. I showed that ectopically expressing SOX9 in epidermis activates polycomb-repressed super-enhancers of HFSC determinants, while sustaining SOX9 in the hair lineage prevents the super-enhancer lineage switch. Cultured HFSCs silence other superenhancer- driven determinants, but retain low SOX9, endowing them with the plasticity to make both SOX9-negative epidermis and SOX9-positive HFs upon engraftment. Together, my findings expose super-enhancers as dynamic and dense transcription factor binding platforms which are exquisitely sensitive to master regulators. Furthermore, by harboring distinct epicenters, super-enhancers possess the ability to adjust reversibly to microenvironmental cues that transiently change transcriptional landscapes. In a second line of research, I focused on functional analyses to uncover the role of superenhancer regulated, putative stemness genes. I found that NFI transcription factors (NFIB and NFIX) act redundantly in mouse skin to maintain the undifferentiated state of progenitors in hair follicles, sebaceous glands and sweat glands. Combining gene expression and chromatin profiling, I discovered that NOTCH signaling, known to drive terminal differentiation in epidermis, is ectopically induced in NFI-deficient HFSCs. These findings provide novel insights into how progenitor status in maintained by a family of transcription factors ubiquitiously active in skin appendages.


A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy

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