Author ORCID Identifier


Date of Graduation


Document Type

Dissertation (PhD)

Program Affiliation

Genes and Development

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Jichao Chen, PhD

Committee Member

Richard Behringer, PhD

Committee Member

Sharon Dent, PhD

Committee Member

Michael Galko, PhD

Committee Member

Harry Karmouty-Quintana, PhD


Lineage transcription factors mark, promote, and maintain multiple distinct cell types originating from a common progenitor. Despite their essential role, how such factors function and bind genome wide to orchestrate the epigenetic changes necessary to form and maintain these identities in vivo is unclear. One lineage transcription factor NK Homeobox 2-1 (NKX2-1) is expressed throughout the lung epithelium during development and was thought to be lost in the extraordinarily thin cell type required for gas exchange– the alveolar type 1 (AT1) cell. Complementing precise genetic knockouts with cell type-specific ChIP-seq, ATAC-seq, and scRNA-seq, our study shows that AT1 and AT2 cells both express and require Nkx2-1 for their development and maintenance through NKX2-1 mediated regulation of cell type-specific genes. Furthermore, NKX2-1 is guided by cell type-specific transcription factors, binding to regulatory elements unique to AT1 or AT2 cells. In the absence of AT1 cell type-specific transcription cofactors in AT1 cells, NKX2-1 reverts to AT2 cell type-specific binding resulting in an AT1 to AT2 cell fate conversion. This remarkable cellular plasticity was further exemplified by loss of Nkx2-1, whereupon both AT1 and AT2 cells first lose chromatin accessibility at their respective cell type-specific and lineage Nkx2-1 binding sites and gain chromatin accessibility at NKX2-1 sites specific to the alternate cell fate within the alveolar epithelium, followed by a final shift to gastrointestinal lineage identity. These data suggest that in vivo, lineage transcription factors positively establish and maintain lineage and cell type identity with the aid of cell type-specific transcription factors, while repressing alternative cellular identities. This study not only demonstrates how a lineage transcription factor regulates the development, and maintenance of distinct cell epigenomes, but also establishes an experimental paradigm to further investigate lineage transcription factors in vivo.


Lung, Development, epigenetics, NKX2-1, lineage transcription factor, alveolar, AT1 cells



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