Author ORCID Identifier

Date of Graduation


Document Type

Dissertation (PhD)

Program Affiliation

Genetics and Epigenetics

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Jichao Chen, PhD

Committee Member

Sharon Dent, Ph.D.

Committee Member

Richard Behringer, Ph.D.

Committee Member

Jain Abhinav, Ph.D.

Committee Member

Michael Green, Ph.D.


Cell plasticity can extend across all possible cell types, yet it naturally diminishes as cells progress through differentiation. This plasticity can be reactivated during injury repair, engaging developmental flexibility. Our investigations reveal the critical role of the transcription factor (TF) CEBPA, specific to lung alveolar type 2 (AT2) cells, in modulating AT2 cell plasticity within the mouse lung. We demonstrate that CEBPA constrains AT2 cell plasticity by promoting the AT2 differentiation program and recruiting the lineage-specific TF NKX2-1. Without CEBPA, AT2 cells, in both neonatal and mature, show a diminished AT2 program; however, only neonatal cells re-activate the SOX9 progenitor program. Intriguingly, mature AT2 cells exhibit neonatal-like plasticity under Sendai virus infection, where Cebpa mutants, unlike their wild-type counterparts, express SOX9, proliferate more readily, and transition into KRT8/CLDN4+ cells. In parallel, our exploration into the gene regulation of Cebpa through single-cell multiome analyses and CRISPR genome engineering uncovers the essential role of distal regulatory elements (REs) in the epithelial expression of Cebpa in mouse lungs. Integrated analysis of single-cell multiome as well as bulk cell-type-specific histone ChIP-seq identifies potential REs across major lung cell types. CRISPR deletion of a +22 kb RE of Cebpa diminishes CEBPA expression in alveolar type 2 (AT2) cells and recapitulates phenotypes of AT2-specific Cebpa knockouts. NKX2-1 binds to and is required for the accessibility and activity of Cebpa. iii Together, these findings not only highlight the dynamic nature of AT2 cell plasticity across developmental stages but also add a new perspective on RE identification and validation, establishing a robust pipeline that could refine our understanding of cell-type-specific gene expression and its implications for cell fate and plasticity.


cell plasticity, transcriptional control, cell fate, epigenome, lung development and regeneration, single-cell multiome

Available for download on Saturday, April 19, 2025