Author ORCID Identifier
https://orcid.org/0000-0003-4339-6239
Date Available
12-11-2026
Year of Publication
2025
Document Type
Doctoral Dissertation
Degree Name
Doctor of Philosophy (PhD)
College
Arts and Sciences
Department/School/Program
Biology
Faculty
Elizabeth Duncan
Faculty
Jakub Famulski
Abstract
Planarian flatworms are masters of regeneration. A key component of this remarkable ability is the neoblasts, a large population of pluripotent and multipotent stem cells distributed throughout the organism and maintained throughout its lifetime. This stem cell population is transcriptionally heterogeneous, a feature that allows differentiation into a diverse array of cell types during regeneration. However, the molecular mechanisms regulating this transcriptional heterogeneity are largely unknown. In this dissertation, I investigate the roles of two chromatin regulators, SET1 and BPTF, in regulating gene expression and stem cell function.
In Chapter 2, I describe my investigation into the role of Set1, a histone methyltransferase (HMT), as a regulator of tumor suppressor genes. By analyzing data from Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq) with an antibody for histone H3 lysine 4 trimethylation (H3K4me3), I found that Set1 establishes a conserved H3K4me3 chromatin signature at both stem cell identity genes and putative tumor suppressor loci, consistent with findings in mammalian systems. Through RNAi-mediated knockdown, I found that loss of set1 disrupts this chromatin landscape and induces profound stem cell phenotypes, including hyperproliferation and abnormal responses to DNA damage. These findings indicate that Set1 is essential not only for maintaining transcriptional programs associated with stem cell identity but also for preserving genome stability in response to genotoxic stress.
In Chapter 3, I describe a study in which I used single-cell RNA-seq (scRNA-seq) to assess transcriptomic changes across both cell populations and time after set1 knockdown. I found that loss of set1 induces strong, early transcriptional effects, particularly in rapidly renewing lineages like the intestine and epidermis. The most significant changes were observed in the stem cell subcluster, and suggest that set1 knockdown affects both self-renewal and differentiation. These functional changes in the stem cell population impact their differentiated progeny, including the relative abundance of secretory and intestinal cell types.
Finally, in Chapter 4, I examined the role of BPTF, the largest subunit of the Nucleosome Remodeling Factor (NuRF) complex. BPTF is known to recognize and bind H3K4me3 through its PHD2 domain, yet it remains unclear whether it preferentially associates with genomic regions modified by Set1 or by the MLL group of histone methyltransferases. I integrated ATAC-seq, ChIP-seq, and RNA-seq datasets from control and bptf(RNAi) stem cells and found that depletion of BPTF primarily reduces chromatin accessibility at promoters near transcription start sites (TSSs). Genes marked by Set1-dependent H3K4me3, but not MLL1/2-dependent H3K4me3, showed increased sensitivity to BPTF-dependent accessibility. Notably, bptf knockdown produced loss-of-function phenotypes similar to those observed with set1, but not mll1/2, knockdown.
Together, these studies establish that chromatin regulators such as Set1 and BPTF are critical for maintaining the transcriptional profiles, genomic integrity, and differentiation potential in planarian stem cells. This work provides new insights into mechanisms of epigenetic regulation that underlie planarian stem cell function and how they contribute to regenerative capacity.
KEYWORDS: Planarian, Stem Cells, Set1, BPTF, single-cell RNA-seq, ChIP-seq, ATAC-seq
Digital Object Identifier (DOI)
https://doi.org/10.13023/etd.2025.591
Funding Information
This study was supported by NIH grant 5R35GM142679 (2021)
COBRE grant P20 GM121327
Elsa U. Pardee Foundation Pilot Grant (2020)
Biology Department Morgan Fellowship, 2022
Biology Department Ribble Pilot Grant, 2021
Biology Department Merit Fellowship, 2020
Recommended Citation
Verma, Prince, "Exploring the Role of Chromatin-Modifying proteins Set1 and BPTF in Planarian Stem Cells" (2025). Theses and Dissertations--Biology. 116.
https://uknowledge.uky.edu/biology_etds/116
