Author ORCID Identifier
Date Available
12-20-2026
Year of Publication
2024
Document Type
Doctoral Dissertation
Degree Name
Doctor of Philosophy (PhD)
College
Medicine
Department/School/Program
Biochemistry
Advisor
Dr. Yvonne Fondufe-Mittendorf
Abstract
Chromatin regulation establishes the fundamental control in maintaining normal development by mediating the accessibility and activity of genes necessary for normal cellular functions. This dynamic structure of chromatin, mediated by the repositioning of nucleosomes, modifications of histones and DNA, and the binding of chromatin-associated proteins, can either activate or repress the expression of key regulatory genes. Therefore, alterations in chromatin structure can impact transcriptional integrity, and its dysregulation can contribute to the development of complex pathological conditions, such as cancer. Understanding how aberrant epigenetic changes can be implicated in the process of epithelial-to-mesenchymal transition (EMT) is crucial for unraveling the complexity of cancer metastasis.
In this study, we investigate the pathological consequences associated with disrupted chromatin dynamics resulting from the incorporation of histone H2B variants into chromatin, with a specific emphasis on breast cancer. Employing bioinformatic analysis, we discovered that H2B genes are highly dysregulated in tumor samples from the most aggressive breast cancer subtypes and its increased expression is associated with younger females of Asian and African descent. Employing multi-omics approaches, we show that the incorporation of various H2B variants, in particular H2B1C, H2B1H, and H2B1O, alter chromatin accessibility to transcription factors and thereby mediating unique functions during disease onset and progression. Additionally, H2B1O activates a well-known pro-inflammatory and oncogenic pathway leading to resistance to common chemotherapeutic drugs used in breast cancer treatments. With biophysical approach, we determined that the incorporation of these histone variants into chromatin not only impact compaction of DNA around the octamer of histones, but also affect high-order chromatin-like structure. Taken together, we show that these perturbations contribute to cellular plasticity and facilitate cancer initiation.
We next investigated the role of PARP1 (Poly (ADP-ribose) polymerase 1), a chromatin-associated enzyme, in gene regulation. PARP1 is crucial for chromatin organization and is often dysregulated in breast cancer. PARP1 and its PARylation activity exert multi-level regulatory control over chromatin, affecting processes from histone modification to the recruitment of elongation factors at actively transcribing regions. To gain a comprehensive understanding of PARP1's role in gene transcription and co-transcriptional splicing, we combined Precision Run-On (PRO), Transient Transcriptome (TT) sequencing, Cut&Run, and RNA-sequencing. Our findings reveal that by influencing the processivity of the transcription machinery, PARP1 affects not only the abundance of transcripts but also the generation of alternative splicing variants.
This work aims to expand our understanding of how the tight regulation of chromatin architecture is essential to maintain the integrity of fundamental biological processes, as demonstrated by PARP1. Additionally, changes to chromatin composition as exemplified by the perturbation of histone H2B variants can modify chromatin structure to fine-tune gene regulation and influence disease progression. Our research highlights that these histone variants could serve as novel prognostic indicators for breast cancer and could potentially guide the development of targeted therapeutic drugs to improve tumor response.
Digital Object Identifier (DOI)
https://doi.org/10.13023/etd.2024.518
Funding Information
This work was supported in part by the Van Andel Institutional support, by National Institute of Environmental Health Sciences (NIEHS) grant R01 ES034253 (YFM), and by National Science Foundation grant MCB 2016515 (YFM).
Recommended Citation
Dhahri, Hejer, "CHROMATIN STRUCTURE AT THE CENTER OF TRANSCRIPTIONAL REGULATION: A FOCUS ON BREAST CANCER" (2024). Theses and Dissertations--Molecular and Cellular Biochemistry. 75.
https://uknowledge.uky.edu/biochem_etds/75
Included in
Disorders of Environmental Origin Commons, Medical Biochemistry Commons, Medical Molecular Biology Commons, Oncology Commons
