Comprehensive classification of pioneer transcription factors: insights into binding characteristics and chromatin interactions

Shapoval, Sofiia (2024) Comprehensive classification of pioneer transcription factors: insights into binding characteristics and chromatin interactions. Masters thesis, Memorial University of Newfoundland.

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Abstract

This study focuses on classifying pioneer transcription factors (pTFs) and understanding their crucial roles in gene regulation across various biological processes like development, differentiation, and responses to environmental cues. Insight into pTFs is valuable for therapeutic interventions, particularly in regenerative medicine, disease treatment, and tissue engineering. They are essential for unpacking chromatin, enabling access to target genes and reprogramming cells into induced pluripotent stem cells (iPSCs), impacting stem cell research and medical applications. Additionally, pTFs are key in cellular responses to environmental changes, especially in cancer biology and immunology, making them significant in industrial and medical contexts. Dysregulation of pTFs can lead to diseases like cancer, underscoring the importance of their classification in identifying potential therapeutic targets. The study outlines methodologies for comprehensive data collection, feature grouping, and categorization related to DNA binding, chromatin accessibility, cell fate alterations, and cancer roles. Results encompass pTFs classification, gene ontology enrichment analysis, pathway analysis, and gene expression analysis under baseline and differential conditions. The classification identified distinct groups of pTFs based on their binding preferences and interactions with chromatin. This detailed understanding highlights the maintenance of cellular identity, differentiation mechanisms, and potential therapeutic interventions targeting specific pTFs. Additionally, the study performed Gene Ontology (GO) enrichment analysis and pathway analysis, offering insights into the functional implications of different pTF groups across cellular components, biological processes, and molecular functions. These analyses enhance our understanding of the roles played by the newly defined groups of pTFs in various cellular processes and regulatory mechanisms. Additionally, gene expression analysis categorized TFs based on their baseline and differential expression patterns across different tissues and processes, revealing distinct functional peculiarities within TF families. This highlights the importance of integrating expression data and functional characteristics for accurate classification and understanding of pTFs' regulatory impact. In conclusion, this comprehensive research significantly advances our understanding of pTFs, unraveling their diverse roles, regulatory mechanisms, and implications across various cellular processes. The findings presented offer a multi-faceted view of pTFs, enriching our knowledge in the field of transcriptional regulation and paving the way for further studies to deepen our understanding of their molecular mechanisms and functional implications.

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