Computational interrogation of Epigenetic Regulation in Cellular Plasticity and Heterogeneity

/ABSTRACT Cell fate determination is modulated by transcription factors (TFs), acting in concert with chromatin remodeling cofactors including enzymes that carry out or remove DNA and histone modifications. Recent advances in next generation–sequencing (NGS)-based molecular methods have illuminated the hierarchical organization of the genome and have shown that changes in the epigenome can promote or prevent the access of TFs to specific DNA sequences, move genes between nuclear compartments, and build or remove the insulation between neighboring genomic regions. As changes in the epigenome and chromatin organization can derail precise transcriptional regulatory programs to change cell differentiation status or induce a pathological state, research in Dr. Li’s laboratory seeks to improve our ability to define and understand the impact of such changes across multiple layers of transcriptional regulation in the cell. Despite this technological progress, significant challenges remain in understanding the functional role of 5mC in regulating gene expression and its implications in cell fate determination. First, researchers lack computational tools to comprehensively assess allele-specific and functional epigenetic heterogeneity in the complete genome, including in previously unmapped genomics regions. Second, researchers have yet to epigenetically annotate the mouse complete genome, despite the recent release of mouse telomere-to-telomere genome reference. Thus, the functions of regulators for 5mC plasticity and heterogeneity still have not been comprehensively determined. Given the aforementioned gaps in knowledge and the unique multi-disciplinary training, my long-term goal is to combine advanced genome technology and computational biology to address to dissect the functions of epigenetic regulation for transcription. Key goals over the next five years include developing a computational framework to mine short- and long-read sequencing data to answer the following questions: (1) What is the epigenetic patterns in the complete mouse genome including those regions that are previously unmappable? (2) What is the allele-specific epigenetic heterogeneity including in those repetitive and duplicated regions? (3) What is the impact of genomic context, specifically TF motifs that impact the functional role of epigenetic heterogeneity? (4) What are the functions of epigenetic regulators on shaping the DNA methylation landscape comprehensive? We will interrogate the impact of the regulators for DNA and histone methylation. The proposed work will deepen our understanding on how epigenetic plasticity and heterogeneity contribute to gene regulation, the crosstalk between DNA methylation and histone methylation, and molecular mechanisms underlying cell differentiation and human diseases. The expected outcome will provide resources for a comprehensive view of the epigenetic organization of a complete mouse genome, and computational tools and examples for the community to leverage to understand the epigenetic regulation in their own system. It will also establish the paradigm for functional dissecting the complete epigenome for other DNA and histone modifications in normal development and disease progress. Project Number: 1R35GM162228-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Sheng Li | Institution: UNIVERSITY OF SOUTHERN CALIFORNIA, Los Angeles, CA | Award Amount: $589,500 | Activity Code: R35 | Study Section: Special Emphasis Panel[ZRG1 MGG-D (55)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11269108