Multiscale Computational Models of Heterochromatin Phase Separation

Although liquid-liquid phase separation (LLPS) driven by multivalent interactions between modified histone tails and their cognate proteins has emerged as a potential mechanism in heterochromatin assembly, the interplay between chromatins, histone modifications, methylated DNA, and their associated binding factors within this phase-separated environment remains enigmatic. Elucidating the orchestration of these factors during LLPS- mediated assembly represents a critical gap in understanding of heterochromatin dynamics. The long-term goal of this project is to fill this gap by deciphering the molecular mechanisms underlying heterochromatin assembly, thereby contributing to a deeper understanding of gene expression regulation and potential therapeutic interventions for chromatin dysfunction. My overall objectives are to (i) uncover the molecular drivers promoting the co-phase separation of heterochromatin protein 1 (HP1) with other associated proteins and (un)methylated DNA, and (ii) characterize the interactions between nucleosomes and heterochromatin constituent proteins. The central hypothesis posits that HP1-mediated phase separation and heterochromatin assembly are governed by a balance of nonspecific electrostatic interactions and specific recognition of H3K9me3 and other binding motifs (such as PXVXL). I propose that paralog-specific sequence features of HP1 across species strategically tune these interactions to regulate heterochromatin organization. I will test this hypothesis through two specific aims: (1) elucidate molecular mechanisms governing co-phase separation of HP1 and other heterochromatin-binding proteins, employing advanced computational and biophysical techniques to refine the understanding of LLPS in chromatin organization, and (2) investigate molecular interactions between nucleosomes and heterochromatin- associated proteins, enriching current models of protein-DNA interactions and exploring the impact on chromatin structure, dynamics, and function. This research stands out by integrating cutting-edge multiscale computational modeling with experimental validation to explore the complex dynamics of heterochromatin assembly, representing a significant advance in the field of chromatin biology and epigenetics. The significance of the proposed work lies in its potential to provide a detailed molecular framework for understanding how heterochromatin assembly regulates gene expression, delivering novel insights with far-reaching implications for developing therapeutic strategies targeting chromatin and epigenetic dysregulation in cancer and other diseases linked to genomic instability. Project Number: 1K99GM159055-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Tien Phan | Institution: TEXAS ENGINEERING EXPERIMENT STATION, COLLEGE STATION, TX | Award Amount: $135,000 | Activity Code: K99 | Study Section: Special Emphasis Panel[ZRG1 MBBC-P (55)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11370746