Computational Framework for Viral RNA–Chromatin Interactions: A Model-Based Approach

Viral RNAs can directly interact with host chromatin through multiple mechanisms, including R-loop formation, triplex structures, and miRNA-like interactions. This study presents a computational framework that integrates five mechanistic classes of RNA–DNA interactions. Using a model retroviral genome, we identified candidate RNA regions with potential regulatory roles in host gene expression. The framework is reproducible, testable, and generalizable across diverse viral families. All predictions are based on publicly available datasets and validated against known host gene targets. This record provides the finalized manuscript version for open access archiving and citation.