Human Coronavirus 229E Infection Alters Histone Proteoforms

Viruses rely on host machinery to replicate, and growing evidence demonstrates that they utilize host epigenetic regulation, including histone modification, to modulate host gene expression for their benefit. Herein, we employed top-down proteomics to quantify histone proteoforms in lung fibroblast (MRC-5) cells following human coronavirus 229E (HCoV-229E) infection and compared them to mock-infected controls. A total of 572 proteoforms were identified, including 461 histone proteoforms that were assigned to histone 2A (H2A), H2B, H3, or H4. 200 histone proteoforms were quantifiable. Differential abundance analysis revealed several changes in both reversible post-translational modifications (e.g., phosphorylation, acetylation) and the truncation states of core histones. Notably, we found a decreased abundance of truncated histones in HCoV-229E-infected samples, specifically C-terminally truncated histone H2A and N-terminally truncated histone H3. These findings underscore the power of top-down proteomics to resolve unique truncation states of proteoforms and support the hypothesis that viruses alter the histone length to influence host gene expression.