PNNL

The Science

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. Pacific Northwest National Laboratory (PNNL) researchers used top-down proteomics to quantify histone proteoforms in lung fibroblast cells following human coronavirus 229E (HCoV-229E) infection and compared them to mock-infected controls. Their findings underscore the power of top-down proteomics to resolve unique truncation states of proteoforms and support the hypothesis that viruses alter histone proteoforms to influence host gene expression. 

The Impact

Characterizing histone proteoforms remains a challenging task for scientists, yet it provides critical information to help researchers understand how to thwart viral infections. Bottom-up strategies have proven limited in revealing specific proteomes from biological samples. In this project, researchers used a top-down proteomics approach to demonstrate statistically significant changes in histone processing following viral infection—results that have not been attainable using bottom-up strategies.

Summary

Post-translational modifications (PTMs) of histones are critical for epigenetic regulation and allow cells to dynamically respond to their environment by mediating changes in transcription, DNA damage repair, and cell-cycle control. Acetylation, methylation, phosphorylation, and removal of PTM sites, along with protein truncation events, are known to create proteoforms that mediate these processes and ultimately regulate transcription activation or repression. In the context of viral infections, emerging research indicates that viruses such as HCoV-229E can influence the host’s epigenetic mechanisms, leading to alterations in chromatin structure, which may affect the outcome of infection.

Using top-down proteomics in this study, researchers characterized intact proteoforms of histones purified from human lung cells following infection from HCoV-229E and found statistically significant changes in histone processing following viral infection. The findings provide an important window into the mechanics of epigenetic regulation during infection and how viruses can change cell events to propagate. Furthermore, this study highlighted the advantages of top-down proteomics in uncovering intact proteoforms and generating deeper insights into histone modifications, particularly protease-driven truncation events that cannot be fully resolved by bottom-up approaches.

Contact

Tong Zhang, tong.zhang@pnnl.gov, Pacific Northwest National Laboratory

Amy Sims, amy.sims@pnnl.gov, Pacific Northwest National Laboratory

Funding

The research described in this paper is part of the Predictive Phenomics Initiative at PNNL and conducted under the Laboratory Directed Research and Development Program. PNNL is a multiprogram national laboratory operated by Battelle for the Department of Energy under Contract No. DE-AC05-76RL01830.