A single-site DNA–histone cross-link causes a global breakdown of nucleosome structure and function

DNA–protein cross-links (DPCs) represent a severe form of DNA damage that can disrupt essential chromatin-based processes. Among them, DNA–histone cross-links (DHCs) occur frequently within nucleosomes, yet their structural and functional consequences remain poorly understood due to their instability and low natural abundance.

Now, researchers from Nankai University and Tsinghua University have discovered that a single covalent bond between DNA and histone proteins can effectively “lock” the nucleosome—the fundamental unit of chromatin—preventing it from moving, being remodeled, or properly processed by polymerase. The findings, published in Protein & Cell, reveal how certain forms of DNA damage can rigidify chromatin and profoundly interfere with key genetic processes.

Using click chemistry, the team engineered nucleosomes containing a single, site-specific DNA–histone cross-link to precisely examine its structural and functional effects. Cryo-electron microscopy showed that while DHC formation does not alter the overall nucleosome architecture, it dramatically increases structural rigidity and stability. The cross-linked nucleosomes resisted disassembly under high-salt and high-temperature conditions, suggesting that a single covalent link significantly strengthens DNA–histone interactions. Functionally, this single DHC was sufficient to completely abolish both thermally induced nucleosome sliding and ATP-dependent remodeling by the chromatin remodeler SNF2h.

Transcription assays using SP6 RNA polymerase further demonstrated that DHC formation blocks transcription elongation within nucleosomes, causing premature termination roughly 15 base pairs upstream of the cross-link site. Mechanistically, this inhibition arises not from steric hindrance but from the inability of RNA polymerase to drive nucleosome translocation along DNA. Additionally, DHCs make histones highly resistant to proteolytic degradation, suggesting that such lesions may evade conventional DNA repair pathways.

Together, these findings establish DNA–histone cross-links as a highly toxic and persistent form of DNA damage that rigidifies nucleosomes, impairs chromatin remodeling, and obstructs transcription. This study provides the first systematic analysis of DHC effects on nucleosome behavior in vitro and offers new insights into how covalent DNA–histone coupling may influence genome stability and epigenetic regulation in living cells.