Histone Core Phosphorylation Regulates DNA Accessibility

Matthew Brehove; Tao Wang; Justin North; Yi Luo; Sarah J. Dreher; John C. Shimko; Jennifer J. Ottesen; Karolin Luger; Michael G. Poirier

doi:10.1074/jbc.M115.661363

Histone Core Phosphorylation Regulates DNA Accessibility*

From the ^‡Department of Physics,
^¶Department of Microbiology,
^‖Biophysics Graduate Program,
^**Ohio State Biochemistry Program, and
^‡‡Department of Chemistry and Biochemistry, The Ohio State University, Columbus Ohio 43210 and
the ^§§Howard Hughes Medical Institute and
^§Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523

↵3 To whom correspondence should be addressed: Dept. of Physics, The Ohio State University, 191 W. Woodruff Ave., Columbus OH, 43214. Tel.: 614-247-4493; E-mail: mpoirier{at}mps.ohio-state.edu.

↵1 Both authors contributed equally to this work.

Background: Transcription and DNA replication are regulated by histone core phosphorylation.

Results: Histone phosphorylation near the DNA entry-exit region of the nucleosome increases DNA unwrapping and accessibility, which are further enhanced when combined with histone acetylation.

Conclusion: Histone core phosphorylation regulates DNA accessibility.

Significance: Histone phosphorylation and acetylation function together to regulate occupancy of DNA regulatory complexes.

Abstract

Nucleosome unwrapping dynamics provide transient access to the complexes involved in DNA transcription, repair, and replication, whereas regulation of nucleosome unwrapping modulates occupancy of these complexes. Histone H3 is phosphorylated at tyrosine 41 (H3Y41ph) and threonine 45 (H3T45ph). H3Y41ph is implicated in regulating transcription, whereas H3T45ph is involved in DNA replication and apoptosis. These modifications are located in the DNA-histone interface near where the DNA exits the nucleosome, and are thus poised to disrupt DNA-histone interactions. However, the impact of histone phosphorylation on nucleosome unwrapping and accessibility is unknown. We find that the phosphorylation mimics H3Y41E and H3T45E, and the chemically correct modification, H3Y41ph, significantly increase nucleosome unwrapping. This enhances DNA accessibility to protein binding by 3-fold. H3K56 acetylation (H3K56ac) is also located in the same DNA-histone interface and increases DNA unwrapping. H3K56ac is implicated in transcription regulation, suggesting that H3Y41ph and H3K56ac could function together. We find that the combination of H3Y41ph with H3K56ac increases DNA accessibility by over an order of magnitude. These results suggest that phosphorylation within the nucleosome DNA entry-exit region increases access to DNA binding complexes and that the combination of phosphorylation with acetylation has the potential to significantly influence DNA accessibility to transcription regulatory complexes.

Footnotes

↵2 Supported by the Howard Hughes Medical Institute.
↵* This work was supported, in whole or in part, by National Institutes of Health Grants GM083055 (to M. G. P. and J. J. O.) and GM088409 to K. L.), by National Science Foundation (NSF) Grant MCB-0845696 (to J. J. O.), and by the Ohio State University Comprehensive Cancer Center (OSU CCC) (Pelotonia Fellowship to J. A. N.). This work was also supported in part by the Joint NSF/NIGMS Initiative to Support Research in the Area of Mathematical Biology Grant R01GM096192 (to K. L.). The authors declare that they have no conflicts of interest with the contents of this article.