The methylation of histones at specific sites has been linked to both transcriptionally active and repressive chromatin. However, the structural basis for these effects has been difficult to study because homogeneous populations of methylated histones were not available for x-ray crystallography.
This situation changed recently with the development of a method to introduce modifications such as methylation at specific sites in recombinant histones. By using this technique in combination with x-ray crystallography, Karolin Luger, Kevan Shokat, and co-workers at Colorado State University and the University of California, San Francisco determined the structural effects of histone H3 dimethylation at lysine 79 (H3K79me2) and H4 trimethylation at lysine 20 (H4K20me3).
The two methylation marks have opposite effects on chromatin: H3K79me2 is enriched at active promoters, whereas H4K20me3 is associated with repressive chromatin. Chemically modified histones (H3Kc79me2 or H4Kc20me3) were assembled into nucleosome core particles on DNA fragments. Then, the crystal structures of the methylated nucleosomes were determined.
Dimethylation of H3K79 partially uncovered a hydrophobic pocket that had been blocked by unmodified H3K79. This reshaping of the local surface of the nucleosome might affect the binding of macromolecules. Trimethylation of H4K20 changed the geometry of the H4 tail, a region that is important for the formation of higher-order chromatin structure. Consistent with this role, H4K20me3 caused a shift toward locally condensed chromatin structures, as shown by sedimentation velocity analysis. This work revealed the first high-resolution structures of nucleosomes that bear analogs of biologically relevant post-translational modifications.
Check out Nature Structure and Molecular Biology, September 2008 for the full download.