An Integrated Approach Based on a DNA Self-Assembly Technique for Characterization of Crosstalk among Combinatorial Histone Modifications

Combinatorial
histone post-translational modifications (HPTMs)
form a complex epigenetic code that can be decoded by specific binding
proteins, termed as readers. Their specific interplays have been thought
to determine gene expression and downstream biological functions.
However, it is still a big challenge to analyze such interactions
due to various limitations including rather weak, transient, and complicated
interactions between HPTMs and readers, the high dynamic property
of HPTMs, and the low abundance of reader proteins. Here we sought
to take advantage of DNA-templated and photo-cross-linking techniques
to design a group of combinatorial histone PTM peptide probes for
the identification of multivalent interactions among histone PTMs
and readers. By use of trimethylation on histone H3K4 (H3K4me3) and
phosphorylation on H3T3, we demonstrated that this approach can be
successfully utilized for identification of the PTM crosstalk on the
same histone. By use of H3K4me3 and acetylation on H4K16, we showed
the potential application of the probe in the multivalent interactions
among PTMs on different histones. Thus, this new chemical proteomics
tool combined with mass spectrometry holds a promising potential in
profiling of the readers of combinatorial HPTMs and characterization
of crosstalk among multiple PTMs on histones and can be adapted for
broad biomedical applications.