Multivalent histone and DNA engagement by the triple reader module of ZMYND8 directs the recruitment of a transcriptional network to genes to regulate gene expression

Elucidation of multivalent interactions involving both DNA and histone post-translational-modifications (PTMs) is essential for providing insight into complex biological functions. We report here the high resolution crystal structure of the N-terminal triple reader module (PHD-Bromo-PWWP) of ZMYND8, which forms a stable unit, capable of simultaneously recognizing histone PTMs and providing a charged platform for DNA interaction. Monte Carlo simulations provide a model whereby the reader module directly engages the core nucleosome particle, extracting the entire histone H3 tail and initiating contacts with the DNA super-coil structure. Systematic mutation of these interaction interfaces reveals cooperativity within the ensemble. Single domain disruption destroys the functional network of interactions initiated by ZMYND8, which impairs recruitment to sites of DNA damage and alters transcription. Taken together, our results establish an important role of the ZMYND8 multivalent reader module in nucleosome binding and chromatin function. Total RNA was extracted from (1) HEK293 T-Rex cells; (2) HEK293 cells stably expressing ZMYND8 following 24 h induction with 100 nM of doxycycline; (3) HEK293 cells stably expressing ZMYND8 mutant (N228F) following 24 h induction with 100 nM of doxycycline; (4) HEK293 T-Rex cells following 48 h treatment with 100 pmol of siRNA (CTRL); (5) HEK293 T-Rex cells following 48 h treatment with 100 pmol of siZMYND8. Each condition was performed in biological triplicates.